{no title found}

BS_00003^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00003`

BS_0000338^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_0000338`

BS_0000339^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_0000339`

BS_0000340^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_0000340`

BS_0000341^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_0000341`

BS_00012^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00012`

BS_00026^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00026`

BS_00027^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00027`

BS_00028^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00028`

BS_00029^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00029`

BS_00032^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00032`

BS_00033^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00033`

BS_00036^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00036`

BS_00040^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00040`

BS_00041^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00041`

BS_00042^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00042`

BS_00052^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00052`

BS_00055^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00055`

BS_00063^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00063`

BS_00067^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00067`

BS_00068^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00068`

BS_00069^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00069`

BS_00070^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00070`

BS_00071^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00071`

BS_00072^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00072`

BS_00073^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00073`

BS_00076^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00076`

BS_00077^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00077`

BS_00124^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00124`

BS_00125^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00125`

BS_00128^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00128`

BS_00129^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00129`

BS_00131^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00131`

BS_00134^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00134`

BS_00136^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00136`

BS_00137^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00137`

BS_00140^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00140`

BS_00141^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00141`

BS_00142^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00142`

BS_00143^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00143`

BS_00144^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00144`

BS_00145^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00145`

BS_00146^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00146`

BS_00147^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00147`

BS_00148^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00148`

BS_00149^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00149`

BS_00151^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00151`

BS_00152^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00152`

BS_00153^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00153`

BS_00154^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00154`

BS_00155^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00155`

BS_00156^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00156`

BS_00157^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00157`

BS_00158^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00158`

BS_00159^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00159`

BS_00178^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00178`

BS_00181^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00181`

BS_00182^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00182`

BS_00185^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00185`

BS_00186^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00186`

BS_00187^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00187`

BS_00202^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00202`

BS_00203^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00203`

BS_00204^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00204`

BS_00205^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00205`

BS_00206^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00206`

BS_00207^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00207`

BS_00208^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00208`

BS_00209^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00209`

BS_00210^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00210`

BS_00211^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00211`

BS_00212^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00212`

BS_00213^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00213`

BS_00214^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00214`

BS_00215^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00215`

BS_00216^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00216`

BS_00219^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00219`

BS_00220^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00220`

BS_00221^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00221`

BS_00222^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00222`

BS_00223^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00223`

BS_00224^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00224`

BS_00225^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00225`

BS_00226^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00226`

BS_00227^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00227`

BS_00228^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00228`

BS_00229^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00229`

BS_00230^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00230`

BS_00231^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00231`

BS_00232^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00232`

BS_00233^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00233`

BS_00234^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00234`

BS_00235^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00235`

BS_00246^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00246`

BS_00331^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00331`

BS_00336^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00336`

BS_00337^c # Classes

URI	`http://purl.obolibrary.org/obo/BS_00337`

Sequence_Ontology^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000000`

region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000001`
Super-classes	obo:SO_0000110^c
Sub-classes	obo:SO_0001411^c obo:SO_0001410^c obo:SO_0001409^c obo:SO_0001412^c

sequence_secondary_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000002`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0000028^c obo:SO_0000591^c obo:SO_0000122^c obo:SO_0000003^c obo:SO_0000142^c

G_quartet^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000003`
Super-classes	obo:SO_0000002^c

interior_coding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000004`
Super-classes	obo:SO_0000195^c

satellite_DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000005`
Super-classes	obo:SO_0000705^c
Sub-classes	obo:SO_0000289^c obo:SO_0000643^c

PCR_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000006`
Description	This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
Super-classes	obo:SO_0000695^c
Sub-classes	obo:SO_0001481^c obo:SO_0001830^c

read_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000007`
Super-classes	obo:SO_0000150^c
Restrictions	so:part_of^op some obo:SO_0001790^c so:part_of^op some obo:SO_0000149^c

gene_sensu_your_favorite_organism^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000008`

gene_class^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000009`

protein_coding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000010`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0000729^c

non_protein_coding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000011`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0000979^c obo:SO_0000578^c obo:SO_0000656^c obo:SO_0000575^c obo:SO_0000663^c obo:SO_0000571^c obo:SO_0000642^c obo:SO_0000623^c obo:SO_0000573^c obo:SO_0000659^c

scRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000012`
Super-classes	obo:SO_0000483^c

scRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000013`
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0000012^c

INR_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000014`
Description	Binds TAF1, TAF2.
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

DPE_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000015`
Description	Binds TAF6, TAF9.
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

BREu_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000016`
Description	Binds TFIIB.
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

PSE_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000017`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000167^c

linkage_group^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000018`
Super-classes	obo:SO_0001411^c

SO_0000019^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000019`

RNA_internal_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000020`
Super-classes	obo:SO_0000715^c
Sub-classes	obo:SO_0000025^c obo:SO_0000021^c

asymmetric_RNA_internal_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000021`
Super-classes	obo:SO_0000020^c
Sub-classes	obo:SO_0000023^c obo:SO_0000024^c

A_minor_RNA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000022`
Super-classes	obo:SO_0000715^c

K_turn_RNA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000023`
Super-classes	obo:SO_0000021^c

sarcin_like_RNA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000024`
Super-classes	obo:SO_0000021^c

symmetric_RNA_internal_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000025`
Super-classes	obo:SO_0000020^c

RNA_junction_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000026`
Super-classes	obo:SO_0000715^c
Sub-classes	obo:SO_0000027^c

RNA_hook_turn^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000027`
Super-classes	obo:SO_0000026^c

base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000028`
Super-classes	obo:SO_0000002^c
Sub-classes	obo:SO_0000501^c obo:SO_0000500^c obo:SO_0000029^c obo:SO_0001015^c obo:SO_0000030^c

WC_base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000029`
Super-classes	obo:SO_0000028^c

sugar_edge_base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000030`
Super-classes	obo:SO_0000028^c

aptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000031`
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0000032^c obo:SO_0000033^c

DNA_aptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000032`
Super-classes	obo:SO_0000031^c

RNA_aptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000033`
Super-classes	obo:SO_0000031^c

morpholino_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000034`
Super-classes	obo:SO_0001247^c
Restrictions	so:has_quality^op some obo:SO_0001183^c

riboswitch^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000035`
Super-classes	obo:SO_0000836^c
Restrictions	so:part_of^op some obo:SO_0000234^c

matrix_attachment_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000036`
Super-classes	obo:SO_0000626^c

locus_control_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000037`
Description	Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene.
Super-classes	obo:SO_0000727^c

match_set^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000038`

match_part^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000039`
Super-classes	obo:SO_0001410^c
Restrictions	so:part_of^op some obo:SO_0000343^c

genomic_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000040`
Super-classes	obo:SO_0000151^c
Restrictions	so:has_quality^op some obo:SO_0000991^c

sequence_operation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000041`

pseudogene_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000042`

processed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000043`
Description	Please not the synonym R psi M uses the spelled out form of the greek letter.
Super-classes	obo:SO_0000336^c
Sub-classes	obo:SO_0002109^c obo:SO_0002105^c

pseudogene_by_unequal_crossing_over^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000044`
Super-classes	obo:SO_0001760^c

delete^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000045`

insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000046`

invert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000047`

substitute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000048`

translocate^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000049`

gene_part^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000050`

probe^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000051`
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0001854^c obo:SO_0000328^c

assortment_derived_deficiency^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000052`

sequence_variant_affecting_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000053`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

aneuploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000054`
Super-classes	obo:SO_1000182^c
Sub-classes	obo:SO_0000055^c obo:SO_0000056^c

hyperploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000055`
Super-classes	obo:SO_0000054^c

hypoploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000056`
Super-classes	obo:SO_0000054^c

operator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000057`
Description	Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.
Super-classes	obo:SO_0001055^c

assortment_derived_aneuploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000058`

nuclease_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000059`
Super-classes	obo:SO_0001654^c
Sub-classes	obo:SO_0001257^c obo:SO_0000684^c obo:SO_0000061^c

compound_chromosome_arm^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000060`
Description	FLAG - this term is should probably be a part of rather than an is_a.
Super-classes	obo:SO_1000042^c

restriction_enzyme_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000061`
Description	A region of a molecule that binds to a restriction enzyme.
Super-classes	obo:SO_0000059^c

deficient_intrachromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000062`
Super-classes	obo:SO_1000029^c obo:SO_1000041^c
Restrictions	so:has_part^op some obo:SO_0000159^c

deficient_interchromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000063`
Super-classes	obo:SO_1000155^c

gene_by_transcript_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000064`
Description	This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.

free_chromosome_arm^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000065`
Super-classes	obo:SO_1000183^c

gene_by_polyadenylation_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000066`

gene_to_gene_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000067`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0000068^c

overlapping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000068`
Super-classes	obo:SO_0000067^c
Sub-classes	obo:SO_0000074^c obo:SO_0000069^c obo:SO_0000075^c obo:SO_0000076^c obo:SO_0000073^c obo:SO_0000077^c

inside_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000069`
Super-classes	obo:SO_0000068^c
Sub-classes	obo:SO_0000070^c obo:SO_0000071^c

inside_intron_antiparallel^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000070`
Super-classes	obo:SO_0000069^c

inside_intron_parallel^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000071`
Super-classes	obo:SO_0000069^c

end_overlapping_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000072`

five_prime_three_prime_overlap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000073`
Super-classes	obo:SO_0000068^c

five_prime_five_prime_overlap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000074`
Super-classes	obo:SO_0000068^c

three_prime_three_prime_overlap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000075`
Super-classes	obo:SO_0000068^c

three_prime_five_prime_overlap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000076`
Super-classes	obo:SO_0000068^c

antisense^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000077`
Super-classes	obo:SO_0000068^c

polycistronic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000078`
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000880^c
Sub-classes	obo:SO_0000079^c obo:SO_0000634^c obo:SO_0000631^c

dicistronic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000079`
Super-classes	obo:SO_0000078^c
Restrictions	so:has_quality^op some obo:SO_0000879^c
Sub-classes	obo:SO_0000716^c obo:SO_1001197^c

operon_member^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000080`
Super-classes	obo:SO_0000081^c

gene_array_member^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000081`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0005849^c obo:SO_0000080^c obo:SO_1001217^c obo:SO_0005848^c

processed_transcript_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000082`

macronuclear_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000083`
Super-classes	obo:SO_0000736^c

micronuclear_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000084`
Super-classes	obo:SO_0000736^c

gene_by_genome_location^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000085`

gene_by_organelle_of_genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000086`

nuclear_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000087`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000738^c

mt_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000088`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000737^c
Sub-classes	obo:SO_0000089^c

kinetoplast_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000089`
Super-classes	obo:SO_0000088^c
Restrictions	so:has_origin^op some obo:SO_0000741^c
Sub-classes	obo:SO_0000975^c obo:SO_0000654^c

plastid_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000090`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000740^c
Sub-classes	obo:SO_0000096^c obo:SO_0000094^c obo:SO_0000091^c obo:SO_0000093^c obo:SO_0000095^c obo:SO_0000092^c

apicoplast_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000091`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000743^c

ct_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000092`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000745^c

chromoplast_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000093`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000744^c

cyanelle_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000094`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000746^c

leucoplast_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000095`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000747^c

proplastid_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000096`
Super-classes	obo:SO_0000090^c
Restrictions	so:has_origin^op some obo:SO_0000748^c

nucleomorph_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000097`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000739^c

plasmid_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000098`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000749^c

proviral_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000099`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_origin^op some obo:SO_0000751^c
Sub-classes	obo:SO_0000100^c

endogenous_retroviral_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000100`
Super-classes	obo:SO_0000099^c
Restrictions	so:has_origin^op some obo:SO_0000903^c

transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000101`
Super-classes	obo:SO_0001039^c
Sub-classes	obo:SO_0001648^c obo:SO_0000720^c obo:SO_0000797^c obo:SO_0000182^c obo:SO_0000798^c obo:SO_0000180^c obo:SO_0000796^c

expressed_sequence_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000102`
Super-classes	obo:SO_0000347^c
Sub-classes	obo:SO_0000689^c obo:SO_0001471^c obo:SO_0001470^c obo:SO_0000668^c

clone_insert_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000103`
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0000753^c

polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000104`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
Super-classes	obo:SO_0001411^c
Restrictions	so:derives_from^op some obo:SO_0000316^c

chromosome_arm^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000105`
Super-classes	obo:SO_0000830^c

non_capped_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000106`

sequencing_primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000107`
Super-classes	obo:SO_0000112^c

mRNA_with_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000108`
Super-classes	obo:SO_0000234^c
Restrictions	so:has_quality^op some obo:SO_0000865^c
Sub-classes	obo:SO_0000329^c obo:SO_0000335^c obo:SO_0000282^c obo:SO_0000321^c

sequence_variant_obs^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000109`

sequence_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000110`
Sub-classes	obo:SO_0000699^c obo:SO_0002072^c obo:SO_0000001^c

transposable_element_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000111`
Super-classes	obo:SO_0000704^c
Restrictions	so:part_of^op some obo:SO_0000101^c
Sub-classes	obo:SO_0000283^c

primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000112`
Super-classes	obo:SO_0000441^c
Sub-classes	obo:SO_0000107^c obo:SO_0001698^c obo:SO_0000121^c obo:SO_0000132^c obo:SO_0001699^c

proviral_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000113`
Super-classes	obo:SO_0001039^c
Sub-classes	obo:SO_0001006^c

methylated_cytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000114`
Super-classes	obo:SO_0001963^c obo:SO_0000306^c
Sub-classes	obo:SO_0001919^c obo:SO_0001918^c obo:SO_0001960^c

transcript_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000115`

edited^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000116`
Super-classes	obo:SO_0000237^c

transcript_with_readthrough_stop_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000117`

transcript_with_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000118`
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000887^c

regulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000119`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0000131^c obo:SO_0000134^c obo:SO_0000123^c obo:SO_0000130^c

protein_coding_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000120`
Description	May contain introns.
Super-classes	obo:SO_0000185^c
Sub-classes	obo:SO_0002114^c obo:SO_0002112^c obo:SO_0000932^c

forward_primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000121`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000112^c
Restrictions	so:has_quality^op some obo:SO_0001030^c

RNA_sequence_secondary_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000122`
Super-classes	obo:SO_0000002^c
Sub-classes	obo:SO_0000313^c obo:SO_0002253^c

transcriptionally_regulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000123`
Description	By:.
Super-classes	obo:SO_0000119^c
Sub-classes	obo:SO_0000126^c obo:SO_0000124^c obo:SO_0000125^c obo:SO_0000471^c

transcriptionally_constitutive^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000124`
Super-classes	obo:SO_0000123^c

transcriptionally_induced^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000125`
Super-classes	obo:SO_0000123^c
Sub-classes	obo:SO_0000475^c

transcriptionally_repressed^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000126`
Super-classes	obo:SO_0000123^c
Sub-classes	obo:SO_0000893^c obo:SO_0000473^c

silenced_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000127`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000893^c
Sub-classes	obo:SO_0000128^c obo:SO_0001224^c obo:SO_0001225^c

gene_silenced_by_DNA_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000128`
Super-classes	obo:SO_0000127^c
Restrictions	so:has_quality^op some obo:SO_0000894^c
Sub-classes	obo:SO_0000129^c

gene_silenced_by_DNA_methylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000129`
Super-classes	obo:SO_0000128^c
Restrictions	so:has_quality^op some obo:SO_0000895^c

post_translationally_regulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000130`
Super-classes	obo:SO_0000119^c
Sub-classes	obo:SO_0000469^c obo:SO_0000467^c

translationally_regulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000131`
Super-classes	obo:SO_0000119^c

reverse_primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000132`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000112^c
Restrictions	so:has_quality^op some obo:SO_0001031^c

epigenetically_modified^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000133`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_0000134^c obo:SO_0000904^c obo:SO_0000137^c

genomically_imprinted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000134`
Super-classes	obo:SO_0000133^c obo:SO_0000119^c
Sub-classes	obo:SO_0000136^c obo:SO_0000135^c

maternally_imprinted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000135`
Super-classes	obo:SO_0000134^c

paternally_imprinted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000136`
Super-classes	obo:SO_0000134^c

allelically_excluded^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000137`
Description	Examples are x-inactivation and immunoglobulin formation.
Super-classes	obo:SO_0000133^c

gene_rearranged_at_DNA_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000138`
Super-classes	obo:SO_0000898^c
Restrictions	so:has_quality^op some obo:SO_0000904^c

ribosome_entry_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000139`
Super-classes	obo:SO_0000836^c
Restrictions	so:part_of^op some obo:SO_0000204^c
Sub-classes	obo:SO_0001647^c obo:SO_0000243^c obo:SO_0000552^c

attenuator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000140`
Super-classes	obo:SO_0001680^c
Restrictions	so:part_of^op some obo:SO_0000234^c

terminator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000141`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c
Restrictions	so:part_of^op some obo:SO_0000673^c
Sub-classes	obo:SO_0000951^c obo:SO_0000614^c

DNA_sequence_secondary_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000142`
Super-classes	obo:SO_0000002^c
Sub-classes	obo:SO_0001010^c

assembly_component^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000143`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0000730^c obo:SO_0000149^c obo:SO_0000412^c obo:SO_0000150^c obo:SO_0001253^c obo:SO_0001790^c obo:SO_0000468^c obo:SO_0000474^c

primary_transcript_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000144`

recoded_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000145`
Super-classes	obo:SO_0000360^c
Sub-classes	obo:SO_0000883^c

capped^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000146`
Super-classes	obo:SO_0000237^c

exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000147`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000833^c
Sub-classes	obo:SO_0005845^c obo:SO_0000198^c obo:SO_0000195^c obo:SO_0000201^c

supercontig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000148`
Super-classes	obo:SO_0001876^c
Restrictions	so:part_of^op some obo:SO_0000719^c
Sub-classes	obo:SO_0001875^c obo:SO_0001922^c

contig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000149`
Super-classes	obo:SO_0000143^c obo:SO_0000353^c
Restrictions	so:part_of^op some obo:SO_0000148^c
Sub-classes	obo:SO_0001921^c obo:SO_0002209^c obo:SO_0001866^c obo:SO_0001829^c

read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000150`
Super-classes	obo:SO_0000143^c
Restrictions	so:part_of^op some obo:SO_0000149^c
Sub-classes	obo:SO_0001480^c obo:SO_0001426^c obo:SO_0001827^c obo:SO_0000999^c obo:SO_0001425^c obo:SO_0001423^c obo:SO_0001498^c obo:SO_0001929^c obo:SO_0001793^c obo:SO_0001828^c obo:SO_0001424^c obo:SO_0000476^c obo:SO_0000007^c obo:SO_0001930^c

clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000151`
Super-classes	obo:SO_0000695^c
Sub-classes	obo:SO_0000317^c obo:SO_0000480^c obo:SO_0000040^c

YAC^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000152`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000440^c

BAC^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000153`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000440^c

PAC^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000154`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
Super-classes	obo:SO_0000440^c

plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000155`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0001235^c
Sub-classes	obo:SO_0001476^c obo:SO_0000768^c obo:SO_0002212^c obo:SO_0002211^c obo:SO_0000637^c

cosmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000156`
Description	Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000440^c

phagemid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000157`
Super-classes	obo:SO_0000440^c

fosmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000158`
Description	Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
Super-classes	obo:SO_0000440^c

deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000159`
Super-classes	obo:SO_0001411^c obo:SO_0001059^c
Sub-classes	obo:SO_0002066^c

lambda_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000160`

methylated_adenine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000161`
Super-classes	obo:SO_0001962^c obo:SO_0000306^c
Sub-classes	obo:SO_0001920^c

splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000162`
Description	With spliceosomal introns, the splice sites bind the spliceosomal machinery.
Super-classes	obo:SO_0000835^c
Sub-classes	obo:SO_0001533^c obo:SO_0001419^c obo:SO_0001420^c

five_prime_cis_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000163`
Super-classes	obo:SO_0001419^c
Sub-classes	obo:SO_0000679^c obo:SO_0000677^c

three_prime_cis_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000164`
Super-classes	obo:SO_0001419^c
Sub-classes	obo:SO_0000678^c obo:SO_0000676^c

enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000165`
Description	An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
Super-classes	obo:SO_0000727^c
Sub-classes	obo:SO_0001482^c obo:SO_0000166^c

enhancer_bound_by_factor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000166`
Super-classes	obo:SO_0000165^c
Restrictions	so:has_quality^op some obo:SO_0000277^c

promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000167`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter.
Super-classes	obo:SO_0001055^c obo:SO_0000842^c
Sub-classes	obo:SO_0002051^c obo:SO_0002310^c obo:SO_0002311^c obo:SO_0002221^c obo:SO_0002222^c obo:SO_0000568^c obo:SO_0002050^c

restriction_enzyme_cut_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000168`

RNApol_I_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000169`
Description	parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
Super-classes	obo:SO_0002221^c

RNApol_II_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000170`
Description	parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
Super-classes	obo:SO_0002221^c
Sub-classes	obo:SO_0001669^c

RNApol_III_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000171`
Description	parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
Super-classes	obo:SO_0002221^c
Sub-classes	obo:SO_0000617^c obo:SO_0000621^c obo:SO_0000618^c

CAAT_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000172`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

GC_rich_promoter_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000173`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

TATA_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000174`
Description	Binds TBP.
Super-classes	obo:SO_0001660^c
Sub-classes	obo:SO_0001662^c obo:SO_0001661^c

minus_10_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000175`
Description	Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001913^c so:part_of^op some obo:SO_0001671^c

minus_35_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000176`
Description	Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021.
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001671^c so:part_of^op some obo:SO_0001913^c

cross_genome_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000177`
Super-classes	obo:SO_0000347^c

operon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000178`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020.
Super-classes	obo:SO_0005855^c
Sub-classes	obo:SO_0002299^c obo:SO_0002298^c

clone_insert_start^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000179`
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0000753^c

retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000180`
Super-classes	obo:SO_0000101^c
Sub-classes	obo:SO_0000189^c obo:SO_0000186^c

translated_nucleotide_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000181`
Super-classes	obo:SO_0000347^c

DNA_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000182`
Super-classes	obo:SO_0000101^c
Sub-classes	obo:SO_0002277^c obo:SO_0000544^c obo:SO_0000238^c obo:SO_0000208^c obo:SO_0000371^c

non_transcribed_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000183`
Super-classes	obo:SO_0000842^c

U2_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000184`
Description	May have either GT-AG or AT-AG 5' and 3' boundaries.
Super-classes	obo:SO_0000662^c

primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000185`
Super-classes	obo:SO_0000673^c
Sub-classes	obo:SO_0000632^c obo:SO_0000861^c obo:SO_0000645^c obo:SO_0000120^c obo:SO_0001905^c obo:SO_0000635^c obo:SO_0000483^c obo:SO_0002115^c obo:SO_0000631^c

LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000186`
Super-classes	obo:SO_0000180^c
Sub-classes	obo:SO_0002265^c obo:SO_0002260^c obo:SO_0002264^c obo:SO_0002267^c obo:SO_0002268^c obo:SO_0002261^c obo:SO_0002266^c

repeat_family^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000187`

intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000188`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000835^c
Sub-classes	obo:SO_0001958^c obo:SO_0000190^c obo:SO_0000446^c obo:SO_0000662^c obo:SO_0000406^c obo:SO_0000191^c obo:SO_0000192^c obo:SO_0001216^c obo:SO_0000666^c obo:SO_0000588^c

non_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000189`
Super-classes	obo:SO_0000180^c
Sub-classes	obo:SO_0000194^c obo:SO_0002290^c obo:SO_0000206^c obo:SO_0002286^c

five_prime_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000190`
Super-classes	obo:SO_0000188^c

interior_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000191`
Super-classes	obo:SO_0000188^c

three_prime_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000192`
Super-classes	obo:SO_0000188^c

RFLP_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000193`
Super-classes	obo:SO_0000412^c

LINE_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000194`
Super-classes	obo:SO_0000189^c
Sub-classes	obo:SO_0002269^c obo:SO_0002272^c obo:SO_0002271^c obo:SO_0002273^c obo:SO_0002270^c

coding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000195`
Super-classes	obo:SO_0000147^c
Sub-classes	obo:SO_0000202^c obo:SO_0000004^c obo:SO_0000200^c

five_prime_coding_exon_coding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000196`
Super-classes	obo:SO_0001215^c
Restrictions	so:part_of^op some obo:SO_0000200^c

three_prime_coding_exon_coding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000197`
Super-classes	obo:SO_0001215^c
Restrictions	so:part_of^op some obo:SO_0000202^c

noncoding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000198`
Super-classes	obo:SO_0000147^c
Sub-classes	obo:SO_0000444^c obo:SO_0000445^c

translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000199`
Super-classes	obo:SO_0001785^c
Sub-classes	obo:SO_1000044^c

five_prime_coding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000200`
Super-classes	obo:SO_0000195^c

interior_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000201`
Super-classes	obo:SO_0000147^c

three_prime_coding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000202`
Super-classes	obo:SO_0000195^c

UTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000203`
Super-classes	obo:SO_0000836^c
Sub-classes	obo:SO_0000242^c obo:SO_0000205^c obo:SO_0000204^c obo:SO_0000241^c

five_prime_UTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000204`
Super-classes	obo:SO_0000203^c

three_prime_UTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000205`
Super-classes	obo:SO_0000203^c

SINE_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000206`
Super-classes	obo:SO_0000189^c
Sub-classes	obo:SO_0002275^c obo:SO_0002276^c obo:SO_0002274^c

simple_sequence_length_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000207`
Super-classes	obo:SO_0000248^c

terminal_inverted_repeat_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000208`
Super-classes	obo:SO_0000182^c
Sub-classes	obo:SO_0001535^c obo:SO_0000973^c obo:SO_0002279^c obo:SO_0002285^c obo:SO_0002282^c obo:SO_0002284^c obo:SO_0002281^c obo:SO_0001170^c obo:SO_0000338^c obo:SO_0002278^c obo:SO_0002280^c obo:SO_0002283^c

rRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000209`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0000325^c obo:SO_0000255^c

tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000210`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0000221^c obo:SO_0000215^c obo:SO_0000226^c obo:SO_0000224^c obo:SO_0000216^c obo:SO_0000220^c obo:SO_0000218^c obo:SO_0000213^c obo:SO_0000219^c obo:SO_0005856^c obo:SO_0000227^c obo:SO_0000217^c obo:SO_0000214^c obo:SO_0000223^c obo:SO_0000229^c obo:SO_0002037^c obo:SO_0001178^c obo:SO_0000230^c obo:SO_0000225^c obo:SO_0000228^c obo:SO_0000212^c obo:SO_0000222^c obo:SO_0000211^c

alanine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000211`
Super-classes	obo:SO_0000210^c

arginine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000212`
Super-classes	obo:SO_0000210^c

asparagine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000213`
Super-classes	obo:SO_0000210^c

aspartic_acid_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000214`
Super-classes	obo:SO_0000210^c

cysteine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000215`
Super-classes	obo:SO_0000210^c

glutamic_acid_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000216`
Super-classes	obo:SO_0000210^c

glutamine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000217`
Super-classes	obo:SO_0000210^c

glycine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000218`
Super-classes	obo:SO_0000210^c

histidine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000219`
Super-classes	obo:SO_0000210^c

isoleucine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000220`
Super-classes	obo:SO_0000210^c

leucine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000221`
Super-classes	obo:SO_0000210^c

lysine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000222`
Super-classes	obo:SO_0000210^c

methionine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000223`
Super-classes	obo:SO_0000210^c

phenylalanine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000224`
Super-classes	obo:SO_0000210^c

proline_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000225`
Super-classes	obo:SO_0000210^c

serine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000226`
Super-classes	obo:SO_0000210^c

threonine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000227`
Super-classes	obo:SO_0000210^c

tryptophan_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000228`
Super-classes	obo:SO_0000210^c

tyrosine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000229`
Super-classes	obo:SO_0000210^c

valine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000230`
Super-classes	obo:SO_0000210^c

snRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000231`
Super-classes	obo:SO_0000483^c

snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000232`
Description	This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520).
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0000595^c obo:SO_0005837^c obo:SO_0000582^c obo:SO_0002034^c obo:SO_0000596^c obo:SO_0000580^c

mature_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000233`
Description	A processed transcript cannot contain introns.
Super-classes	obo:SO_0000673^c
Restrictions	so:derives_from^op some obo:SO_0000185^c
Sub-classes	obo:SO_0000655^c obo:SO_0000234^c

mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000234`
Description	An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000233^c
Sub-classes	obo:SO_0000633^c obo:SO_0002292^c obo:SO_0000862^c obo:SO_0000734^c obo:SO_0002130^c obo:SO_0000872^c obo:SO_0000995^c obo:SO_0000108^c obo:SO_0000634^c obo:SO_1001261^c obo:SO_0000871^c obo:SO_0000929^c

TF_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000235`
Description	Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001654^c obo:SO_0001055^c
Restrictions	so:part_of^op some obo:SO_0000727^c
Sub-classes	obo:SO_0002295^c obo:SO_0001840^c obo:SO_0001653^c obo:SO_0001715^c obo:SO_0002045^c

ORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000236`
Description	The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000717^c
Sub-classes	obo:SO_0002028^c obo:SO_0002027^c obo:SO_0002029^c obo:SO_0000815^c

transcript_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000237`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000870^c obo:SO_0000877^c obo:SO_0000880^c obo:SO_0000863^c obo:SO_0000146^c obo:SO_0000878^c obo:SO_0000116^c

foldback_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000238`
Super-classes	obo:SO_0000182^c

flanking_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000239`
Super-classes	obo:SO_0001412^c
Sub-classes	obo:SO_0001416^c obo:SO_0000364^c obo:SO_0001417^c

chromosome_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000240`
Super-classes	obo:SO_0001507^c
Restrictions	so:part_of^op some obo:SO_0001524^c
Sub-classes	obo:SO_1000183^c obo:SO_1000182^c obo:SO_0001504^c

internal_UTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000241`
Super-classes	obo:SO_0000203^c

untranslated_region_polycistronic_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000242`
Super-classes	obo:SO_0000203^c

internal_ribosome_entry_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000243`
Super-classes	obo:SO_0000139^c
Sub-classes	obo:SO_1001260^c

four_cutter_restriction_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000244`

mRNA_by_polyadenylation_status^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000245`

polyadenylated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000246`
Super-classes	obo:SO_0000863^c

mRNA_not_polyadenylated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000247`

sequence_length_alteration^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000248`
Super-classes	obo:SO_0001059^c
Sub-classes	obo:SO_0002096^c obo:SO_0000207^c obo:SO_0001019^c

six_cutter_restriction_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000249`

modified_RNA_base_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000250`
Super-classes	obo:SO_0001236^c
Sub-classes	obo:SO_0001232^c obo:SO_0001276^c obo:SO_0001231^c obo:SO_0001230^c obo:SO_0001275^c obo:SO_0001277^c obo:SO_0001273^c

eight_cutter_restriction_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000251`

rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000252`
Description	Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0000209^c
Sub-classes	obo:SO_0002346^c obo:SO_0002343^c obo:SO_0002128^c

tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000253`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0002247^c
Restrictions	so:derives_from^op some obo:SO_0000210^c
Sub-classes	obo:SO_0000259^c obo:SO_0005857^c obo:SO_0000256^c obo:SO_0000269^c obo:SO_0000262^c obo:SO_0000268^c obo:SO_0000258^c obo:SO_0002129^c obo:SO_0000270^c obo:SO_0000271^c obo:SO_0000261^c obo:SO_0000265^c obo:SO_0000257^c obo:SO_0000266^c obo:SO_0000272^c obo:SO_0000254^c obo:SO_0000766^c obo:SO_0000264^c obo:SO_0000263^c obo:SO_0000267^c obo:SO_0000273^c obo:SO_0001036^c obo:SO_0000260^c

alanyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000254`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000211^c

rRNA_small_subunit_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000255`
Super-classes	obo:SO_0000209^c

asparaginyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000256`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000213^c

aspartyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000257`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000214^c

cysteinyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000258`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000215^c

glutaminyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000259`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000216^c

glutamyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000260`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000217^c

glycyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000261`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000218^c

histidyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000262`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000219^c

isoleucyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000263`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000220^c

leucyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000264`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000221^c

lysyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000265`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000222^c

methionyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000266`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000223^c

phenylalanyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000267`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000224^c

prolyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000268`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000225^c

seryl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000269`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000226^c

threonyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000270`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000227^c

tryptophanyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000271`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000228^c

tyrosyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000272`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000229^c

valyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000273`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000230^c

snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000274`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0002247^c
Restrictions	so:derives_from^op some obo:SO_0000231^c
Sub-classes	obo:SO_0000394^c obo:SO_0000396^c obo:SO_0000397^c obo:SO_0000393^c obo:SO_0000391^c obo:SO_0002338^c obo:SO_0000395^c obo:SO_0000398^c obo:SO_0000399^c obo:SO_0000392^c

snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000275`
Super-classes	obo:SO_0002247^c
Restrictions	so:derives_from^op some obo:SO_0000232^c
Sub-classes	obo:SO_0000594^c obo:SO_0000593^c obo:SO_0002095^c

miRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000276`
Super-classes	obo:SO_0000370^c
Restrictions	so:derives_from^op some obo:SO_0001244^c
Sub-classes	obo:SO_0002167^c obo:SO_0002166^c

bound_by_factor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000277`
Description	Formerly called transcript_by_bound_factor.
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000876^c obo:SO_0000875^c

transcript_bound_by_nucleic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000278`
Description	Formerly called transcript_by_bound_nucleic_acid.
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000876^c

transcript_bound_by_protein^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000279`
Description	Formerly called transcript_by_bound_protein.
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000875^c

engineered_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000280`
Super-classes	obo:SO_0000704^c obo:SO_0000804^c
Restrictions	so:has_quality^op some obo:SO_0000783^c
Sub-classes	obo:SO_0000281^c obo:SO_0000288^c

engineered_foreign_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000281`
Super-classes	obo:SO_0000805^c obo:SO_0000280^c obo:SO_0000285^c
Restrictions	so:has_quality^op some obo:SO_0000783^c so:has_quality^op some obo:SO_0000784^c
Sub-classes	obo:SO_0000283^c

mRNA_with_minus_1_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000282`
Super-classes	obo:SO_0000108^c
Restrictions	so:has_quality^op some obo:SO_0000866^c

engineered_foreign_transposable_element_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000283`
Super-classes	obo:SO_0000111^c obo:SO_0000281^c
Restrictions	so:has_quality^op some obo:SO_0000784^c so:has_quality^op some obo:SO_0000783^c

type_I_enzyme_restriction_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000284`

foreign_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000285`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000784^c
Sub-classes	obo:SO_0000281^c

long_terminal_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000286`
Super-classes	obo:SO_0000657^c
Restrictions	so:part_of^op some obo:SO_0000186^c
Sub-classes	obo:SO_0000426^c obo:SO_0000425^c obo:SO_0001003^c

fusion_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000287`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000806^c
Sub-classes	obo:SO_0000288^c

engineered_fusion_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000288`
Super-classes	obo:SO_0000280^c obo:SO_0000287^c
Restrictions	so:has_quality^op some obo:SO_0000783^c

microsatellite^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000289`
Super-classes	obo:SO_0000005^c
Sub-classes	obo:SO_0000290^c obo:SO_0000641^c obo:SO_0000291^c

dinucleotide_repeat_microsatellite_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000290`
Super-classes	obo:SO_0000289^c
Sub-classes	obo:SO_0001862^c

trinucleotide_repeat_microsatellite_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000291`
Super-classes	obo:SO_0000289^c
Sub-classes	obo:SO_0001863^c

repetitive_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000292`

engineered_foreign_repetitive_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000293`
Super-classes	obo:SO_0000657^c obo:SO_0000805^c
Restrictions	so:has_quality^op some obo:SO_0000783^c so:has_quality^op some obo:SO_0000784^c

inverted_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000294`
Super-classes	obo:SO_0000657^c
Sub-classes	obo:SO_0000481^c

U12_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000295`
Description	May have either GT-AC or AT-AC 5' and 3' boundaries.
Super-classes	obo:SO_0000662^c

origin_of_replication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000296`
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0001235^c
Sub-classes	obo:SO_0000750^c obo:SO_0000724^c obo:SO_0000952^c obo:SO_0002203^c obo:SO_0002140^c obo:SO_0002293^c obo:SO_0000436^c obo:SO_0002141^c obo:SO_0000953^c obo:SO_0002171^c

D_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000297`
Description	Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0002294^c

recombination_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000298`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0002154^c obo:SO_0000669^c obo:SO_0000723^c obo:SO_0002155^c obo:SO_0000355^c obo:SO_0000339^c

specific_recombination_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000299`
Super-classes	obo:SO_0000669^c
Sub-classes	obo:SO_0000342^c obo:SO_0000300^c obo:SO_0001532^c

recombination_feature_of_rearranged_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000300`
Super-classes	obo:SO_0000299^c
Sub-classes	obo:SO_0000301^c

vertebrate_immune_system_gene_recombination_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000301`
Super-classes	obo:SO_0000300^c
Sub-classes	obo:SO_0000460^c obo:SO_0000938^c obo:SO_0000563^c obo:SO_0000482^c obo:SO_0001835^c obo:SO_0000939^c obo:SO_0000936^c obo:SO_0001836^c

J_gene_recombination_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000302`
Super-classes	obo:SO_0000939^c

clip^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000303`
Super-classes	obo:SO_0000835^c
Sub-classes	obo:SO_0000555^c obo:SO_0000557^c

type_II_enzyme_restriction_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000304`

modified_DNA_base^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000305`
Description	Modified base:.
Super-classes	obo:SO_0001720^c obo:SO_0001236^c
Sub-classes	obo:SO_0001963^c obo:SO_0000306^c obo:SO_0001964^c obo:SO_0001962^c

methylated_DNA_base_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000306`
Super-classes	obo:SO_0000305^c
Sub-classes	obo:SO_0000161^c obo:SO_0000114^c

CpG_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000307`
Super-classes	obo:SO_0001411^c

sequence_feature_locating_method^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000308`

computed_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000309`

predicted_ab_initio_computation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000310`

computed_feature_by_similarity^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000311`
Description	similar to:

experimentally_determined^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000312`
Super-classes	obo:SO_0000789^c

stem_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000313`
Super-classes	obo:SO_0000122^c
Sub-classes	obo:SO_0001008^c

direct_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000314`
Super-classes	obo:SO_0000657^c
Sub-classes	obo:SO_0001459^c obo:SO_0000434^c

TSS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000315`
Description	Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant.
Super-classes	obo:SO_0002309^c obo:SO_0000835^c
Sub-classes	obo:SO_0001238^c obo:SO_0001239^c

CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000316`
Super-classes	obo:SO_0000836^c
Sub-classes	obo:SO_0001384^c obo:SO_1001254^c obo:SO_0001896^c obo:SO_0002227^c obo:SO_1001246^c obo:SO_0000935^c

cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000317`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000151^c
Restrictions	so:has_quality^op some obo:SO_0000756^c
Sub-classes	obo:SO_0001433^c obo:SO_0000808^c obo:SO_0000809^c

start_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000318`
Super-classes	obo:SO_0000360^c
Sub-classes	obo:SO_0000680^c

stop_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000319`
Super-classes	obo:SO_0000360^c
Sub-classes	obo:SO_0002334^c obo:SO_0002333^c obo:SO_0002335^c

intronic_splice_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000320`
Super-classes	obo:SO_0000344^c
Restrictions	so:part_of^op some obo:SO_0000841^c

mRNA_with_plus_1_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000321`
Super-classes	obo:SO_0000108^c
Restrictions	so:has_quality^op some obo:SO_0000868^c

nuclease_hypersensitive_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000322`
Description	Relationship to accessible_DNA_region added 11 Feb 2021. GREEKC pointed out that this is an assay based term, but we need a biological term for the accessible DNA. See GitHub Issue #531.
Super-classes	obo:SO_0002331^c obo:SO_0000684^c
Sub-classes	obo:SO_0000685^c

coding_start^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000323`
Super-classes	obo:SO_0000851^c

tag^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000324`
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0000345^c obo:SO_0002023^c obo:SO_0000807^c obo:SO_0001916^c obo:SO_0000331^c obo:SO_0000326^c

rRNA_large_subunit_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000325`
Super-classes	obo:SO_0000209^c

SAGE_tag^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000326`
Super-classes	obo:SO_0000324^c

coding_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000327`
Super-classes	obo:SO_0000851^c

microarray_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000328`
Super-classes	obo:SO_0000051^c

mRNA_with_plus_2_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000329`
Super-classes	obo:SO_0000108^c
Restrictions	so:has_quality^op some obo:SO_0000869^c

conserved_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000330`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0001494^c obo:SO_0001495^c obo:SO_0001497^c obo:SO_0005858^c obo:SO_0000435^c obo:SO_0000332^c obo:SO_0001788^c obo:SO_0001493^c obo:SO_0001796^c obo:SO_0000853^c obo:SO_0000334^c

STS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000331`
Super-classes	obo:SO_0000324^c

coding_conserved_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000332`
Super-classes	obo:SO_0000330^c

exon_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000333`
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0000233^c

nc_conserved_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000334`
Super-classes	obo:SO_0000330^c

mRNA_with_minus_2_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000335`
Super-classes	obo:SO_0000108^c
Restrictions	so:has_quality^op some obo:SO_0000867^c

pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000336`
Super-classes	obo:SO_0001411^c
Restrictions	so:non_functional_homolog_of^op some obo:SO_0000704^c
Sub-classes	obo:SO_0002097^c obo:SO_0001841^c obo:SO_0001760^c obo:SO_0001897^c obo:SO_0000043^c

RNAi_reagent^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000337`
Super-classes	obo:SO_0000442^c

MITE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000338`
Super-classes	obo:SO_0000208^c

recombination_hotspot^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000339`
Super-classes	obo:SO_0000298^c
Sub-classes	obo:SO_0002094^c

chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000340`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0001235^c
Sub-classes	obo:SO_0000822^c obo:SO_0000819^c obo:SO_0000821^c obo:SO_0000828^c obo:SO_0000820^c obo:SO_0000823^c obo:SO_0000961^c obo:SO_0000954^c obo:SO_0000829^c obo:SO_0000824^c obo:SO_0001259^c obo:SO_0000825^c

chromosome_band^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000341`
Super-classes	obo:SO_0000830^c

site_specific_recombination_target_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000342`
Super-classes	obo:SO_0000299^c
Sub-classes	obo:SO_0001048^c obo:SO_0000947^c obo:SO_0000948^c obo:SO_0000946^c

match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000343`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0000347^c obo:SO_0000349^c

splice_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000344`
Super-classes	obo:SO_0001056^c
Sub-classes	obo:SO_0000320^c obo:SO_0000683^c

EST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000345`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000324^c
Restrictions	so:derives_from^op some obo:SO_0000234^c
Sub-classes	obo:SO_0001464^c obo:SO_0001209^c obo:SO_0001467^c obo:SO_0001208^c

loxP_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000346`
Super-classes	obo:SO_0000947^c

nucleotide_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000347`
Super-classes	obo:SO_0000343^c
Sub-classes	obo:SO_0000181^c obo:SO_0001472^c obo:SO_0000102^c obo:SO_0000177^c

nucleic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000348`
Super-classes	obo:SO_0000443^c
Sub-classes	obo:SO_0000352^c obo:SO_0001190^c obo:SO_0001184^c obo:SO_0000356^c obo:SO_0001192^c obo:SO_0001183^c obo:SO_0001188^c

protein_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000349`
Super-classes	obo:SO_0000343^c
Sub-classes	obo:SO_0001831^c

FRT_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000350`
Super-classes	obo:SO_0000948^c

synthetic_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000351`
Super-classes	obo:SO_0000443^c
Sub-classes	obo:SO_0000546^c obo:SO_0000449^c

DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000352`
Super-classes	obo:SO_0000348^c
Sub-classes	obo:SO_0000756^c obo:SO_0000991^c

sequence_assembly^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000353`
Super-classes	obo:SO_0001248^c
Sub-classes	obo:SO_0000149^c obo:SO_0001428^c obo:SO_0000688^c obo:SO_0001876^c obo:SO_0000472^c obo:SO_0000499^c

group_1_intron_homing_endonuclease_target_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000354`
Super-classes	obo:SO_0000684^c

haplotype_block^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000355`
Super-classes	obo:SO_0000298^c

RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000356`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000348^c

flanked^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000357`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000359^c obo:SO_0000361^c

SO_0000358^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000358`

floxed^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000359`
Super-classes	obo:SO_0000357^c

codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000360`
Super-classes	obo:SO_0000851^c
Sub-classes	obo:SO_0000145^c obo:SO_0000319^c obo:SO_0000318^c

FRT_flanked^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000361`
Super-classes	obo:SO_0000357^c

invalidated_by_chimeric_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000362`
Super-classes	obo:SO_0000790^c

floxed_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000363`
Super-classes	obo:SO_0000902^c
Restrictions	so:has_quality^op some obo:SO_0000359^c

transposable_element_flanking_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000364`
Super-classes	obo:SO_0000239^c

integron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000365`
Super-classes	obo:SO_0001039^c

insertion_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000366`
Super-classes	obo:SO_0000699^c
Sub-classes	obo:SO_0000368^c

attI_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000367`
Super-classes	obo:SO_0000946^c
Restrictions	so:part_of^op some obo:SO_0000365^c

transposable_element_insertion_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000368`
Super-classes	obo:SO_0000366^c

integrase_coding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000369`

small_regulatory_ncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000370`
Super-classes	obo:SO_0002247^c
Sub-classes	obo:SO_0001035^c obo:SO_0000388^c obo:SO_0000384^c obo:SO_0002032^c obo:SO_0000377^c obo:SO_0000389^c obo:SO_0000584^c obo:SO_0000376^c obo:SO_0000276^c obo:SO_0000387^c obo:SO_0000378^c obo:SO_0002033^c obo:SO_0000646^c

conjugative_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000371`
Super-classes	obo:SO_0000182^c

enzymatic_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000372`
Description	This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533.
Super-classes	obo:SO_0000655^c
Restrictions	so:has_quality^op some obo:SO_0001185^c
Sub-classes	obo:SO_0000385^c obo:SO_0000374^c obo:SO_0000386^c

recombinationally_inverted_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000373`
Super-classes	obo:SO_0000456^c
Restrictions	so:has_quality^op some obo:SO_1000036^c

ribozyme^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000374`
Super-classes	obo:SO_0000372^c
Restrictions	so:has_quality^op some obo:SO_0001186^c
Sub-classes	obo:SO_0002231^c

cytosolic_5_8S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000375`
Description	Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

RNA_6S^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000376`
Super-classes	obo:SO_0000370^c

CsrB_RsmB_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000377`
Super-classes	obo:SO_0000370^c

DsrA_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000378`
Super-classes	obo:SO_0000370^c
Sub-classes	obo:SO_0000379^c

GcvB_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000379`
Super-classes	obo:SO_0000378^c

hammerhead_ribozyme^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000380`
Super-classes	obo:SO_0000715^c
Restrictions	so:has_quality^op some obo:SO_0001186^c

group_IIA_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000381`
Super-classes	obo:SO_0000603^c

group_IIB_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000382`
Super-classes	obo:SO_0000603^c

MicF_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000383`
Super-classes	obo:SO_0000644^c

OxyS_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000384`
Super-classes	obo:SO_0000370^c

RNase_MRP_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000385`
Description	Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.
Super-classes	obo:SO_0000372^c

RNase_P_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000386`
Description	Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533.
Super-classes	obo:SO_0000372^c

RprA_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000387`
Super-classes	obo:SO_0000370^c

RRE_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000388`
Super-classes	obo:SO_0000370^c

spot_42_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000389`
Super-classes	obo:SO_0000370^c

telomerase_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000390`
Super-classes	obo:SO_0000655^c

U1_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000391`
Super-classes	obo:SO_0000274^c

U2_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000392`
Super-classes	obo:SO_0000274^c

U4_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000393`
Super-classes	obo:SO_0000274^c

U4atac_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000394`
Super-classes	obo:SO_0000274^c

U5_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000395`
Super-classes	obo:SO_0000274^c

U6_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000396`
Super-classes	obo:SO_0000274^c

U6atac_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000397`
Super-classes	obo:SO_0000274^c

U11_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000398`
Super-classes	obo:SO_0000274^c

U12_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000399`
Super-classes	obo:SO_0000274^c

sequence_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000400`
Sub-classes	obo:SO_0000443^c obo:SO_0000733^c obo:SO_0000735^c obo:SO_0001761^c obo:SO_0002206^c

gene_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000401`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000133^c obo:SO_0000067^c obo:SO_0000463^c obo:SO_0000011^c obo:SO_0001241^c obo:SO_0000119^c obo:SO_0000081^c obo:SO_0000010^c

enhancer_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000402`

U14_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000403`
Description	An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
Super-classes	obo:SO_0000593^c
Restrictions	so:derives_from^op some obo:SO_0005837^c

vault_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000404`
Super-classes	obo:SO_0000655^c

Y_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000405`
Super-classes	obo:SO_0000655^c

twintron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000406`
Super-classes	obo:SO_0000188^c

cytosolic_18S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000407`
Description	Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000650^c

site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000408`

binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000409`
Description	See GO:0005488 : binding.
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0001018^c obo:SO_0001656^c obo:SO_0001655^c obo:SO_0001657^c obo:SO_0000410^c obo:SO_0002233^c

protein_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000410`
Description	See GO:0042277 : peptide binding.
Super-classes	obo:SO_0000409^c
Sub-classes	obo:SO_0001093^c obo:SO_0001654^c

rescue_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000411`
Super-classes	obo:SO_0000695^c
Restrictions	so:has_quality^op some obo:SO_0000814^c
Sub-classes	obo:SO_0000794^c

restriction_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000412`
Super-classes	obo:SO_0000143^c
Sub-classes	obo:SO_0000193^c

sequence_difference^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000413`
Super-classes	obo:SO_0000700^c
Sub-classes	obo:SO_0000702^c obo:SO_0000701^c obo:SO_0001525^c obo:SO_0002172^c obo:SO_0001526^c

invalidated_by_genomic_contamination^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000414`
Super-classes	obo:SO_0000790^c

invalidated_by_genomic_polyA_primed_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000415`
Super-classes	obo:SO_0000790^c

invalidated_by_partial_processing^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000416`
Super-classes	obo:SO_0000790^c

polypeptide_domain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000417`
Description	Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
Super-classes	obo:SO_0001070^c obo:SO_0100021^c

signal_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000418`
Description	Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
Super-classes	obo:SO_0001527^c
Restrictions	so:part_of^op some obo:SO_0001062^c so:derives_from^op some obo:SO_0002251^c
Sub-classes	obo:SO_0001809^c

mature_protein_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000419`
Description	This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
Super-classes	obo:SO_0000839^c
Restrictions	so:part_of^op some obo:SO_0001063^c so:derives_from^op some obo:SO_0002249^c
Sub-classes	obo:SO_0001064^c

five_prime_terminal_inverted_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000420`
Super-classes	obo:SO_0000481^c

three_prime_terminal_inverted_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000421`
Super-classes	obo:SO_0000481^c

U5_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000422`
Super-classes	obo:SO_0000848^c
Sub-classes	obo:SO_0000428^c

R_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000423`
Super-classes	obo:SO_0000848^c
Sub-classes	obo:SO_0000427^c

U3_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000424`
Super-classes	obo:SO_0000848^c
Sub-classes	obo:SO_0000429^c

five_prime_LTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000425`
Super-classes	obo:SO_0000286^c

three_prime_LTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000426`
Super-classes	obo:SO_0000286^c

R_five_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000427`
Super-classes	obo:SO_0000423^c obo:SO_0000850^c

U5_five_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000428`
Super-classes	obo:SO_0000422^c obo:SO_0000850^c

U3_five_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000429`
Super-classes	obo:SO_0000850^c obo:SO_0000424^c

R_three_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000430`
Super-classes	obo:SO_0000849^c

U3_three_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000431`
Super-classes	obo:SO_0000849^c

U5_three_prime_LTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000432`
Super-classes	obo:SO_0000849^c

non_LTR_retrotransposon_polymeric_tract^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000433`
Super-classes	obo:SO_0000657^c obo:SO_0000840^c
Restrictions	so:part_of^op some obo:SO_0000189^c

target_site_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000434`
Super-classes	obo:SO_0000314^c
Restrictions	so:derives_from^op some obo:SO_0000101^c

RR_tract^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000435`
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0000186^c

ARS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000436`
Super-classes	obo:SO_0000296^c

assortment_derived_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000437`

gene_not_polyadenylated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000438`

inverted_ring_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000439`
Super-classes	obo:SO_1000030^c obo:SO_1000045^c

vector_replicon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000440`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0001235^c
Restrictions	so:part_of^op some obo:SO_0000151^c
Sub-classes	obo:SO_0000754^c obo:SO_0000154^c obo:SO_0000153^c obo:SO_0000156^c obo:SO_0001644^c obo:SO_0000152^c obo:SO_0000755^c obo:SO_0000157^c obo:SO_0000158^c

ss_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000441`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0000112^c

ds_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000442`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0001009^c obo:SO_0000337^c

polymer_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000443`
Super-classes	obo:SO_0000400^c
Sub-classes	obo:SO_0000986^c obo:SO_0000348^c obo:SO_0001407^c obo:SO_0000351^c

three_prime_noncoding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000444`
Super-classes	obo:SO_0000198^c

five_prime_noncoding_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000445`
Super-classes	obo:SO_0000198^c

UTR_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000446`
Super-classes	obo:SO_0000188^c
Sub-classes	obo:SO_0000448^c obo:SO_0000447^c

five_prime_UTR_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000447`
Super-classes	obo:SO_0000446^c

three_prime_UTR_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000448`
Super-classes	obo:SO_0000446^c

random_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000449`
Super-classes	obo:SO_0000351^c

interband^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000450`
Super-classes	obo:SO_0000830^c

gene_with_polyadenylated_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000451`
Super-classes	obo:SO_0001217^c
Restrictions	so:transcribed_to^op some obo:SO_0000871^c

transgene_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000452`

chromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000453`
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_1000155^c obo:SO_1000041^c

rasiRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000454`
Super-classes	obo:SO_0000655^c

gene_with_mRNA_with_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000455`
Super-classes	obo:SO_0001217^c
Restrictions	so:has_quality^op some obo:SO_0000865^c

recombinationally_rearranged_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000456`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000940^c
Sub-classes	obo:SO_0000941^c obo:SO_0000373^c

interchromosomal_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000457`
Super-classes	obo:SO_1000037^c

D_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000458`
Super-classes	obo:SO_0000460^c

gene_with_trans_spliced_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000459`
Super-classes	obo:SO_0000704^c
Restrictions	so:transcribed_to^op some obo:SO_0000479^c

vertebrate_immunoglobulin_T_cell_receptor_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000460`
Description	I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000478^c obo:SO_0000458^c obo:SO_0000470^c obo:SO_0000466^c

inversion_derived_bipartite_deficiency^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000461`
Super-classes	obo:SO_1000029^c

pseudogenic_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000462`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0000516^c obo:SO_0000507^c obo:SO_0002087^c obo:SO_0000464^c

encodes_alternately_spliced_transcripts^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000463`
Super-classes	obo:SO_0000401^c
Sub-classes	obo:SO_1001189^c obo:SO_1001188^c

decayed_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000464`
Description	Does not have to be part of a pseudogene.
Super-classes	obo:SO_0000462^c
Restrictions	so:non_functional_homolog_of^op some obo:SO_0000147^c

inversion_derived_deficiency_plus_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000465`
Super-classes	obo:SO_1000029^c obo:SO_1000038^c

V_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000466`
Super-classes	obo:SO_0000460^c

post_translationally_regulated_by_protein_stability^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000467`
Super-classes	obo:SO_0000130^c

golden_path_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000468`
Super-classes	obo:SO_0000143^c
Restrictions	so:part_of^op some obo:SO_0000688^c

post_translationally_regulated_by_protein_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000469`
Super-classes	obo:SO_0000130^c

J_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000470`
Super-classes	obo:SO_0000460^c

autoregulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000471`
Super-classes	obo:SO_0000123^c
Sub-classes	obo:SO_0000475^c obo:SO_0000473^c

tiling_path^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000472`
Super-classes	obo:SO_0000353^c

negatively_autoregulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000473`
Super-classes	obo:SO_0000471^c obo:SO_0000126^c

tiling_path_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000474`
Super-classes	obo:SO_0000143^c
Restrictions	so:part_of^op some obo:SO_0000472^c
Sub-classes	obo:SO_0000480^c

positively_autoregulated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000475`
Super-classes	obo:SO_0000471^c obo:SO_0000125^c

contig_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000476`
Super-classes	obo:SO_0000150^c

polycistronic_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000477`

C_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000478`
Super-classes	obo:SO_0000460^c

trans_spliced_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000479`
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000870^c
Sub-classes	obo:SO_0000872^c

tiling_path_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000480`
Super-classes	obo:SO_0000474^c obo:SO_0000151^c

terminal_inverted_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000481`
Super-classes	obo:SO_0000294^c
Restrictions	so:part_of^op some obo:SO_0000208^c
Sub-classes	obo:SO_0000420^c obo:SO_0000421^c

vertebrate_immunoglobulin_T_cell_receptor_gene_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000482`
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000559^c obo:SO_0000534^c obo:SO_0000513^c obo:SO_0000509^c obo:SO_0000560^c obo:SO_0000535^c obo:SO_0000511^c obo:SO_0000526^c obo:SO_0000558^c

nc_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000483`
Super-classes	obo:SO_0000185^c
Sub-classes	obo:SO_0000209^c obo:SO_0000231^c obo:SO_0002042^c obo:SO_0000589^c obo:SO_0000647^c obo:SO_0000210^c obo:SO_0002035^c obo:SO_0002038^c obo:SO_0001801^c obo:SO_0000012^c obo:SO_0000586^c obo:SO_0000232^c obo:SO_0002040^c

three_prime_coding_exon_noncoding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000484`
Super-classes	obo:SO_0001214^c
Restrictions	so:part_of^op some obo:SO_0000202^c

DJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000485`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000572^c

five_prime_coding_exon_noncoding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000486`
Super-classes	obo:SO_0001214^c
Restrictions	so:part_of^op some obo:SO_0000200^c

VDJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000487`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000574^c so:has_part^op some obo:SO_0000478^c

VDJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000488`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000574^c so:has_part^op some obo:SO_0000470^c

VJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000489`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000576^c

VJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000490`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000470^c

VJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000491`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000470^c

D_gene_recombination_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000492`
Super-classes	obo:SO_0000939^c
Sub-classes	obo:SO_0000556^c obo:SO_0000570^c

three_prime_D_heptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000493`
Super-classes	obo:SO_0000561^c
Restrictions	so:part_of^op some obo:SO_0000570^c

three_prime_D_nonamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000494`
Super-classes	obo:SO_0000562^c
Restrictions	so:part_of^op some obo:SO_0000570^c

three_prime_D_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000495`
Super-classes	obo:SO_0000563^c
Restrictions	so:part_of^op some obo:SO_0000570^c

five_prime_D_heptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000496`
Super-classes	obo:SO_0000561^c
Restrictions	so:part_of^op some obo:SO_0000556^c

five_prime_D_nonamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000497`
Super-classes	obo:SO_0000562^c
Restrictions	so:part_of^op some obo:SO_0000556^c

five_prime_D_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000498`
Super-classes	obo:SO_0000563^c
Restrictions	so:part_of^op some obo:SO_0000556^c

virtual_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000499`
Super-classes	obo:SO_0000353^c

Hoogsteen_base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000500`
Super-classes	obo:SO_0000028^c

reverse_Hoogsteen_base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000501`
Super-classes	obo:SO_0000028^c

transcribed_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000502`
Description	This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.

alternately_spliced_gene_encodeing_one_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000503`

D_DJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000504`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000572^c

D_DJ_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000505`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000572^c

D_DJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000506`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000470^c

pseudogenic_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000507`
Description	This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
Super-classes	obo:SO_0000462^c
Restrictions	so:non_functional_homolog_of^op some obo:SO_0000147^c so:part_of^op some obo:SO_0000516^c

D_DJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000508`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000572^c

D_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000509`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000458^c

VD_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000510`
Super-classes	obo:SO_0000936^c

J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000511`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000478^c

inversion_derived_deficiency_plus_aneuploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000512`
Super-classes	obo:SO_1000029^c

J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000513`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000470^c

J_nonamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000514`
Super-classes	obo:SO_0000562^c
Restrictions	so:part_of^op some obo:SO_0000302^c

J_heptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000515`
Super-classes	obo:SO_0000561^c
Restrictions	so:part_of^op some obo:SO_0000302^c

pseudogenic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000516`
Description	This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
Super-classes	obo:SO_0000462^c
Restrictions	so:part_of^op some obo:SO_0000336^c so:non_functional_homolog_of^op some obo:SO_0000673^c
Sub-classes	obo:SO_0000777^c obo:SO_0000778^c

J_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000517`
Super-classes	obo:SO_0000563^c
Restrictions	so:part_of^op some obo:SO_0000302^c

V_DJ_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000518`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000466^c

V_DJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000519`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000470^c

V_VDJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000520`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000574^c so:has_part^op some obo:SO_0000466^c

V_VDJ_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000521`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000574^c so:has_part^op some obo:SO_0000466^c

V_VDJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000522`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000574^c

V_VJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000523`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000466^c

V_VJ_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000524`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000466^c

V_VJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000525`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000466^c

V_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000526`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000466^c

V_D_DJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000527`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000466^c

V_D_DJ_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000528`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000572^c

V_D_DJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000529`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000470^c

V_D_DJ_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000530`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000458^c

V_D_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000531`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000458^c

V_D_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000532`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000470^c

V_heptamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000533`
Super-classes	obo:SO_0000561^c
Restrictions	so:part_of^op some obo:SO_0000538^c

V_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000534`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000470^c

V_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000535`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000466^c

V_nonamer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000536`
Super-classes	obo:SO_0000562^c
Restrictions	so:part_of^op some obo:SO_0000538^c

V_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000537`
Super-classes	obo:SO_0000563^c
Restrictions	so:part_of^op some obo:SO_0000538^c

V_gene_recombination_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000538`
Super-classes	obo:SO_0000939^c

DJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000539`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000478^c

DJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000540`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000470^c

VDJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000541`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000574^c

V_DJ_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000542`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000572^c

alternately_spliced_gene_encoding_greater_than_one_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000543`

helitron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000544`
Super-classes	obo:SO_0000182^c

recoding_pseudoknot^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000545`
Super-classes	obo:SO_0000591^c
Restrictions	so:part_of^op some obo:SO_1001268^c

designed_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000546`
Super-classes	obo:SO_0000351^c

inversion_derived_bipartite_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000547`
Super-classes	obo:SO_1000038^c

gene_with_edited_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000548`
Super-classes	obo:SO_0001217^c
Restrictions	so:transcribed_to^op some obo:SO_0000873^c

inversion_derived_duplication_plus_aneuploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000549`
Super-classes	obo:SO_1000038^c

aneuploid_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000550`
Description	Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_0000567^c

polyA_signal_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000551`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c

Shine_Dalgarno_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000552`
Description	Not found in Eukaryotic sequence.
Super-classes	obo:SO_0000139^c

polyA_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000553`
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0000233^c so:part_of^op some obo:SO_0000205^c

assortment_derived_deficiency_plus_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000554`

five_prime_clip^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000555`
Super-classes	obo:SO_0000303^c

five_prime_D_recombination_signal_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000556`
Super-classes	obo:SO_0000492^c

three_prime_clip^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000557`
Super-classes	obo:SO_0000303^c

C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000558`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000478^c

D_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000559`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000458^c

D_J_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000560`
Super-classes	obo:SO_0000482^c
Restrictions	so:has_part^op some obo:SO_0000458^c so:has_part^op some obo:SO_0000470^c

heptamer_of_recombination_feature_of_vertebrate_immune_system_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000561`
Super-classes	obo:SO_0000939^c
Sub-classes	obo:SO_0000496^c obo:SO_0000533^c obo:SO_0000493^c obo:SO_0000515^c

nonamer_of_recombination_feature_of_vertebrate_immune_system_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000562`
Super-classes	obo:SO_0000939^c
Sub-classes	obo:SO_0000494^c obo:SO_0000514^c obo:SO_0000536^c obo:SO_0000497^c

vertebrate_immune_system_gene_recombination_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000563`
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000498^c obo:SO_0000517^c obo:SO_0000495^c obo:SO_0000537^c

V_DJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000564`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000572^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000470^c

V_VDJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000565`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000574^c so:has_part^op some obo:SO_0000470^c so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000466^c

V_VJ_J_C_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000566`
Super-classes	obo:SO_0000938^c
Restrictions	so:has_part^op some obo:SO_0000478^c so:has_part^op some obo:SO_0000466^c so:has_part^op some obo:SO_0000576^c so:has_part^op some obo:SO_0000470^c

inversion_derived_aneuploid_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000567`
Super-classes	obo:SO_0000550^c

bidirectional_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000568`
Description	Definition updated in Aug 2020 by Dave Sant.
Super-classes	obo:SO_0000167^c

retrotransposed^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000569`
Description	GO:0003964 RNA-directed DNA polymerase activity.
Super-classes	obo:SO_0000733^c

three_prime_D_recombination_signal_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000570`
Super-classes	obo:SO_0000492^c

miRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000571`
Super-classes	obo:SO_0000011^c

DJ_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000572`
Super-classes	obo:SO_0000936^c

rRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000573`
Super-classes	obo:SO_0000011^c

VDJ_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000574`
Super-classes	obo:SO_0000936^c

scRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000575`
Super-classes	obo:SO_0000011^c

VJ_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000576`
Super-classes	obo:SO_0000936^c

centromere^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000577`
Super-classes	obo:SO_0000628^c
Sub-classes	obo:SO_0001795^c obo:SO_0001794^c

snoRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000578`
Super-classes	obo:SO_0000011^c
Sub-classes	obo:SO_0000608^c obo:SO_0000585^c

edited_transcript_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000579`
Super-classes	obo:SO_0000833^c
Sub-classes	obo:SO_0000604^c obo:SO_0000607^c obo:SO_0000606^c obo:SO_0000583^c

methylation_guide_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000580`
Super-classes	obo:SO_0000232^c

cap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000581`
Super-classes	obo:SO_0001411^c

rRNA_cleavage_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000582`
Super-classes	obo:SO_0000232^c

pre_edited_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000583`
Super-classes	obo:SO_0000579^c

tmRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000584`
Super-classes	obo:SO_0000370^c

C_D_box_snoRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000585`
Super-classes	obo:SO_0000578^c

tmRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000586`
Super-classes	obo:SO_0000483^c

group_I_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000587`
Description	GO:0000372.
Super-classes	obo:SO_0000588^c

autocatalytically_spliced_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000588`
Super-classes	obo:SO_0000188^c
Restrictions	so:has_quality^op some obo:SO_0001186^c
Sub-classes	obo:SO_0000603^c obo:SO_0000587^c obo:SO_0001213^c

SRP_RNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000589`
Super-classes	obo:SO_0000483^c

SRP_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000590`
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0000589^c

pseudoknot^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000591`
Super-classes	obo:SO_0000002^c
Sub-classes	obo:SO_0000545^c obo:SO_0000592^c

H_pseudoknot^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000592`
Super-classes	obo:SO_0000591^c

C_D_box_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000593`
Super-classes	obo:SO_0000275^c
Restrictions	so:derives_from^op some obo:SO_0000595^c
Sub-classes	obo:SO_0001179^c obo:SO_0005841^c obo:SO_0000403^c

H_ACA_box_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000594`
Super-classes	obo:SO_0000275^c
Restrictions	so:derives_from^op some obo:SO_0000596^c
Sub-classes	obo:SO_0001187^c

C_D_box_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000595`
Super-classes	obo:SO_0000232^c

H_ACA_box_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000596`
Super-classes	obo:SO_0000232^c

transcript_edited_by_U_insertion/deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000597`

edited_by_C_insertion_and_dinucleotide_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000598`

edited_by_C_to_U_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000599`

edited_by_A_to_I_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000600`

edited_by_G_addition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000601`

guide_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000602`
Super-classes	obo:SO_0000655^c

group_II_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000603`
Description	GO:0000373.
Super-classes	obo:SO_0000588^c
Sub-classes	obo:SO_0000382^c obo:SO_0000381^c obo:SO_0002226^c

editing_block^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000604`
Super-classes	obo:SO_0000579^c

intergenic_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000605`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0001411^c

editing_domain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000606`
Super-classes	obo:SO_0000579^c

unedited_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000607`
Super-classes	obo:SO_0000579^c

H_ACA_box_snoRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000608`
Super-classes	obo:SO_0000578^c

oligo_U_tail^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000609`
Super-classes	obo:SO_0001411^c
Restrictions	so:adjacent_to^op some obo:SO_0000602^c

polyA_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000610`
Super-classes	obo:SO_0001411^c
Restrictions	so:adjacent_to^op some obo:SO_0000234^c

branch_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000611`
Super-classes	obo:SO_0000841^c

polypyrimidine_tract^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000612`
Super-classes	obo:SO_0000841^c

bacterial_RNApol_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000613`
Description	former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.
Super-classes	obo:SO_0002222^c
Sub-classes	obo:SO_0001672^c obo:SO_0001913^c obo:SO_0001671^c

bacterial_terminator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000614`
Description	Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529.
Super-classes	obo:SO_0000141^c
Sub-classes	obo:SO_0000981^c obo:SO_0000982^c

terminator_of_type_2_RNApol_III_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000615`
Super-classes	obo:SO_0000951^c

transcription_end_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000616`
Super-classes	obo:SO_0000835^c

RNApol_III_promoter_type_1^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000617`
Super-classes	obo:SO_0000171^c

RNApol_III_promoter_type_2^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000618`
Super-classes	obo:SO_0000171^c

A_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000619`
Description	Binds TFIIIC.
Super-classes	obo:SO_0001660^c
Sub-classes	obo:SO_0001675^c obo:SO_0001676^c

B_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000620`
Description	Binds TFIIIC.
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0000618^c

RNApol_III_promoter_type_3^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000621`
Super-classes	obo:SO_0000171^c

C_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000622`
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0000617^c

snRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000623`
Super-classes	obo:SO_0000011^c

telomere^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000624`
Super-classes	obo:SO_0000628^c

silencer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000625`
Super-classes	obo:SO_0000727^c
Sub-classes	obo:SO_0002058^c obo:SO_0002056^c

chromosomal_regulatory_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000626`
Super-classes	obo:SO_0000830^c
Sub-classes	obo:SO_0000036^c

insulator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000627`
Description	moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
Super-classes	obo:SO_0000727^c
Sub-classes	obo:SO_0002020^c obo:SO_0002190^c

chromosomal_structural_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000628`
Super-classes	obo:SO_0000830^c
Sub-classes	obo:SO_0000624^c obo:SO_0000577^c obo:SO_0001997^c

five_prime_open_reading_frame^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000629`
Super-classes	obo:SO_0000836^c
Restrictions	so:part_of^op some obo:SO_0000204^c

upstream_AUG_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000630`
Super-classes	obo:SO_0000837^c
Restrictions	so:part_of^op some obo:SO_0000203^c

polycistronic_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000631`
Super-classes	obo:SO_0000078^c obo:SO_0000185^c
Restrictions	so:has_quality^op some obo:SO_0000880^c
Sub-classes	obo:SO_1001197^c

monocistronic_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000632`
Super-classes	obo:SO_0000185^c obo:SO_0000665^c
Restrictions	so:has_quality^op some obo:SO_0000878^c

monocistronic_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000633`
Super-classes	obo:SO_0000234^c obo:SO_0000665^c
Restrictions	so:has_quality^op some obo:SO_0000878^c

polycistronic_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000634`
Super-classes	obo:SO_0000234^c obo:SO_0000078^c
Restrictions	so:has_quality^op some obo:SO_0000880^c
Sub-classes	obo:SO_0000716^c

mini_exon_donor_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000635`
Super-classes	obo:SO_0000185^c

spliced_leader_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000636`
Super-classes	obo:SO_0000835^c
Restrictions	so:part_of^op some obo:SO_0000635^c

engineered_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000637`
Super-classes	obo:SO_0000804^c obo:SO_0000155^c
Restrictions	so:has_quality^op some obo:SO_0000783^c
Sub-classes	obo:SO_0000779^c obo:SO_0001478^c obo:SO_0001477^c obo:SO_0001479^c

transcribed_spacer_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000638`
Super-classes	obo:SO_0000838^c
Sub-classes	obo:SO_0000640^c obo:SO_0000639^c

internal_transcribed_spacer_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000639`
Super-classes	obo:SO_0000638^c

external_transcribed_spacer_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000640`
Super-classes	obo:SO_0000638^c

tetranucleotide_repeat_microsatellite_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000641`
Super-classes	obo:SO_0000289^c

SRP_RNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000642`
Super-classes	obo:SO_0000011^c

minisatellite^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000643`
Super-classes	obo:SO_0000005^c

antisense_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000644`
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0000645^c
Sub-classes	obo:SO_0000383^c obo:SO_0001904^c

antisense_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000645`
Super-classes	obo:SO_0000185^c

siRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000646`
Super-classes	obo:SO_0000370^c

miRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000647`
Super-classes	obo:SO_0000483^c
Restrictions	so:has_part^op some obo:SO_0001244^c

SO_0000648^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000648`

SO_0000649^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000649`

cytosolic_SSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000650`
Description	Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Super-classes	obo:SO_0002343^c
Restrictions	so:derives_from^op some obo:SO_0000255^c
Sub-classes	obo:SO_0001000^c obo:SO_0000407^c

cytosolic_LSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000651`
Description	Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Super-classes	obo:SO_0002343^c
Restrictions	so:derives_from^op some obo:SO_0000325^c
Sub-classes	obo:SO_0002337^c obo:SO_0000375^c obo:SO_0001001^c obo:SO_0000653^c obo:SO_0001002^c obo:SO_0000652^c

cytosolic_5S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000652`
Description	Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

cytosolic_28S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000653`
Description	Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

maxicircle_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000654`
Super-classes	obo:SO_0000089^c
Restrictions	so:part_of^op some obo:SO_0000742^c
Sub-classes	obo:SO_1001196^c

ncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000655`
Description	A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
Super-classes	obo:SO_0000233^c
Sub-classes	obo:SO_0000252^c obo:SO_0000990^c obo:SO_0000404^c obo:SO_0002031^c obo:SO_0000390^c obo:SO_0000644^c obo:SO_0000454^c obo:SO_0002356^c obo:SO_0005843^c obo:SO_0001927^c obo:SO_0000013^c obo:SO_0002352^c obo:SO_0001800^c obo:SO_0000989^c obo:SO_0000602^c obo:SO_0001870^c obo:SO_0001877^c obo:SO_0002022^c obo:SO_0002247^c obo:SO_0002120^c obo:SO_0000590^c obo:SO_0002291^c obo:SO_0002354^c obo:SO_0002340^c obo:SO_0000372^c obo:SO_0000405^c

stRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000656`
Super-classes	obo:SO_0000011^c

repeat_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000657`
Super-classes	obo:SO_0001411^c
Restrictions	so:has_part^op some obo:SO_0000726^c
Sub-classes	obo:SO_0000314^c obo:SO_0002201^c obo:SO_0000433^c obo:SO_0000658^c obo:SO_0001649^c obo:SO_0001484^c obo:SO_0000293^c obo:SO_0002192^c obo:SO_0001496^c obo:SO_0001485^c obo:SO_0001797^c obo:SO_0000286^c obo:SO_0000705^c obo:SO_0000294^c obo:SO_0002257^c

dispersed_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000658`
Super-classes	obo:SO_0000657^c

tmRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000659`
Super-classes	obo:SO_0000011^c

DNA_invertase_target_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000660`

intron_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000661`

spliceosomal_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000662`
Description	GO:0000398.
Super-classes	obo:SO_0000188^c
Sub-classes	obo:SO_0000184^c obo:SO_0000295^c

tRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000663`
Super-classes	obo:SO_0000011^c

introgressed_chromosome_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000664`
Super-classes	obo:SO_0000830^c

monocistronic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000665`
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000878^c
Sub-classes	obo:SO_0000632^c obo:SO_0000633^c

mobile_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000666`
Super-classes	obo:SO_0001037^c obo:SO_0000188^c
Restrictions	so:has_quality^op some obo:SO_0001234^c

insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000667`
Super-classes	obo:SO_0001059^c obo:SO_0001411^c
Sub-classes	obo:SO_0001218^c obo:SO_0001837^c obo:SO_1000035^c obo:SO_0001838^c

EST_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000668`
Super-classes	obo:SO_0000102^c

sequence_rearrangement_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000669`
Super-classes	obo:SO_0000298^c
Sub-classes	obo:SO_0000672^c obo:SO_0000671^c obo:SO_0000299^c obo:SO_0000670^c

chromosome_breakage_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000670`
Super-classes	obo:SO_0000669^c

internal_eliminated_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000671`
Super-classes	obo:SO_0000669^c

macronucleus_destined_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000672`
Super-classes	obo:SO_0000669^c

transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000673`
Description	Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.
Super-classes	obo:SO_0000831^c
Restrictions	so:overlaps^op some obo:SO_0002300^c
Sub-classes	obo:SO_0000681^c obo:SO_0000278^c obo:SO_0000185^c obo:SO_0000479^c obo:SO_0002208^c obo:SO_0002138^c obo:SO_0000118^c obo:SO_0000233^c obo:SO_0000078^c obo:SO_0001503^c obo:SO_1001187^c obo:SO_0000873^c obo:SO_0000279^c obo:SO_0000665^c

non_canonical_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000674`

canonical_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000675`

canonical_three_prime_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000676`
Super-classes	obo:SO_0000164^c

canonical_five_prime_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000677`
Super-classes	obo:SO_0000163^c

non_canonical_three_prime_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000678`
Super-classes	obo:SO_0000164^c

non_canonical_five_prime_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000679`
Super-classes	obo:SO_0000163^c

non_canonical_start_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000680`
Super-classes	obo:SO_0000318^c
Sub-classes	obo:SO_1001273^c obo:SO_1001269^c

aberrant_processed_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000681`
Super-classes	obo:SO_0000673^c

splicing_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000682`

exonic_splice_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000683`
Super-classes	obo:SO_0000344^c

nuclease_sensitive_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000684`
Super-classes	obo:SO_0000059^c
Sub-classes	obo:SO_0000354^c obo:SO_0000322^c

DNaseI_hypersensitive_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000685`
Super-classes	obo:SO_0000322^c

translocation_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000686`
Super-classes	obo:SO_1000044^c

deletion_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000687`
Super-classes	obo:SO_0000699^c

golden_path^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000688`
Super-classes	obo:SO_0000353^c

cDNA_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000689`
Super-classes	obo:SO_0000102^c

gene_with_polycistronic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000690`
Super-classes	obo:SO_0000704^c
Restrictions	so:transcribed_to^op some obo:SO_0000078^c
Sub-classes	obo:SO_0000692^c

cleaved_initiator_methionine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000691`
Super-classes	obo:SO_0100011^c

gene_with_dicistronic_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000692`
Super-classes	obo:SO_0000690^c
Restrictions	so:transcribed_to^op some obo:SO_0000079^c
Sub-classes	obo:SO_0000721^c obo:SO_0000722^c

gene_with_recoded_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000693`
Super-classes	obo:SO_0001217^c
Restrictions	so:has_quality^op some obo:SO_0000881^c
Sub-classes	obo:SO_0000711^c obo:SO_0000697^c obo:SO_0000712^c

SNP^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000694`
Super-classes	obo:SO_0001483^c

reagent^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000695`
Description	Requested by Lynn Crosby, jan 2006.
Super-classes	obo:SO_0001409^c
Sub-classes	obo:SO_0000411^c obo:SO_0000785^c obo:SO_0000696^c obo:SO_0000151^c obo:SO_0000006^c obo:SO_0000753^c obo:SO_2000061^c

oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000696`
Super-classes	obo:SO_0000695^c
Sub-classes	obo:SO_0000031^c obo:SO_0001012^c obo:SO_0000442^c obo:SO_0001998^c obo:SO_0000324^c obo:SO_0001247^c obo:SO_0000051^c obo:SO_0000441^c

gene_with_stop_codon_read_through^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000697`
Super-classes	obo:SO_0000693^c
Restrictions	so:has_part^op some obo:SO_0000883^c
Sub-classes	obo:SO_0000698^c obo:SO_0000710^c

gene_with_stop_codon_redefined_as_pyrrolysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000698`
Super-classes	obo:SO_0000697^c
Restrictions	so:has_part^op some obo:SO_0000884^c

junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000699`
Description	A junction is a boundary between regions. A boundary has an extent of zero.
Super-classes	obo:SO_0000110^c
Sub-classes	obo:SO_0002204^c obo:SO_0000333^c obo:SO_0000687^c obo:SO_0000553^c obo:SO_0000179^c obo:SO_0000366^c obo:SO_0000103^c obo:SO_0001421^c obo:SO_0002305^c obo:SO_0001021^c obo:SO_0001474^c

remark^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000700`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0000703^c obo:SO_0001082^c obo:SO_0000413^c

possible_base_call_error^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000701`
Super-classes	obo:SO_0000413^c

possible_assembly_error^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000702`
Super-classes	obo:SO_0000413^c

experimental_result_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000703`
Super-classes	obo:SO_0000700^c
Sub-classes	obo:SO_0001261^c obo:SO_0100010^c

gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000704`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
Super-classes	obo:SO_0001411^c
Restrictions	so:member_of^op some obo:SO_0005855^c
Sub-classes	obo:SO_0000459^c obo:SO_0001263^c obo:SO_0000097^c obo:SO_0001217^c obo:SO_0000087^c obo:SO_0000111^c obo:SO_0000456^c obo:SO_0005853^c obo:SO_0000287^c obo:SO_0000816^c obo:SO_0000099^c obo:SO_0000285^c obo:SO_0000892^c obo:SO_0000902^c obo:SO_0001431^c obo:SO_0000088^c obo:SO_0002121^c obo:SO_0001739^c obo:SO_0000996^c obo:SO_0000890^c obo:SO_0000898^c obo:SO_0000280^c obo:SO_0001867^c obo:SO_0000891^c obo:SO_0000690^c obo:SO_0001219^c obo:SO_0000098^c obo:SO_0000090^c obo:SO_0000896^c obo:SO_0000127^c

tandem_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000705`
Super-classes	obo:SO_0000657^c
Sub-classes	obo:SO_0000005^c obo:SO_0001934^c obo:SO_0002202^c

trans_splice_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000706`
Description	This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
Super-classes	obo:SO_0001420^c
Sub-classes	obo:SO_0000709^c obo:SO_0000708^c

trans_splice_donor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000707`
Description	SL RNA contains a donor site.
Super-classes	obo:SO_0001420^c

SL1_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000708`
Super-classes	obo:SO_0000706^c

SL2_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000709`
Super-classes	obo:SO_0000706^c
Sub-classes	obo:SO_0001750^c obo:SO_0001753^c obo:SO_0001752^c obo:SO_0001755^c obo:SO_0001757^c obo:SO_0001756^c obo:SO_0001751^c obo:SO_0001748^c obo:SO_0001754^c obo:SO_0001749^c

gene_with_stop_codon_redefined_as_selenocysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000710`
Super-classes	obo:SO_0000697^c
Restrictions	so:has_part^op some obo:SO_0000885^c

gene_with_mRNA_recoded_by_translational_bypass^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000711`
Super-classes	obo:SO_0000693^c
Restrictions	so:has_quality^op some obo:SO_0000886^c

gene_with_transcript_with_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000712`
Super-classes	obo:SO_0000693^c
Restrictions	so:has_quality^op some obo:SO_0000887^c

DNA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000713`
Super-classes	obo:SO_0000714^c
Sub-classes	obo:SO_0001158^c obo:SO_0000175^c obo:SO_0001665^c obo:SO_0002004^c obo:SO_0000017^c obo:SO_0001673^c obo:SO_0001258^c obo:SO_0000176^c obo:SO_0002025^c obo:SO_0001853^c obo:SO_0002021^c obo:SO_0001860^c obo:SO_0001666^c obo:SO_0001667^c obo:SO_0001156^c obo:SO_0000172^c obo:SO_0001999^c obo:SO_0002215^c obo:SO_0001163^c obo:SO_0001659^c obo:SO_0002005^c obo:SO_0001674^c obo:SO_0001166^c obo:SO_0001864^c obo:SO_0001914^c obo:SO_0002258^c

nucleotide_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000714`
Super-classes	obo:SO_0001683^c
Sub-classes	obo:SO_0000715^c obo:SO_0000713^c

RNA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000715`
Super-classes	obo:SO_0000714^c
Sub-classes	obo:SO_0000380^c obo:SO_0000020^c obo:SO_0001979^c obo:SO_0000026^c obo:SO_0000022^c

dicistronic_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000716`
Super-classes	obo:SO_0000634^c obo:SO_0000079^c
Restrictions	so:has_quality^op some obo:SO_0000879^c

reading_frame^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000717`
Description	This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0000718^c obo:SO_0000236^c obo:SO_0002048^c

blocked_reading_frame^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000718`
Description	Term requested by Rama from SGD.
Super-classes	obo:SO_0000717^c

ultracontig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000719`
Super-classes	obo:SO_0001876^c

foreign_transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000720`
Description	requested by Michael on 19 Nov 2004.
Super-classes	obo:SO_0000101^c
Restrictions	so:has_quality^op some obo:SO_0000784^c
Sub-classes	obo:SO_0000799^c

gene_with_dicistronic_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000721`
Description	Requested by Michael, 19 nov 2004.
Super-classes	obo:SO_0000692^c
Restrictions	so:transcribed_to^op some obo:SO_1001197^c

gene_with_dicistronic_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000722`
Description	Requested by MA nov 19 2004.
Super-classes	obo:SO_0000692^c
Restrictions	so:transcribed_to^op some obo:SO_0000716^c

iDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000723`
Super-classes	obo:SO_0000298^c

oriT^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000724`
Super-classes	obo:SO_0000296^c

transit_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000725`
Description	Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
Super-classes	obo:SO_0001527^c
Restrictions	so:derives_from^op some obo:SO_0002252^c

repeat_unit^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000726`
Description	Added to comply with the feature table. A single repeat.
Super-classes	obo:SO_0001411^c

cis_regulatory_module^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000727`
Description	Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534.
Super-classes	obo:SO_0001055^c
Sub-classes	obo:SO_0000627^c obo:SO_0002308^c obo:SO_0000037^c obo:SO_0000625^c obo:SO_0000165^c

intein^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000728`
Description	Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
Super-classes	obo:SO_0100011^c

intein_containing^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000729`
Super-classes	obo:SO_0000010^c

gap^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000730`
Super-classes	obo:SO_0000143^c
Restrictions	so:part_of^op some obo:SO_0000353^c

fragmentary^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000731`
Description	Term added because of request by MO people.
Super-classes	obo:SO_0000905^c

predicted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000732`
Super-classes	obo:SO_0000905^c
Sub-classes	obo:SO_0000911^c obo:SO_0000907^c obo:SO_0000910^c

feature_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000733`
Super-classes	obo:SO_0000400^c
Sub-classes	obo:SO_0000905^c obo:SO_0001508^c obo:SO_0000401^c obo:SO_0001234^c obo:SO_0000814^c obo:SO_0000781^c obo:SO_0000277^c obo:SO_0000933^c obo:SO_0000817^c obo:SO_0001185^c obo:SO_0000357^c obo:SO_0000569^c obo:SO_0001029^c obo:SO_0000940^c obo:SO_0000806^c obo:SO_0000856^c obo:SO_0000976^c obo:SO_0000784^c obo:SO_0001684^c obo:SO_0000783^c obo:SO_0000983^c obo:SO_0000237^c obo:SO_0000782^c

exemplar_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000734`
Description	Added for the MO people.
Super-classes	obo:SO_0000234^c
Restrictions	so:has_quality^op some obo:SO_0000864^c

sequence_location^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000735`
Super-classes	obo:SO_0000400^c
Sub-classes	obo:SO_0000736^c obo:SO_0000751^c obo:SO_0000738^c obo:SO_0000749^c

organelle_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000736`
Super-classes	obo:SO_0000735^c
Sub-classes	obo:SO_0000737^c obo:SO_0000740^c obo:SO_0000739^c obo:SO_0000084^c obo:SO_0000083^c

mitochondrial_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000737`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000736^c
Sub-classes	obo:SO_0001032^c

nuclear_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000738`
Description	Moved from is_a SO:0000736 (organelle_sequence) when brought to our attention by GitHub issue #489.
Super-classes	obo:SO_0000735^c

nucleomorphic_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000739`
Super-classes	obo:SO_0000736^c

plastid_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000740`
Super-classes	obo:SO_0000736^c
Sub-classes	obo:SO_0000745^c obo:SO_0000743^c obo:SO_0000746^c obo:SO_0000748^c obo:SO_0000744^c obo:SO_0000747^c

kinetoplast^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000741`
Super-classes	obo:SO_0001026^c
Restrictions	so:has_part^op some obo:SO_0000980^c so:has_part^op some obo:SO_0000742^c

maxicircle^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000742`
Super-classes	obo:SO_0001235^c

apicoplast_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000743`
Super-classes	obo:SO_0000740^c

chromoplast_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000744`
Super-classes	obo:SO_0000740^c

chloroplast_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000745`
Super-classes	obo:SO_0000740^c
Sub-classes	obo:SO_0001033^c

cyanelle_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000746`
Super-classes	obo:SO_0000740^c

leucoplast_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000747`
Super-classes	obo:SO_0000740^c

proplastid_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000748`
Super-classes	obo:SO_0000740^c

plasmid_location^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000749`
Super-classes	obo:SO_0000735^c

amplification_origin^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000750`
Super-classes	obo:SO_0000296^c

proviral_location^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000751`
Super-classes	obo:SO_0000735^c
Sub-classes	obo:SO_0000903^c

gene_group_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000752`
Description	Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529.

clone_insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000753`
Super-classes	obo:SO_0000695^c
Restrictions	so:part_of^op some obo:SO_0000151^c
Sub-classes	obo:SO_0000913^c obo:SO_0000914^c obo:SO_0000915^c

lambda_vector^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000754`
Super-classes	obo:SO_0000440^c

plasmid_vector^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000755`
Super-classes	obo:SO_0000440^c
Restrictions	so:derives_from^op some obo:SO_0000155^c

cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000756`
Super-classes	obo:SO_0000352^c
Sub-classes	obo:SO_0000757^c obo:SO_0000758^c

single_stranded_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000757`
Super-classes	obo:SO_0000756^c

double_stranded_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000758`
Super-classes	obo:SO_0000756^c

plasmid_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000759`

YAC_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000760`

phagemid_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000761`

PAC_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000762`

fosmid_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000763`

BAC_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000764`

cosmid_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000765`

pyrrolysyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000766`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0001178^c

clone_insert_start^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000767`

episome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000768`
Super-classes	obo:SO_0000155^c
Sub-classes	obo:SO_0000779^c

tmRNA_coding_piece^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000769`
Description	Added in response to comment from Kelly Williams from Indiana. Nov 2005.
Super-classes	obo:SO_0000847^c

tmRNA_acceptor_piece^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000770`
Description	Added in response to Kelly Williams from Indiana. Date: Nov 2005.
Super-classes	obo:SO_0000847^c

QTL^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000771`
Description	Added in respose to request by Simon Twigger November 14th 2005.
Super-classes	obo:SO_0001411^c

genomic_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000772`
Description	Genomic islands are transmissible elements characterized by large size (>10kb).
Super-classes	obo:SO_0001039^c
Sub-classes	obo:SO_0000775^c obo:SO_0000774^c obo:SO_0001049^c obo:SO_0000773^c obo:SO_0000776^c obo:SO_0001007^c

pathogenic_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000773`
Description	Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
Super-classes	obo:SO_0000772^c

metabolic_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000774`
Description	Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
Super-classes	obo:SO_0000772^c

adaptive_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000775`
Description	The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
Super-classes	obo:SO_0000772^c

symbiosis_island^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000776`
Description	Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
Super-classes	obo:SO_0000772^c

pseudogenic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000777`
Description	Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
Super-classes	obo:SO_0000516^c
Sub-classes	obo:SO_0002193^c obo:SO_0002196^c obo:SO_0002194^c obo:SO_0002195^c

pseudogenic_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000778`
Description	Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
Super-classes	obo:SO_0000516^c
Sub-classes	obo:SO_0002199^c obo:SO_0002198^c obo:SO_0002197^c obo:SO_0002200^c

engineered_episome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000779`
Description	Requested by Lynn Crosby Jan 2006.
Super-classes	obo:SO_0000637^c obo:SO_0000768^c
Restrictions	so:has_quality^op some obo:SO_0000783^c

transposable_element_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000780`
Description	Added by KE Jan 2006 to capture the kinds of attributes of TEs

transgenic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000781`
Super-classes	obo:SO_0000733^c

natural^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000782`
Super-classes	obo:SO_0000733^c

engineered^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000783`
Super-classes	obo:SO_0000733^c

foreign^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000784`
Super-classes	obo:SO_0000733^c

cloned_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000785`
Description	Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
Super-classes	obo:SO_0000695^c
Restrictions	so:part_of^op some obo:SO_0000753^c

reagent_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000786`
Description	Added jan 2006 by KE.

clone_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000787`

cloned^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000788`

validated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000789`
Super-classes	obo:SO_0000905^c
Sub-classes	obo:SO_0000312^c

invalidated^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000790`
Super-classes	obo:SO_0000905^c
Sub-classes	obo:SO_0000362^c obo:SO_0000415^c obo:SO_0000416^c obo:SO_0000414^c

cloned_genomic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000791`

cloned_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000792`

engineered_DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000793`

engineered_rescue_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000794`
Super-classes	obo:SO_0000411^c obo:SO_0000804^c
Restrictions	so:has_quality^op some obo:SO_0000783^c

rescue_mini_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000795`
Super-classes	obo:SO_0000815^c
Restrictions	so:has_quality^op some obo:SO_0000814^c

transgenic_transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000796`
Description	Modified as requested by Lynn - FB. May 2007.
Super-classes	obo:SO_0000101^c
Restrictions	so:derives_from^op some obo:SO_0000151^c so:has_quality^op some obo:SO_0000781^c

natural_transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000797`
Super-classes	obo:SO_0000101^c obo:SO_0001038^c
Restrictions	so:has_quality^op some obo:SO_0000782^c

engineered_transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000798`
Super-classes	obo:SO_0000101^c obo:SO_0000804^c
Restrictions	so:has_quality^op some obo:SO_0000783^c
Sub-classes	obo:SO_0000799^c

engineered_foreign_transposable_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000799`
Super-classes	obo:SO_0000798^c obo:SO_0000720^c obo:SO_0000805^c
Restrictions	so:has_quality^op some obo:SO_0000784^c so:has_quality^op some obo:SO_0000783^c

assortment_derived_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000800`
Super-classes	obo:SO_0001504^c

assortment_derived_deficiency_plus_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000801`
Super-classes	obo:SO_0001504^c

assortment_derived_deficiency^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000802`
Super-classes	obo:SO_0001504^c

assortment_derived_aneuploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000803`
Super-classes	obo:SO_0001504^c

engineered_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000804`
Super-classes	obo:SO_0001409^c
Restrictions	so:has_quality^op some obo:SO_0000783^c
Sub-classes	obo:SO_0001978^c obo:SO_0000637^c obo:SO_0000915^c obo:SO_0001644^c obo:SO_0000798^c obo:SO_0000805^c obo:SO_0000807^c obo:SO_0000794^c obo:SO_0000280^c

engineered_foreign_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000805`
Super-classes	obo:SO_0000804^c
Restrictions	so:has_quality^op some obo:SO_0000784^c so:has_quality^op some obo:SO_0000783^c
Sub-classes	obo:SO_0000281^c obo:SO_0000799^c obo:SO_0000293^c

fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000806`
Super-classes	obo:SO_0000733^c

engineered_tag^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000807`
Super-classes	obo:SO_0000324^c obo:SO_0000804^c
Restrictions	so:has_quality^op some obo:SO_0000783^c

validated_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000808`
Super-classes	obo:SO_0000317^c
Restrictions	so:has_quality^op some obo:SO_0000789^c

invalidated_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000809`
Super-classes	obo:SO_0000317^c
Restrictions	so:has_quality^op some obo:SO_0000790^c
Sub-classes	obo:SO_0000813^c obo:SO_0000811^c obo:SO_0000810^c obo:SO_0000812^c

chimeric_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000810`
Super-classes	obo:SO_0000809^c
Restrictions	so:has_quality^op some obo:SO_0000362^c

genomically_contaminated_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000811`
Super-classes	obo:SO_0000809^c
Restrictions	so:has_quality^op some obo:SO_0000414^c

polyA_primed_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000812`
Super-classes	obo:SO_0000809^c
Restrictions	so:has_quality^op some obo:SO_0000415^c

partially_processed_cDNA_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000813`
Super-classes	obo:SO_0000809^c
Restrictions	so:has_quality^op some obo:SO_0000416^c

rescue^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000814`
Super-classes	obo:SO_0000733^c

mini_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000815`
Super-classes	obo:SO_0000236^c
Sub-classes	obo:SO_0000795^c

rescue_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000816`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000814^c
Sub-classes	obo:SO_0000818^c

wild_type^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000817`
Super-classes	obo:SO_0000733^c

wild_type_rescue_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000818`
Super-classes	obo:SO_0000816^c
Restrictions	so:has_quality^op some obo:SO_0000817^c

mitochondrial_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000819`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000737^c

chloroplast_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000820`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000745^c

chromoplast_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000821`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000744^c

cyanelle_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000822`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000746^c

leucoplast_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000823`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000747^c

macronuclear_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000824`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000083^c

micronuclear_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000825`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000084^c

SO_0000826^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000826`

SO_0000827^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000827`

nuclear_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000828`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000738^c

nucleomorphic_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000829`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000739^c

chromosome_part^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000830`
Description	This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0000340^c
Sub-classes	obo:SO_0000664^c obo:SO_0002307^c obo:SO_0000105^c obo:SO_0000341^c obo:SO_0000450^c obo:SO_0002263^c obo:SO_0002306^c obo:SO_0002262^c obo:SO_0000626^c obo:SO_0000628^c

gene_member_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000831`
Description	A manufactured term used to allow the parts of a gene to have an is_a path to the root.
Super-classes	obo:SO_0001411^c
Restrictions	so:member_of^op some obo:SO_0000704^c
Sub-classes	obo:SO_0000673^c obo:SO_0002188^c obo:SO_0005836^c

promoter_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000832`
Description	This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.

transcript_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000833`
Description	This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0000673^c
Sub-classes	obo:SO_0000977^c obo:SO_0000834^c obo:SO_0000579^c obo:SO_0000852^c obo:SO_0001977^c obo:SO_0000147^c obo:SO_0000835^c

mature_transcript_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000834`
Description	A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
Super-classes	obo:SO_0000833^c
Sub-classes	obo:SO_0001172^c obo:SO_0000847^c obo:SO_0000836^c obo:SO_0000930^c

primary_transcript_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000835`
Description	This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
Super-classes	obo:SO_0000833^c
Restrictions	so:part_of^op some obo:SO_0000185^c
Sub-classes	obo:SO_0000616^c obo:SO_0000162^c obo:SO_0001475^c obo:SO_0001014^c obo:SO_0000636^c obo:SO_0000188^c obo:SO_0000841^c obo:SO_0001243^c obo:SO_0001902^c obo:SO_0000303^c obo:SO_0000315^c obo:SO_0000838^c

mRNA_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000836`
Description	This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
Super-classes	obo:SO_0000834^c
Restrictions	so:part_of^op some obo:SO_0000234^c
Sub-classes	obo:SO_0000035^c obo:SO_0000139^c obo:SO_0000316^c obo:SO_0001210^c obo:SO_0000203^c obo:SO_0002168^c obo:SO_0000837^c obo:SO_1001268^c obo:SO_0000629^c obo:SO_0000851^c

UTR_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000837`
Description	A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
Super-classes	obo:SO_0000836^c
Sub-classes	obo:SO_0000630^c obo:SO_0001180^c obo:SO_0001181^c obo:SO_0001182^c obo:SO_0002234^c

rRNA_primary_transcript_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000838`
Description	To allow transcribed_spacer_region to have a path to the root.
Super-classes	obo:SO_0000835^c
Restrictions	so:part_of^op some obo:SO_0000209^c
Sub-classes	obo:SO_0000638^c

polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000839`
Description	Added to allow the polypeptide regions to have is_a paths back to the root.
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0000104^c
Sub-classes	obo:SO_0001063^c obo:SO_0100011^c obo:SO_0100013^c obo:SO_0001146^c obo:SO_0100021^c obo:SO_0001527^c obo:SO_0001832^c obo:SO_0001070^c obo:SO_0001955^c obo:SO_0002224^c obo:SO_0001066^c obo:SO_0000419^c obo:SO_0001956^c

repeat_component^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000840`
Description	A manufactured to group the parts of repeats, to give them an is_a path back to the root.
Super-classes	obo:SO_0001412^c
Sub-classes	obo:SO_0001054^c obo:SO_0001050^c obo:SO_0000848^c obo:SO_0000433^c

spliceosomal_intron_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000841`
Description	A terms added to allow the parts of introns to have is_a paths to the root.
Super-classes	obo:SO_0000835^c
Restrictions	so:part_of^op some obo:SO_0000662^c
Sub-classes	obo:SO_0000611^c obo:SO_0000612^c

gene_component_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000842`
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0000704^c
Sub-classes	obo:SO_0000997^c obo:SO_0000183^c obo:SO_0000167^c obo:SO_3000000^c obo:SO_0002026^c

bacterial_RNApol_promoter_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000843`
Description	This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.

RNApol_II_promoter_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000844`
Description	This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.

RNApol_III_promoter_type_1_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000845`
Description	This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.

RNApol_III_promoter_type_2_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000846`
Description	This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.

tmRNA_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000847`
Description	This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
Super-classes	obo:SO_0000834^c
Restrictions	so:part_of^op some obo:SO_0000584^c
Sub-classes	obo:SO_0000770^c obo:SO_0000769^c

LTR_component^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000848`
Super-classes	obo:SO_0000840^c
Restrictions	so:part_of^op some obo:SO_0000286^c
Sub-classes	obo:SO_0000849^c obo:SO_0000423^c obo:SO_0000424^c obo:SO_0000850^c obo:SO_0000422^c

three_prime_LTR_component^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000849`
Super-classes	obo:SO_0000848^c
Restrictions	so:part_of^op some obo:SO_0000426^c
Sub-classes	obo:SO_0000431^c obo:SO_0000430^c obo:SO_0000432^c

five_prime_LTR_component^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000850`
Super-classes	obo:SO_0000848^c
Restrictions	so:part_of^op some obo:SO_0000425^c
Sub-classes	obo:SO_0000428^c obo:SO_0000427^c obo:SO_0000429^c

CDS_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000851`
Super-classes	obo:SO_0000836^c
Restrictions	so:part_of^op some obo:SO_0000316^c
Sub-classes	obo:SO_0000360^c obo:SO_0000327^c obo:SO_0002250^c obo:SO_0002251^c obo:SO_0002252^c obo:SO_0000323^c obo:SO_0002249^c

exon_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000852`
Super-classes	obo:SO_0000833^c
Restrictions	so:part_of^op some obo:SO_0000147^c
Sub-classes	obo:SO_0001215^c obo:SO_0002058^c obo:SO_0001214^c

homologous_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000853`
Super-classes	obo:SO_0000330^c
Restrictions	so:has_quality^op some obo:SO_0000857^c
Sub-classes	obo:SO_0000854^c obo:SO_0000855^c

paralogous_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000854`
Description	A term to be used in conjunction with the paralogous_to relationship.
Super-classes	obo:SO_0000853^c
Restrictions	so:has_quality^op some obo:SO_0000859^c

orthologous_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000855`
Description	This term should be used in conjunction with the similarity relationships defined in SO.
Super-classes	obo:SO_0000853^c
Restrictions	so:has_quality^op some obo:SO_0000858^c

conserved^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000856`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000860^c obo:SO_0000857^c

homologous^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000857`
Super-classes	obo:SO_0000856^c
Sub-classes	obo:SO_0000859^c obo:SO_0000858^c

orthologous^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000858`
Super-classes	obo:SO_0000857^c

paralogous^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000859`
Super-classes	obo:SO_0000857^c

syntenic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000860`
Super-classes	obo:SO_0000856^c

capped_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000861`
Super-classes	obo:SO_0000185^c
Restrictions	so:has_quality^op some obo:SO_0000146^c so:adjacent_to^op some obo:SO_0000581^c

capped_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000862`
Super-classes	obo:SO_0000234^c
Restrictions	so:adjacent_to^op some obo:SO_0000581^c so:has_quality^op some obo:SO_0000146^c

mRNA_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000863`
Super-classes	obo:SO_0000237^c
Sub-classes	obo:SO_0000246^c obo:SO_0000865^c obo:SO_0000864^c obo:SO_0001817^c obo:SO_0000881^c

exemplar^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000864`
Super-classes	obo:SO_0000863^c

frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000865`
Super-classes	obo:SO_0000863^c
Sub-classes	obo:SO_0000868^c obo:SO_0000866^c obo:SO_0000867^c obo:SO_0000869^c

minus_1_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000866`
Super-classes	obo:SO_0000865^c

minus_2_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000867`
Super-classes	obo:SO_0000865^c

plus_1_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000868`
Super-classes	obo:SO_0000865^c

plus_2_framshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000869`
Super-classes	obo:SO_0000865^c

trans_spliced^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000870`
Super-classes	obo:SO_0000237^c

polyadenylated_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000871`
Super-classes	obo:SO_0000234^c
Restrictions	so:adjacent_to^op some obo:SO_0000610^c so:has_quality^op some obo:SO_0000246^c

trans_spliced_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000872`
Super-classes	obo:SO_0000479^c obo:SO_0000234^c
Restrictions	so:has_quality^op some obo:SO_0000870^c so:adjacent_to^op some obo:SO_0000636^c

edited_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000873`
Super-classes	obo:SO_0000673^c
Restrictions	so:guided_by^op some obo:SO_0000602^c so:has_part^op some obo:SO_0000977^c so:has_quality^op some obo:SO_0000116^c
Sub-classes	obo:SO_0000874^c obo:SO_0000929^c

edited_transcript_by_A_to_I_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000874`
Super-classes	obo:SO_0000873^c

bound_by_protein^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000875`
Super-classes	obo:SO_0000277^c

bound_by_nucleic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000876`
Super-classes	obo:SO_0000277^c

alternatively_spliced^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000877`
Super-classes	obo:SO_0000237^c

monocistronic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000878`
Super-classes	obo:SO_0000237^c

dicistronic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000879`
Super-classes	obo:SO_0000880^c

polycistronic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000880`
Super-classes	obo:SO_0000237^c
Sub-classes	obo:SO_0000879^c

recoded^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000881`
Super-classes	obo:SO_0000863^c
Sub-classes	obo:SO_0000886^c obo:SO_0000887^c obo:SO_0000882^c

codon_redefined^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000882`
Super-classes	obo:SO_0000881^c

stop_codon_read_through^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000883`
Super-classes	obo:SO_0000145^c
Sub-classes	obo:SO_0000884^c obo:SO_0000885^c

stop_codon_redefined_as_pyrrolysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000884`
Super-classes	obo:SO_0000883^c

stop_codon_redefined_as_selenocysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000885`
Super-classes	obo:SO_0000883^c

recoded_by_translational_bypass^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000886`
Super-classes	obo:SO_0000881^c

translationally_frameshifted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000887`
Super-classes	obo:SO_0000881^c
Sub-classes	obo:SO_1001263^c obo:SO_1001262^c

maternally_imprinted_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000888`
Super-classes	obo:SO_0000898^c
Restrictions	so:has_quality^op some obo:SO_0000135^c

paternally_imprinted_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000889`
Super-classes	obo:SO_0000898^c
Restrictions	so:has_quality^op some obo:SO_0000136^c

post_translationally_regulated_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000890`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000130^c

negatively_autoregulated_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000891`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000473^c

positively_autoregulated_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000892`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000475^c

silenced^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000893`
Super-classes	obo:SO_0000126^c
Sub-classes	obo:SO_0001220^c obo:SO_0000894^c obo:SO_0001221^c

silenced_by_DNA_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000894`
Super-classes	obo:SO_0000893^c
Sub-classes	obo:SO_0000895^c

silenced_by_DNA_methylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000895`
Super-classes	obo:SO_0000894^c

translationally_regulated_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000896`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000131^c

allelically_excluded_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000897`
Super-classes	obo:SO_0000898^c
Restrictions	so:has_quality^op some obo:SO_0000137^c

epigenetically_modified_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000898`
Super-classes	obo:SO_0001720^c obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000133^c
Sub-classes	obo:SO_0000889^c obo:SO_0000138^c obo:SO_0000888^c obo:SO_0000897^c

nuclear_mitochondrial^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000899`

processed^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000900`

unequally_crossed_over^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000901`

transgene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000902`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000781^c
Sub-classes	obo:SO_0000363^c

endogenous_retroviral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000903`
Super-classes	obo:SO_0000751^c

rearranged_at_DNA_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000904`
Super-classes	obo:SO_0000133^c

status^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000905`
Description	This term is the hypernym of attributes and should not be annotated to.
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000789^c obo:SO_0000993^c obo:SO_0001004^c obo:SO_0001499^c obo:SO_0000906^c obo:SO_0000731^c obo:SO_0000732^c obo:SO_0000790^c

independently_known^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000906`
Super-classes	obo:SO_0000905^c

supported_by_sequence_similarity^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000907`
Super-classes	obo:SO_0000732^c
Sub-classes	obo:SO_0000908^c obo:SO_0000909^c

supported_by_domain_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000908`
Super-classes	obo:SO_0000907^c

supported_by_EST_or_cDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000909`
Super-classes	obo:SO_0000907^c

orphan^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000910`
Super-classes	obo:SO_0000732^c

predicted_by_ab_initio_computation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000911`
Super-classes	obo:SO_0000732^c

asx_turn^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000912`
Super-classes	obo:SO_0001128^c
Sub-classes	obo:SO_0001131^c obo:SO_0001130^c obo:SO_0001132^c obo:SO_0001129^c

cloned_cDNA_insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000913`
Super-classes	obo:SO_0000753^c
Restrictions	so:has_quality^op some obo:SO_0000756^c

cloned_genomic_insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000914`
Super-classes	obo:SO_0000753^c
Restrictions	so:has_quality^op some obo:SO_0000991^c
Sub-classes	obo:SO_0000992^c

engineered_insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000915`
Super-classes	obo:SO_0000804^c obo:SO_0000753^c
Restrictions	so:has_quality^op some obo:SO_0000783^c

edit_operation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000916`

insert_U^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000917`
Description	The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

delete_U^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000918`
Description	The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.

substitute_A_to_I^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000919`

insert_C^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000920`

insert_dinucleotide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000921`

substitute_C_to_U^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000922`

insert_G^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000923`

insert_GC^c # Classes

URI http://purl.obolibrary.org/obo/SO_0000924

Description

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_GU^c # Classes

URI http://purl.obolibrary.org/obo/SO_0000925

Description

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_CU^c # Classes

URI http://purl.obolibrary.org/obo/SO_0000926

Description

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_AU^c # Classes

URI http://purl.obolibrary.org/obo/SO_0000927

Description

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

insert_AA^c # Classes

URI http://purl.obolibrary.org/obo/SO_0000928

Description

The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.

edited_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000929`
Super-classes	obo:SO_0000873^c obo:SO_0000234^c
Restrictions	so:has_quality^op some obo:SO_0000116^c

guide_RNA_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000930`
Super-classes	obo:SO_0000834^c
Restrictions	so:part_of^op some obo:SO_0000602^c
Sub-classes	obo:SO_0000978^c obo:SO_0000931^c

anchor_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000931`
Super-classes	obo:SO_0000930^c

pre_edited_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000932`
Super-classes	obo:SO_0000120^c

intermediate^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000933`
Super-classes	obo:SO_0000733^c

miRNA_target_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000934`
Super-classes	obo:SO_0001655^c

edited_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000935`
Super-classes	obo:SO_0000316^c
Restrictions	so:has_quality^op some obo:SO_0000116^c

vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000936`
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000572^c obo:SO_0000510^c obo:SO_0000576^c obo:SO_0000574^c

vertebrate_immune_system_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000937`

vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000938`
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000519^c obo:SO_0000527^c obo:SO_0000530^c obo:SO_0000542^c obo:SO_0000531^c obo:SO_0000524^c obo:SO_0000485^c obo:SO_0000523^c obo:SO_0000540^c obo:SO_0000508^c obo:SO_0000521^c obo:SO_0000505^c obo:SO_0000520^c obo:SO_0000522^c obo:SO_0000489^c obo:SO_0000528^c obo:SO_0000539^c obo:SO_0000491^c obo:SO_0000518^c obo:SO_0000541^c obo:SO_0000488^c obo:SO_0000529^c obo:SO_0000564^c obo:SO_0000565^c obo:SO_0000490^c obo:SO_0000532^c obo:SO_0000525^c obo:SO_0000487^c obo:SO_0000566^c obo:SO_0000504^c obo:SO_0000506^c

vertebrate_immune_system_gene_recombination_signal_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000939`
Super-classes	obo:SO_0000301^c
Sub-classes	obo:SO_0000538^c obo:SO_0000561^c obo:SO_0000492^c obo:SO_0000562^c obo:SO_0000302^c

recombinationally_rearranged^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000940`
Super-classes	obo:SO_0000733^c

recombinationally_rearranged_vertebrate_immune_system_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000941`
Super-classes	obo:SO_0000456^c

attP_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000942`
Super-classes	obo:SO_0000946^c
Restrictions	so:part_of^op some obo:SO_0001042^c

attB_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000943`
Super-classes	obo:SO_0000946^c

attL_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000944`
Super-classes	obo:SO_0000946^c

attR_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000945`
Super-classes	obo:SO_0000946^c

integration_excision_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000946`
Super-classes	obo:SO_0000342^c
Sub-classes	obo:SO_0000943^c obo:SO_0000950^c obo:SO_0000942^c obo:SO_0000367^c obo:SO_0000944^c obo:SO_0000945^c obo:SO_0001043^c

resolution_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000947`
Super-classes	obo:SO_0000342^c
Sub-classes	obo:SO_0000949^c obo:SO_0000346^c

inversion_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000948`
Description	A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
Super-classes	obo:SO_0000342^c
Sub-classes	obo:SO_0000350^c

dif_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000949`
Super-classes	obo:SO_0000947^c

attC_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000950`
Super-classes	obo:SO_0000946^c
Restrictions	so:part_of^op some obo:SO_0000365^c

eukaryotic_terminator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000951`
Super-classes	obo:SO_0000141^c
Sub-classes	obo:SO_0000615^c obo:SO_0002213^c

oriV^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000952`
Super-classes	obo:SO_0000296^c

oriC^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000953`
Super-classes	obo:SO_0000296^c

DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000954`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_quality^op some obo:SO_0000352^c
Sub-classes	obo:SO_0000956^c obo:SO_0000955^c

double_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000955`
Super-classes	obo:SO_0000954^c
Restrictions	so:has_quality^op some obo:SO_0000985^c
Sub-classes	obo:SO_0000958^c obo:SO_0000957^c

single_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000956`
Super-classes	obo:SO_0000954^c
Restrictions	so:has_quality^op some obo:SO_0000984^c
Sub-classes	obo:SO_0000959^c obo:SO_0000960^c

linear_double_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000957`
Super-classes	obo:SO_0000955^c
Restrictions	so:has_quality^op some obo:SO_0000987^c

circular_double_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000958`
Super-classes	obo:SO_0000955^c
Restrictions	so:has_quality^op some obo:SO_0000988^c

linear_single_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000959`
Super-classes	obo:SO_0000956^c
Restrictions	so:has_quality^op some obo:SO_0000987^c

circular_single_stranded_DNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000960`
Super-classes	obo:SO_0000956^c
Restrictions	so:has_quality^op some obo:SO_0000988^c

RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000961`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_quality^op some obo:SO_0000356^c
Sub-classes	obo:SO_0000965^c obo:SO_0000962^c

single_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000962`
Super-classes	obo:SO_0000961^c
Restrictions	so:has_quality^op some obo:SO_0000984^c
Sub-classes	obo:SO_0000963^c obo:SO_0000966^c

linear_single_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000963`
Super-classes	obo:SO_0000962^c
Restrictions	so:has_quality^op some obo:SO_0000987^c

linear_double_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000964`
Super-classes	obo:SO_0000965^c
Restrictions	so:has_quality^op some obo:SO_0000987^c

double_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000965`
Super-classes	obo:SO_0000961^c
Restrictions	so:has_quality^op some obo:SO_0000985^c
Sub-classes	obo:SO_0000967^c obo:SO_0000964^c

circular_single_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000966`
Super-classes	obo:SO_0000962^c
Restrictions	so:has_quality^op some obo:SO_0000988^c

circular_double_stranded_RNA_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000967`
Super-classes	obo:SO_0000965^c
Restrictions	so:has_quality^op some obo:SO_0000988^c

sequence_replication_mode^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000968`
Description	This has been obsoleted as it represents a process. replaced_by: GO:0034961.

rolling_circle^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000969`
Description	This has been obsoleted as it represents a process. replaced_by: GO:0070581.

theta_replication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000970`
Description	This has been obsoleted as it represents a process. replaced_by: GO:0070582

DNA_replication_mode^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000971`
Description	This has been obsoleted as it represents a process. replaced_by: GO:0006260.

RNA_replication_mode^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000972`
Description	This has been obsoleted as it represents a process. replaced_by: GO:0034961.

insertion_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000973`
Super-classes	obo:SO_0000208^c

SO_0000974^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000974`

minicircle_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000975`
Super-classes	obo:SO_0000089^c
Restrictions	so:part_of^op some obo:SO_0000980^c

cryptic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000976`
Super-classes	obo:SO_0000733^c

anchor_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000977`
Description	Part of an edited transcript only.
Super-classes	obo:SO_0000833^c

template_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000978`
Super-classes	obo:SO_0000930^c

gRNA_encoding^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000979`
Super-classes	obo:SO_0000011^c

minicircle^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000980`
Super-classes	obo:SO_0001235^c

rho_dependent_bacterial_terminator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000981`
Super-classes	obo:SO_0000614^c

rho_independent_bacterial_terminator^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000982`
Super-classes	obo:SO_0000614^c

strand_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000983`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0000985^c obo:SO_0000984^c

single^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000984`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000983^c

double^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000985`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000983^c

topology_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000986`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000443^c
Sub-classes	obo:SO_0000988^c obo:SO_0000987^c

linear^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000987`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000986^c

circular^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000988`
Description	Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
Super-classes	obo:SO_0000986^c

class_II_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000989`
Super-classes	obo:SO_0000655^c

class_I_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000990`
Description	Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
Super-classes	obo:SO_0000655^c

genomic_DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000991`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000352^c

BAC_cloned_genomic_insert^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000992`
Description	Requested by Andy Schroder - Flybase Harvard, Nov 2006.
Super-classes	obo:SO_0000914^c
Restrictions	so:derives_from^op some obo:SO_0000153^c

consensus^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000993`
Description	Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
Super-classes	obo:SO_0000905^c

consensus_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000994`
Description	DO not obsolete without considering MGED mapping.
Super-classes	obo:SO_0001410^c
Restrictions	so:has_quality^op some obo:SO_0000993^c
Sub-classes	obo:SO_0001991^c obo:SO_0001931^c obo:SO_0000995^c

consensus_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000995`
Description	DO not obsolete without considering MGED mapping.
Super-classes	obo:SO_0000234^c obo:SO_0000994^c
Restrictions	so:has_quality^op some obo:SO_0000993^c

predicted_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000996`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000732^c

gene_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000997`
Description	This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
Super-classes	obo:SO_0000842^c
Restrictions	so:has_quality^op some obo:SO_0000731^c

recursive_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000998`
Super-classes	obo:SO_0001419^c

BAC_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0000999`
Description	Requested by Keith Boroevich December, 2006.
Super-classes	obo:SO_0000150^c
Restrictions	so:part_of^op some obo:SO_0000153^c

cytosolic_16S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001000`
Description	Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000650^c

cytosolic_23S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001001`
Description	Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

cytosolic_25S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001002`
Description	Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

solo_LTR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001003`
Description	Requested by Hadi Quesneville January 2007.
Super-classes	obo:SO_0000286^c

low_complexity^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001004`
Super-classes	obo:SO_0000905^c

low_complexity_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001005`
Super-classes	obo:SO_0001410^c
Restrictions	so:has_quality^op some obo:SO_0001004^c

prophage^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001006`
Super-classes	obo:SO_0000113^c

cryptic_prophage^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001007`
Description	This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
Super-classes	obo:SO_0000772^c

tetraloop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001008`
Super-classes	obo:SO_0000313^c

DNA_constraint_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001009`
Super-classes	obo:SO_0000442^c

i_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001010`
Super-classes	obo:SO_0000142^c

PNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001011`
Super-classes	obo:SO_0001247^c
Restrictions	so:has_quality^op some obo:SO_0001184^c

DNAzyme^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001012`
Description	Added by request from Colin Batchelor.
Super-classes	obo:SO_0000696^c
Restrictions	so:has_quality^op some obo:SO_0001185^c

MNP^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001013`
Super-classes	obo:SO_0002007^c

intron_domain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001014`
Description	Requested by Colin Batchelor, Feb 2007.
Super-classes	obo:SO_0000835^c
Restrictions	so:part_of^op some obo:SO_0000188^c
Sub-classes	obo:SO_0001996^c obo:SO_0001016^c obo:SO_0001994^c obo:SO_0001034^c

wobble_base_pair^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001015`
Super-classes	obo:SO_0000028^c

internal_guide_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001016`
Super-classes	obo:SO_0001014^c
Restrictions	so:part_of^op some obo:SO_0000587^c

silent_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001017`
Description	Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
Super-classes	obo:SO_0001878^c

epitope^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001018`
Description	Requested by Trish Whetzel.
Super-classes	obo:SO_0000409^c

copy_number_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001019`
Super-classes	obo:SO_0000248^c
Sub-classes	obo:SO_0002210^c obo:SO_0001743^c obo:SO_0001742^c

sequence_variant_affecting_copy_number^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001020`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

chromosome_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001021`
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0000340^c
Sub-classes	obo:SO_0001874^c obo:SO_0001415^c obo:SO_0001414^c obo:SO_0001873^c obo:SO_0001413^c obo:SO_0002349^c obo:SO_0001022^c

inversion_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001022`
Super-classes	obo:SO_0001021^c

allele^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001023`
Super-classes	obo:SO_0001507^c
Restrictions	so:variant_of^op some obo:SO_0000704^c
Sub-classes	obo:SO_0001025^c

haplotype^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001024`
Super-classes	obo:SO_0001507^c
Restrictions	so:variant_of^op some obo:SO_0000355^c

polymorphic_sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001025`
Super-classes	obo:SO_0001023^c

genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001026`
Super-classes	obo:SO_0001260^c
Restrictions	so:has_part^op some obo:SO_0001235^c
Sub-classes	obo:SO_0001505^c obo:SO_0000741^c obo:SO_0001506^c

genotype^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001027`
Super-classes	obo:SO_0001507^c
Restrictions	so:variant_of^op some obo:SO_0001026^c

diplotype^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001028`
Super-classes	obo:SO_0001507^c

direction_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001029`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0001030^c obo:SO_0001031^c

forward^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001030`
Super-classes	obo:SO_0001029^c

reverse^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001031`
Super-classes	obo:SO_0001029^c

mitochondrial_DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001032`
Description	This terms is used by MO.
Super-classes	obo:SO_0000737^c
Restrictions	so:has_quality^op some obo:SO_0000352^c

chloroplast_DNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001033`
Description	This term is used by MO.
Super-classes	obo:SO_0000745^c
Restrictions	so:has_quality^op some obo:SO_0000352^c

miRtron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001034`
Description	Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
Super-classes	obo:SO_0001014^c
Restrictions	so:has_part^op some obo:SO_0001244^c

piRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001035`
Super-classes	obo:SO_0000370^c

arginyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001036`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0000212^c

mobile_genetic_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001037`
Super-classes	obo:SO_0001411^c
Restrictions	so:has_quality^op some obo:SO_0001234^c
Sub-classes	obo:SO_0000666^c obo:SO_0001039^c obo:SO_0001038^c

extrachromosomal_mobile_genetic_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001038`
Super-classes	obo:SO_0001037^c
Sub-classes	obo:SO_0001041^c obo:SO_0001476^c obo:SO_0000797^c

integrated_mobile_genetic_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001039`
Super-classes	obo:SO_0001037^c
Sub-classes	obo:SO_0001045^c obo:SO_0000113^c obo:SO_0000772^c obo:SO_0001040^c obo:SO_0000365^c obo:SO_0000101^c

integrated_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001040`
Super-classes	obo:SO_0001039^c
Restrictions	so:derives_from^op some obo:SO_0000155^c

viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001041`
Description	The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
Super-classes	obo:SO_0001038^c obo:SO_0001235^c
Sub-classes	obo:SO_0001199^c obo:SO_0001042^c obo:SO_0001169^c obo:SO_0001198^c

phage_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001042`
Super-classes	obo:SO_0001041^c

attCtn_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001043`
Super-classes	obo:SO_0000946^c
Restrictions	so:part_of^op some obo:SO_0000371^c

nuclear_mt_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001044`
Description	Definition change requested by Val, 3172757.
Super-classes	obo:SO_0001760^c

cointegrated_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001045`
Super-classes	obo:SO_0001039^c

IRLinv_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001046`
Super-classes	obo:SO_0001048^c
Restrictions	so:part_of^op some obo:SO_0000948^c

IRRinv_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001047`
Super-classes	obo:SO_0001048^c
Restrictions	so:part_of^op some obo:SO_0000948^c

inversion_site_part^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001048`
Description	A term created to allow the parts of an inversion site have an is_a path back to the root.
Super-classes	obo:SO_0000342^c
Sub-classes	obo:SO_0001047^c obo:SO_0001046^c

defective_conjugative_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001049`
Super-classes	obo:SO_0000772^c

repeat_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001050`
Description	Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
Super-classes	obo:SO_0000840^c
Restrictions	so:part_of^op some obo:SO_0001649^c

nested_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001051`

nested_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001052`

nested_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001053`

transposon_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001054`
Super-classes	obo:SO_0000840^c
Restrictions	so:part_of^op some obo:SO_0001648^c

transcriptional_cis_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001055`
Description	Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0005836^c
Sub-classes	obo:SO_0001492^c obo:SO_0002297^c obo:SO_0002047^c obo:SO_0000141^c obo:SO_0000167^c obo:SO_0002296^c obo:SO_0000235^c obo:SO_0001427^c obo:SO_0002205^c obo:SO_0001058^c obo:SO_0000057^c obo:SO_0001952^c obo:SO_0000551^c obo:SO_0000727^c obo:SO_0001056^c

splicing_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001056`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c
Sub-classes	obo:SO_0000344^c

enhanceosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001057`

promoter_targeting_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001058`
Description	Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field.
Super-classes	obo:SO_0001055^c

sequence_alteration^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001059`
Description	Merged with partially characterized change in nucleotide sequence.
Super-classes	obo:SO_0002072^c
Sub-classes	obo:SO_0000667^c obo:SO_0001744^c obo:SO_0000248^c obo:SO_0001785^c obo:SO_1000036^c obo:SO_1000002^c obo:SO_0002217^c obo:SO_0000159^c obo:SO_1000032^c

sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001060`
Sub-classes	obo:SO_0001537^c obo:SO_0001536^c

propeptide_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001061`
Description	Discrete.
Super-classes	obo:SO_0100011^c
Restrictions	so:part_of^op some obo:SO_0001062^c

propeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001062`
Description	Range.
Super-classes	obo:SO_0100011^c
Restrictions	so:derives_from^op some obo:SO_0002250^c

immature_peptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001063`
Description	Range.
Super-classes	obo:SO_0000839^c

active_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001064`
Description	Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
Super-classes	obo:SO_0000419^c

SO_0001065^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001065`

compositionally_biased_region_of_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001066`
Description	Range.
Super-classes	obo:SO_0000839^c

polypeptide_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001067`
Description	Range.
Super-classes	obo:SO_0100021^c
Sub-classes	obo:SO_0100017^c obo:SO_0100001^c

polypeptide_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001068`
Description	Range.
Super-classes	obo:SO_0100021^c

SO_0001069^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001069`

polypeptide_structural_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001070`
Description	Range.
Super-classes	obo:SO_0000839^c
Sub-classes	obo:SO_0001071^c obo:SO_0001079^c obo:SO_0100003^c obo:SO_0001075^c obo:SO_0001072^c obo:SO_0000417^c obo:SO_0001078^c

membrane_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001071`
Description	Range.
Super-classes	obo:SO_0001070^c

extramembrane_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001072`
Description	Range.
Super-classes	obo:SO_0001070^c
Restrictions	so:part_of^op some obo:SO_0001071^c
Sub-classes	obo:SO_0001074^c obo:SO_0001073^c

cytoplasmic_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001073`
Super-classes	obo:SO_0001072^c

non_cytoplasmic_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001074`
Description	This could be inside an organelle within the cell.
Super-classes	obo:SO_0001072^c

intramembrane_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001075`
Super-classes	obo:SO_0001070^c
Restrictions	so:part_of^op some obo:SO_0001071^c
Sub-classes	obo:SO_0001077^c obo:SO_0001076^c

membrane_peptide_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001076`
Super-classes	obo:SO_0001075^c

transmembrane_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001077`
Super-classes	obo:SO_0001075^c

polypeptide_secondary_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001078`
Description	Biosapien term was secondary_structure.
Super-classes	obo:SO_0001070^c
Sub-classes	obo:SO_0001106^c obo:SO_0001126^c obo:SO_0001120^c obo:SO_0100006^c obo:SO_0100004^c obo:SO_0001107^c obo:SO_0100007^c obo:SO_0001114^c obo:SO_0100005^c obo:SO_0001127^c obo:SO_0001111^c obo:SO_0001108^c obo:SO_0100012^c obo:SO_0001123^c obo:SO_0100008^c obo:SO_0001128^c

polypeptide_structural_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001079`
Super-classes	obo:SO_0001070^c
Sub-classes	obo:SO_0001080^c obo:SO_0001081^c

coiled_coil^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001080`
Description	Range.
Super-classes	obo:SO_0001079^c

helix_turn_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001081`
Super-classes	obo:SO_0001079^c
Restrictions	so:has_part^op some obo:SO_0001114^c so:has_part^op some obo:SO_0001128^c

polypeptide_sequencing_information^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001082`
Description	Range.
Super-classes	obo:SO_0000700^c
Sub-classes	obo:SO_0001083^c obo:SO_0001084^c obo:SO_0001085^c obo:SO_0001086^c

non_adjacent_residues^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001083`
Super-classes	obo:SO_0001082^c

non_terminal_residue^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001084`
Description	Discrete.
Super-classes	obo:SO_0001082^c

sequence_conflict^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001085`
Description	Discrete.
Super-classes	obo:SO_0001082^c
Sub-classes	obo:SO_0001462^c

sequence_uncertainty^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001086`
Super-classes	obo:SO_0001082^c

cross_link^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001087`

disulfide_bond^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001088`
Description	2 discreet & joined.

post_translationally_modified_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001089`
Description	Discrete.
Super-classes	obo:SO_0100001^c
Sub-classes	obo:SO_0001700^c obo:SO_0001811^c

covalent_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001090`

non_covalent_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001091`
Description	Discrete.

polypeptide_metal_contact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001092`
Description	Residue is part of a binding site for a metal ion.
Super-classes	obo:SO_0001656^c obo:SO_0100002^c
Sub-classes	obo:SO_0001097^c obo:SO_0001095^c obo:SO_0001101^c obo:SO_0001100^c obo:SO_0001099^c obo:SO_0001103^c obo:SO_0001094^c obo:SO_0001096^c obo:SO_0001098^c obo:SO_0001102^c

protein_protein_contact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001093`
Super-classes	obo:SO_0000410^c obo:SO_0100002^c
Sub-classes	obo:SO_0001810^c obo:SO_0001804^c obo:SO_0002235^c

polypeptide_calcium_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001094`
Description	Residue involved in contact with calcium.
Super-classes	obo:SO_0001092^c

polypeptide_cobalt_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001095`
Super-classes	obo:SO_0001092^c

polypeptide_copper_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001096`
Super-classes	obo:SO_0001092^c

polypeptide_iron_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001097`
Super-classes	obo:SO_0001092^c

polypeptide_magnesium_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001098`
Super-classes	obo:SO_0001092^c

polypeptide_manganese_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001099`
Super-classes	obo:SO_0001092^c

polypeptide_molybdenum_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001100`
Super-classes	obo:SO_0001092^c

polypeptide_nickel_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001101`
Super-classes	obo:SO_0001092^c

polypeptide_tungsten_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001102`
Super-classes	obo:SO_0001092^c

polypeptide_zinc_ion_contact_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001103`
Super-classes	obo:SO_0001092^c

catalytic_residue^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001104`
Description	Discrete.
Super-classes	obo:SO_0001237^c
Restrictions	so:part_of^op some obo:SO_0100019^c

polypeptide_ligand_contact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001105`
Super-classes	obo:SO_0001657^c obo:SO_0100002^c

asx_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001106`
Super-classes	obo:SO_0001078^c

beta_bulge^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001107`
Super-classes	obo:SO_0001078^c

beta_bulge_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001108`
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0001109^c obo:SO_0001110^c

beta_bulge_loop_five^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001109`
Super-classes	obo:SO_0001108^c

beta_bulge_loop_six^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001110`
Super-classes	obo:SO_0001108^c

beta_strand^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001111`
Description	Range.
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0001112^c obo:SO_0001113^c

antiparallel_beta_strand^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001112`
Description	Range.
Super-classes	obo:SO_0001111^c

parallel_beta_strand^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001113`
Description	Range.
Super-classes	obo:SO_0001111^c

peptide_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001114`
Description	Range.
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0001812^c obo:SO_0001116^c obo:SO_0001115^c

left_handed_peptide_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001115`
Super-classes	obo:SO_0001114^c

right_handed_peptide_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001116`
Super-classes	obo:SO_0001114^c
Sub-classes	obo:SO_0001118^c obo:SO_0001117^c obo:SO_0001119^c

alpha_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001117`
Description	Range.
Super-classes	obo:SO_0001116^c

pi_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001118`
Description	Range.
Super-classes	obo:SO_0001116^c

three_ten_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001119`
Description	Range.
Super-classes	obo:SO_0001116^c

polypeptide_nest_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001120`
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0001122^c obo:SO_0001121^c

polypeptide_nest_left_right_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001121`
Super-classes	obo:SO_0001120^c

polypeptide_nest_right_left_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001122`
Super-classes	obo:SO_0001120^c

schellmann_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001123`
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0001125^c obo:SO_0001124^c

schellmann_loop_seven^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001124`
Super-classes	obo:SO_0001123^c

schellmann_loop_six^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001125`
Super-classes	obo:SO_0001123^c

serine_threonine_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001126`
Super-classes	obo:SO_0001078^c

serine_threonine_staple_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001127`
Super-classes	obo:SO_0001078^c

polypeptide_turn_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001128`
Description	Range.
Super-classes	obo:SO_0001078^c
Sub-classes	obo:SO_0000912^c obo:SO_0001141^c obo:SO_0001138^c obo:SO_0001133^c

asx_turn_left_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001129`
Super-classes	obo:SO_0000912^c

asx_turn_left_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001130`
Super-classes	obo:SO_0000912^c

asx_turn_right_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001131`
Super-classes	obo:SO_0000912^c

asx_turn_right_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001132`
Super-classes	obo:SO_0000912^c

beta_turn^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001133`
Super-classes	obo:SO_0001128^c
Sub-classes	obo:SO_0001136^c obo:SO_0001150^c obo:SO_0001134^c obo:SO_0001135^c obo:SO_0001137^c obo:SO_0001155^c

beta_turn_left_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001134`
Super-classes	obo:SO_0001133^c

beta_turn_left_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001135`
Super-classes	obo:SO_0001133^c

beta_turn_right_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001136`
Super-classes	obo:SO_0001133^c

beta_turn_right_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001137`
Super-classes	obo:SO_0001133^c

gamma_turn^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001138`
Super-classes	obo:SO_0001128^c
Sub-classes	obo:SO_0001139^c obo:SO_0001140^c

gamma_turn_classic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001139`
Super-classes	obo:SO_0001138^c

gamma_turn_inverse^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001140`
Super-classes	obo:SO_0001138^c

serine_threonine_turn^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001141`
Super-classes	obo:SO_0001128^c
Sub-classes	obo:SO_0001145^c obo:SO_0001143^c obo:SO_0001144^c obo:SO_0001142^c

st_turn_left_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001142`
Super-classes	obo:SO_0001141^c

st_turn_left_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001143`
Super-classes	obo:SO_0001141^c

st_turn_right_handed_type_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001144`
Super-classes	obo:SO_0001141^c

st_turn_right_handed_type_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001145`
Super-classes	obo:SO_0001141^c

polypeptide_variation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001146`
Description	For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
Super-classes	obo:SO_0000839^c
Sub-classes	obo:SO_0001148^c obo:SO_0001147^c obo:SO_0001149^c

natural_variant_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001147`
Description	Discrete.
Super-classes	obo:SO_0001146^c

mutated_variant_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001148`
Description	Discrete.
Super-classes	obo:SO_0001146^c

alternate_sequence_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001149`
Description	Discrete.
Super-classes	obo:SO_0001146^c

beta_turn_type_six^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001150`
Super-classes	obo:SO_0001133^c
Sub-classes	obo:SO_0001151^c obo:SO_0001154^c

beta_turn_type_six_a^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001151`
Super-classes	obo:SO_0001150^c
Sub-classes	obo:SO_0001153^c obo:SO_0001152^c

beta_turn_type_six_a_one^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001152`
Super-classes	obo:SO_0001151^c

beta_turn_type_six_a_two^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001153`
Super-classes	obo:SO_0001151^c

beta_turn_type_six_b^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001154`
Super-classes	obo:SO_0001150^c

beta_turn_type_eight^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001155`
Super-classes	obo:SO_0001133^c

DRE_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001156`
Description	This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DMv4_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001157`
Super-classes	obo:SO_0001659^c

E_box_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001158`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DMv5_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001159`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DMv3_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001160`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DMv2_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001161`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

MTE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001162`
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

INR1_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001163`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DPE1_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001164`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

DMv1_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001165`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

GAGA_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001166`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

NDM2_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001167`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

NDM3_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001168`
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000170^c

ds_RNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001169`
Super-classes	obo:SO_0001041^c

polinton^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001170`
Super-classes	obo:SO_0000208^c

rRNA_21S^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001171`
Description	This term has been merged into mt_LSU_rRNA (SO:0002345) as part of reorganization of rRNA child terms 10 June 2021. Requested by EBI. See GitHub Issue #493.

tRNA_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001172`
Super-classes	obo:SO_0000834^c
Restrictions	so:part_of^op some obo:SO_0000253^c
Sub-classes	obo:SO_0001174^c obo:SO_0001173^c obo:SO_0001175^c obo:SO_0001176^c obo:SO_0001177^c

anticodon_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001173`
Super-classes	obo:SO_0001172^c

anticodon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001174`
Super-classes	obo:SO_0001172^c
Restrictions	so:part_of^op some obo:SO_0001173^c

CCA_tail^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001175`
Super-classes	obo:SO_0001172^c

DHU_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001176`
Super-classes	obo:SO_0001172^c

T_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001177`
Super-classes	obo:SO_0001172^c

pyrrolysine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001178`
Super-classes	obo:SO_0000210^c

U3_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001179`
Description	The definition is most of the old definition for snoRNA (SO:0000275).
Super-classes	obo:SO_0000593^c

AU_rich_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001180`
Super-classes	obo:SO_0000837^c
Restrictions	so:part_of^op some obo:SO_0000205^c

Bruno_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001181`
Description	Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
Super-classes	obo:SO_0000837^c
Restrictions	so:part_of^op some obo:SO_0000205^c

iron_responsive_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001182`
Super-classes	obo:SO_0000837^c
Restrictions	so:part_of^op some obo:SO_0000203^c

morpholino_backbone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001183`
Description	Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
Super-classes	obo:SO_0000348^c

PNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001184`
Description	Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
Super-classes	obo:SO_0000348^c

enzymatic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001185`
Description	Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0001186^c

ribozymic^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001186`
Description	Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
Super-classes	obo:SO_0001185^c

pseudouridylation_guide_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001187`
Description	Has RNA pseudouridylation guide activity (GO:0030558).
Super-classes	obo:SO_0000594^c

LNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001188`
Description	Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
Super-classes	obo:SO_0000348^c

LNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001189`
Super-classes	obo:SO_0001247^c
Restrictions	so:has_quality^op some obo:SO_0001188^c

TNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001190`
Description	Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
Super-classes	obo:SO_0000348^c

TNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001191`
Super-classes	obo:SO_0001247^c
Restrictions	so:has_quality^op some obo:SO_0001190^c

GNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001192`
Description	Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
Super-classes	obo:SO_0000348^c
Sub-classes	obo:SO_0001196^c obo:SO_0001194^c

GNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001193`
Super-classes	obo:SO_0001247^c
Restrictions	so:has_quality^op some obo:SO_0001192^c
Sub-classes	obo:SO_0001195^c obo:SO_0001197^c

R_GNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001194`
Description	Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
Super-classes	obo:SO_0001192^c

R_GNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001195`
Super-classes	obo:SO_0001193^c
Restrictions	so:has_quality^op some obo:SO_0001194^c

S_GNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001196`
Description	Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
Super-classes	obo:SO_0001192^c

S_GNA_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001197`
Super-classes	obo:SO_0001193^c
Restrictions	so:has_quality^op some obo:SO_0001196^c

ds_DNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001198`
Super-classes	obo:SO_0001041^c

ss_RNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001199`
Super-classes	obo:SO_0001041^c
Sub-classes	obo:SO_0001200^c obo:SO_0001201^c obo:SO_0001202^c

negative_sense_ssRNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001200`
Super-classes	obo:SO_0001199^c

positive_sense_ssRNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001201`
Super-classes	obo:SO_0001199^c

ambisense_ssRNA_viral_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001202`
Super-classes	obo:SO_0001199^c

RNA_polymerase_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001203`
Description	Term merged with promoter SO:0000167 in August 2020 as part of GREEKC initiative. See GitHub Issue 492 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/492)

Phage_RNA_Polymerase_Promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001204`
Description	former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.
Super-classes	obo:SO_0002311^c
Sub-classes	obo:SO_0001207^c obo:SO_0001205^c obo:SO_0001206^c

SP6_RNA_Polymerase_Promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001205`
Super-classes	obo:SO_0001204^c

T3_RNA_Polymerase_Promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001206`
Super-classes	obo:SO_0001204^c

T7_RNA_Polymerase_Promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001207`
Super-classes	obo:SO_0001204^c

five_prime_EST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001208`
Super-classes	obo:SO_0000345^c

three_prime_EST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001209`
Super-classes	obo:SO_0000345^c

translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001210`
Description	Added synonym 'ribosomal_slippage' on Feb 1, 2021, a term in INSDC and GenBank. See GitHub Issue #522.
Super-classes	obo:SO_0000836^c
Sub-classes	obo:SO_0001211^c obo:SO_0001212^c obo:SO_0002329^c obo:SO_0002330^c

plus_1_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001211`
Super-classes	obo:SO_0001210^c

plus_2_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001212`
Super-classes	obo:SO_0001210^c

group_III_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001213`
Description	GO:0000374.
Super-classes	obo:SO_0000588^c

noncoding_region_of_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001214`
Description	An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
Super-classes	obo:SO_0000852^c
Sub-classes	obo:SO_0000486^c obo:SO_0000484^c

coding_region_of_exon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001215`
Description	An exon containing either a start or stop codon will be partially coding and partially non coding.
Super-classes	obo:SO_0000852^c
Sub-classes	obo:SO_0000197^c obo:SO_0000196^c

endonuclease_spliced_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001216`
Super-classes	obo:SO_0000188^c
Sub-classes	obo:SO_1001271^c obo:SO_1001272^c

protein_coding_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001217`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000010^c
Sub-classes	obo:SO_0000548^c obo:SO_0000451^c obo:SO_0000693^c obo:SO_0000455^c

transgenic_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001218`
Super-classes	obo:SO_0000667^c
Restrictions	so:has_quality^op some obo:SO_0000781^c

retrogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001219`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000569^c

silenced_by_RNA_interference^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001220`
Description	RNA interference is GO:0016246.
Super-classes	obo:SO_0000893^c

silenced_by_histone_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001221`
Description	Histone modification is GO:0016570.
Super-classes	obo:SO_0000893^c
Sub-classes	obo:SO_0001222^c obo:SO_0001223^c

silenced_by_histone_methylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001222`
Description	Histone methylation is GO:0016571.
Super-classes	obo:SO_0001221^c

silenced_by_histone_deacetylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001223`
Description	Histone deacetylation is GO:0016573.
Super-classes	obo:SO_0001221^c

gene_silenced_by_RNA_interference^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001224`
Super-classes	obo:SO_0000127^c
Restrictions	so:has_quality^op some obo:SO_0001220^c

gene_silenced_by_histone_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001225`
Super-classes	obo:SO_0000127^c
Restrictions	so:has_quality^op some obo:SO_0001221^c
Sub-classes	obo:SO_0001226^c obo:SO_0001227^c

gene_silenced_by_histone_methylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001226`
Super-classes	obo:SO_0001225^c
Restrictions	so:has_quality^op some obo:SO_0001222^c

gene_silenced_by_histone_deacetylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001227`
Super-classes	obo:SO_0001225^c
Restrictions	so:has_quality^op some obo:SO_0001223^c

dihydrouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001228`
Super-classes	obo:SO_0001277^c

pseudouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001229`
Description	The free molecule is CHEBI:17802.
Super-classes	obo:SO_0001277^c

inosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001230`
Description	The free molecule is CHEBI:17596.
Super-classes	obo:SO_0000250^c
Sub-classes	obo:SO_0001274^c

seven_methylguanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001231`
Description	The free molecule is CHEBI:2274.
Super-classes	obo:SO_0000250^c

ribothymidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001232`
Description	The free molecule is CHEBI:30832.
Super-classes	obo:SO_0000250^c

methylinosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001233`
Super-classes	obo:SO_0001274^c

mobile^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001234`
Super-classes	obo:SO_0000733^c

replicon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001235`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0000340^c obo:SO_0001041^c obo:SO_0000155^c obo:SO_0000980^c obo:SO_0000440^c obo:SO_0000742^c

base^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001236`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0000250^c obo:SO_0000305^c

amino_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001237`
Description	Probably in the future this will cross reference to Chebi.
Super-classes	obo:SO_0001411^c
Restrictions	so:part_of^op some obo:SO_0000104^c
Sub-classes	obo:SO_0001445^c obo:SO_0001437^c obo:SO_0001452^c obo:SO_0001440^c obo:SO_0001454^c obo:SO_0001450^c obo:SO_0001438^c obo:SO_0001443^c obo:SO_0001451^c obo:SO_0001442^c obo:SO_0001447^c obo:SO_0001436^c obo:SO_0001444^c obo:SO_0001449^c obo:SO_0001435^c obo:SO_0001453^c obo:SO_0001455^c obo:SO_0001456^c obo:SO_0001448^c obo:SO_0001441^c obo:SO_0001385^c obo:SO_0001439^c obo:SO_0001104^c obo:SO_0001446^c

major_TSS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001238`
Super-classes	obo:SO_0000315^c

minor_TSS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001239`
Super-classes	obo:SO_0000315^c

TSS_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001240`
Description	Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528

encodes_alternate_transcription_start_sites^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001241`
Super-classes	obo:SO_0000401^c

SO_0001242^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001242`

miRNA_primary_transcript_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001243`
Super-classes	obo:SO_0000835^c
Sub-classes	obo:SO_0001473^c obo:SO_0001245^c obo:SO_0001244^c obo:SO_0001246^c

pre_miRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001244`
Super-classes	obo:SO_0001243^c

miRNA_stem^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001245`
Super-classes	obo:SO_0001243^c
Restrictions	so:part_of^op some obo:SO_0001244^c

miRNA_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001246`
Super-classes	obo:SO_0001243^c
Restrictions	so:part_of^op some obo:SO_0001244^c

synthetic_oligo^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001247`
Super-classes	obo:SO_0000696^c
Sub-classes	obo:SO_0001189^c obo:SO_0001011^c obo:SO_0000034^c obo:SO_0001191^c obo:SO_0001193^c

assembly^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001248`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0001249^c obo:SO_0000353^c

fragment_assembly^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001249`
Super-classes	obo:SO_0001248^c
Sub-classes	obo:SO_0001250^c obo:SO_0001252^c obo:SO_0001251^c

fingerprint_map^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001250`
Super-classes	obo:SO_0001249^c
Restrictions	so:has_part^op some obo:SO_0000412^c

STS_map^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001251`
Super-classes	obo:SO_0001249^c
Restrictions	so:has_part^op some obo:SO_0000331^c

RH_map^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001252`
Super-classes	obo:SO_0001249^c
Restrictions	so:has_part^op some obo:SO_0000331^c

sonicate_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001253`
Super-classes	obo:SO_0000143^c

polyploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001254`
Super-classes	obo:SO_1000182^c
Sub-classes	obo:SO_0001256^c obo:SO_0001255^c

autopolyploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001255`
Super-classes	obo:SO_0001254^c

allopolyploid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001256`
Super-classes	obo:SO_0001254^c

homing_endonuclease_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001257`
Super-classes	obo:SO_0000059^c

octamer_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001258`
Description	Nature. 1986 Oct 16-22;323(6089):640-3.
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000170^c

apicoplast_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001259`
Super-classes	obo:SO_0000340^c
Restrictions	so:has_origin^op some obo:SO_0000743^c

sequence_collection^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001260`
Sub-classes	obo:SO_0001026^c obo:SO_0001507^c obo:SO_0001501^c obo:SO_0001462^c

overlapping_feature_set^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001261`
Description	This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
Super-classes	obo:SO_0000703^c
Sub-classes	obo:SO_0001262^c

overlapping_EST_set^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001262`
Super-classes	obo:SO_0001261^c
Restrictions	so:has_part^op some obo:SO_0000345^c

ncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001263`
Super-classes	obo:SO_0000704^c
Sub-classes	obo:SO_0001266^c obo:SO_0001264^c obo:SO_0002180^c obo:SO_0002341^c obo:SO_0002359^c obo:SO_0002353^c obo:SO_0002355^c obo:SO_0001643^c obo:SO_0002358^c obo:SO_0002127^c obo:SO_0001637^c obo:SO_0002342^c obo:SO_0001269^c

gRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001264`
Super-classes	obo:SO_0001263^c
Restrictions	so:has_quality^op some obo:SO_0000979^c

miRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001265`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
Super-classes	obo:SO_0002342^c
Restrictions	so:has_quality^op some obo:SO_0000656^c so:has_quality^op some obo:SO_0000571^c

scRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001266`
Super-classes	obo:SO_0001263^c
Restrictions	so:has_quality^op some obo:SO_0000575^c

snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001267`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. Added additional children of snoRNA on 18 Nov 2021 at the request of Steven Marygold. See GitHub Issue #519.
Super-classes	obo:SO_0002342^c
Restrictions	so:has_quality^op some obo:SO_0000578^c
Sub-classes	obo:SO_0002339^c obo:SO_0002376^c obo:SO_0002375^c

snRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001268`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
Super-classes	obo:SO_0002342^c

SRP_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001269`
Super-classes	obo:SO_0001263^c
Restrictions	so:has_quality^op some obo:SO_0000642^c

SO_0001270^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001270`

tmRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001271`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
Super-classes	obo:SO_0002342^c
Restrictions	so:has_quality^op some obo:SO_0000659^c

tRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001272`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
Super-classes	obo:SO_0002342^c
Restrictions	so:has_quality^op some obo:SO_0000663^c

modified_adenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001273`
Super-classes	obo:SO_0000250^c
Sub-classes	obo:SO_0001305^c obo:SO_0001300^c obo:SO_0001306^c obo:SO_0001302^c obo:SO_0001314^c obo:SO_0001297^c obo:SO_0001313^c obo:SO_0001309^c obo:SO_0001298^c obo:SO_0001299^c obo:SO_0001311^c obo:SO_0001296^c obo:SO_0001310^c obo:SO_0001315^c obo:SO_0001312^c obo:SO_0001304^c obo:SO_0001308^c obo:SO_0001301^c obo:SO_0001295^c obo:SO_0001303^c obo:SO_0001307^c

modified_inosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001274`
Super-classes	obo:SO_0001230^c
Sub-classes	obo:SO_0001280^c obo:SO_0001278^c obo:SO_0001279^c obo:SO_0001233^c

modified_cytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001275`
Super-classes	obo:SO_0000250^c
Sub-classes	obo:SO_0001290^c obo:SO_0001282^c obo:SO_0001287^c obo:SO_0001289^c obo:SO_0001281^c obo:SO_0001288^c obo:SO_0001283^c obo:SO_0001293^c obo:SO_0001291^c obo:SO_0001294^c obo:SO_0001285^c obo:SO_0001284^c obo:SO_0001292^c obo:SO_0001286^c

modified_guanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001276`
Super-classes	obo:SO_0000250^c
Sub-classes	obo:SO_0001341^c obo:SO_0001332^c obo:SO_0001342^c obo:SO_0001330^c obo:SO_0001316^c obo:SO_0001336^c obo:SO_0001329^c obo:SO_0001326^c obo:SO_0001324^c obo:SO_0001334^c obo:SO_0001343^c obo:SO_0001337^c obo:SO_0001339^c obo:SO_0001340^c obo:SO_0001333^c obo:SO_0001331^c obo:SO_0001327^c obo:SO_0001328^c obo:SO_0001335^c obo:SO_0001338^c obo:SO_0001325^c

modified_uridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001277`
Super-classes	obo:SO_0000250^c
Sub-classes	obo:SO_0001376^c obo:SO_0001378^c obo:SO_0001351^c obo:SO_0001357^c obo:SO_0001373^c obo:SO_0001375^c obo:SO_0001361^c obo:SO_0001372^c obo:SO_0001356^c obo:SO_0001345^c obo:SO_0001382^c obo:SO_0001350^c obo:SO_0001364^c obo:SO_0001355^c obo:SO_0001346^c obo:SO_0001368^c obo:SO_0001369^c obo:SO_0001360^c obo:SO_0001363^c obo:SO_0001370^c obo:SO_0001380^c obo:SO_0001381^c obo:SO_0001367^c obo:SO_0001352^c obo:SO_0001362^c obo:SO_0001379^c obo:SO_0001365^c obo:SO_0001347^c obo:SO_0001358^c obo:SO_0001348^c obo:SO_0001349^c obo:SO_0001377^c obo:SO_0001228^c obo:SO_0001229^c obo:SO_0001366^c obo:SO_0001374^c obo:SO_0001354^c obo:SO_0001344^c obo:SO_0001371^c obo:SO_0001353^c obo:SO_0001359^c

one_methylinosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001278`
Super-classes	obo:SO_0001274^c

one_two_prime_O_dimethylinosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001279`
Super-classes	obo:SO_0001274^c

two_prime_O_methylinosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001280`
Super-classes	obo:SO_0001274^c

three_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001281`
Super-classes	obo:SO_0001275^c

five_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001282`
Super-classes	obo:SO_0001275^c

two_prime_O_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001283`
Super-classes	obo:SO_0001275^c

two_thiocytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001284`
Super-classes	obo:SO_0001275^c

N4_acetylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001285`
Super-classes	obo:SO_0001275^c

five_formylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001286`
Super-classes	obo:SO_0001275^c

five_two_prime_O_dimethylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001287`
Super-classes	obo:SO_0001275^c

N4_acetyl_2_prime_O_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001288`
Super-classes	obo:SO_0001275^c

lysidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001289`
Super-classes	obo:SO_0001275^c

N4_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001290`
Super-classes	obo:SO_0001275^c

N4_2_prime_O_dimethylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001291`
Super-classes	obo:SO_0001275^c

five_hydroxymethylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001292`
Super-classes	obo:SO_0001275^c

five_formyl_two_prime_O_methylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001293`
Super-classes	obo:SO_0001275^c

N4_N4_2_prime_O_trimethylcytidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001294`
Super-classes	obo:SO_0001275^c

one_methyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001295`
Super-classes	obo:SO_0001273^c

two_methyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001296`
Super-classes	obo:SO_0001273^c

N6_methyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001297`
Super-classes	obo:SO_0001273^c

two_prime_O_methyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001298`
Super-classes	obo:SO_0001273^c

two_methylthio_N6_methyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001299`
Super-classes	obo:SO_0001273^c

N6_isopentenyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001300`
Super-classes	obo:SO_0001273^c

two_methylthio_N6_isopentenyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001301`
Super-classes	obo:SO_0001273^c

N6_cis_hydroxyisopentenyl_adenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001302`
Super-classes	obo:SO_0001273^c

two_methylthio_N6_cis_hydroxyisopentenyl_adenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001303`
Super-classes	obo:SO_0001273^c

N6_glycinylcarbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001304`
Super-classes	obo:SO_0001273^c

N6_threonylcarbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001305`
Super-classes	obo:SO_0001273^c

two_methylthio_N6_threonyl_carbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001306`
Super-classes	obo:SO_0001273^c

N6_methyl_N6_threonylcarbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001307`
Super-classes	obo:SO_0001273^c

N6_hydroxynorvalylcarbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001308`
Super-classes	obo:SO_0001273^c

two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001309`
Super-classes	obo:SO_0001273^c

two_prime_O_ribosyladenosine_phosphate^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001310`
Super-classes	obo:SO_0001273^c

N6_N6_dimethyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001311`
Super-classes	obo:SO_0001273^c

N6_2_prime_O_dimethyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001312`
Super-classes	obo:SO_0001273^c

N6_N6_2_prime_O_trimethyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001313`
Super-classes	obo:SO_0001273^c

one_two_prime_O_dimethyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001314`
Super-classes	obo:SO_0001273^c

N6_acetyladenosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001315`
Super-classes	obo:SO_0001273^c

seven_deazaguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001316`
Super-classes	obo:SO_0001276^c
Sub-classes	obo:SO_0001322^c obo:SO_0001320^c obo:SO_0001318^c obo:SO_0001323^c obo:SO_0001321^c obo:SO_0001319^c obo:SO_0001317^c

queuosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001317`
Super-classes	obo:SO_0001316^c

epoxyqueuosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001318`
Super-classes	obo:SO_0001316^c

galactosyl_queuosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001319`
Super-classes	obo:SO_0001316^c

mannosyl_queuosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001320`
Super-classes	obo:SO_0001316^c

seven_cyano_seven_deazaguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001321`
Super-classes	obo:SO_0001316^c

seven_aminomethyl_seven_deazaguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001322`
Super-classes	obo:SO_0001316^c

archaeosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001323`
Super-classes	obo:SO_0001316^c

one_methylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001324`
Super-classes	obo:SO_0001276^c

N2_methylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001325`
Super-classes	obo:SO_0001276^c

seven_methylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001326`
Super-classes	obo:SO_0001276^c

two_prime_O_methylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001327`
Super-classes	obo:SO_0001276^c

N2_N2_dimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001328`
Super-classes	obo:SO_0001276^c

N2_2_prime_O_dimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001329`
Super-classes	obo:SO_0001276^c

N2_N2_2_prime_O_trimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001330`
Super-classes	obo:SO_0001276^c

two_prime_O_ribosylguanosine_phosphate^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001331`
Super-classes	obo:SO_0001276^c

wybutosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001332`
Super-classes	obo:SO_0001276^c

peroxywybutosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001333`
Super-classes	obo:SO_0001276^c

hydroxywybutosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001334`
Super-classes	obo:SO_0001276^c

undermodified_hydroxywybutosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001335`
Super-classes	obo:SO_0001276^c

wyosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001336`
Super-classes	obo:SO_0001276^c

methylwyosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001337`
Super-classes	obo:SO_0001276^c

N2_7_dimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001338`
Super-classes	obo:SO_0001276^c

N2_N2_7_trimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001339`
Super-classes	obo:SO_0001276^c

one_two_prime_O_dimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001340`
Super-classes	obo:SO_0001276^c

four_demethylwyosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001341`
Super-classes	obo:SO_0001276^c

isowyosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001342`
Super-classes	obo:SO_0001276^c

N2_7_2prirme_O_trimethylguanosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001343`
Super-classes	obo:SO_0001276^c

five_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001344`
Super-classes	obo:SO_0001277^c

two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001345`
Super-classes	obo:SO_0001277^c

five_two_prime_O_dimethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001346`
Super-classes	obo:SO_0001277^c

one_methylpseudouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001347`
Super-classes	obo:SO_0001277^c

two_prime_O_methylpseudouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001348`
Super-classes	obo:SO_0001277^c

two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001349`
Super-classes	obo:SO_0001277^c

four_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001350`
Super-classes	obo:SO_0001277^c

five_methyl_2_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001351`
Super-classes	obo:SO_0001277^c

two_thio_two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001352`
Super-classes	obo:SO_0001277^c

three_three_amino_three_carboxypropyl_uridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001353`
Super-classes	obo:SO_0001277^c

five_hydroxyuridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001354`
Super-classes	obo:SO_0001277^c

five_methoxyuridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001355`
Super-classes	obo:SO_0001277^c

uridine_five_oxyacetic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001356`
Super-classes	obo:SO_0001277^c

uridine_five_oxyacetic_acid_methyl_ester^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001357`
Super-classes	obo:SO_0001277^c

five_carboxyhydroxymethyl_uridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001358`
Super-classes	obo:SO_0001277^c

five_carboxyhydroxymethyl_uridine_methyl_ester^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001359`
Super-classes	obo:SO_0001277^c

five_methoxycarbonylmethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001360`
Super-classes	obo:SO_0001277^c

five_methoxycarbonylmethyl_two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001361`
Super-classes	obo:SO_0001277^c

five_methoxycarbonylmethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001362`
Super-classes	obo:SO_0001277^c

five_aminomethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001363`
Super-classes	obo:SO_0001277^c

five_methylaminomethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001364`
Super-classes	obo:SO_0001277^c

five_methylaminomethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001365`
Super-classes	obo:SO_0001277^c

five_methylaminomethyl_two_selenouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001366`
Super-classes	obo:SO_0001277^c

five_carbamoylmethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001367`
Super-classes	obo:SO_0001277^c

five_carbamoylmethyl_two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001368`
Super-classes	obo:SO_0001277^c

five_carboxymethylaminomethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001369`
Super-classes	obo:SO_0001277^c

five_carboxymethylaminomethyl_two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001370`
Super-classes	obo:SO_0001277^c

five_carboxymethylaminomethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001371`
Super-classes	obo:SO_0001277^c

three_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001372`
Super-classes	obo:SO_0001277^c

one_methyl_three_three_amino_three_carboxypropyl_pseudouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001373`
Super-classes	obo:SO_0001277^c

five_carboxymethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001374`
Super-classes	obo:SO_0001277^c

three_two_prime_O_dimethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001375`
Super-classes	obo:SO_0001277^c

five_methyldihydrouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001376`
Super-classes	obo:SO_0001277^c

three_methylpseudouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001377`
Super-classes	obo:SO_0001277^c

five_taurinomethyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001378`
Super-classes	obo:SO_0001277^c

five_taurinomethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001379`
Super-classes	obo:SO_0001277^c

five_isopentenylaminomethyl_uridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001380`
Super-classes	obo:SO_0001277^c

five_isopentenylaminomethyl_two_thiouridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001381`
Super-classes	obo:SO_0001277^c

five_isopentenylaminomethyl_two_prime_O_methyluridine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001382`
Super-classes	obo:SO_0001277^c

histone_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001383`
Super-classes	obo:SO_0001654^c

CDS_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001384`
Super-classes	obo:SO_0000316^c
Restrictions	so:has_quality^op some obo:SO_0000731^c

modified_amino_acid_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001385`
Super-classes	obo:SO_0001237^c
Sub-classes	obo:SO_0001402^c obo:SO_0001400^c obo:SO_0001404^c obo:SO_0001395^c obo:SO_0001401^c obo:SO_0001386^c obo:SO_0001387^c obo:SO_0001398^c obo:SO_0001405^c obo:SO_0001390^c obo:SO_0001397^c obo:SO_0001391^c obo:SO_0001388^c obo:SO_0001392^c obo:SO_0001394^c obo:SO_0001393^c obo:SO_0001399^c obo:SO_0001403^c obo:SO_0001406^c obo:SO_0001389^c obo:SO_0001396^c

modified_glycine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001386`
Super-classes	obo:SO_0001385^c

modified_L_alanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001387`
Super-classes	obo:SO_0001385^c

modified_L_asparagine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001388`
Super-classes	obo:SO_0001385^c

modified_L_aspartic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001389`
Super-classes	obo:SO_0001385^c

modified_L_cysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001390`
Super-classes	obo:SO_0001385^c

modified_L_glutamic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001391`
Super-classes	obo:SO_0001385^c

modified_L_threonine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001392`
Super-classes	obo:SO_0001385^c

modified_L_tryptophan^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001393`
Super-classes	obo:SO_0001385^c

modified_L_glutamine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001394`
Super-classes	obo:SO_0001385^c

modified_L_methionine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001395`
Super-classes	obo:SO_0001385^c

modified_L_isoleucine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001396`
Super-classes	obo:SO_0001385^c

modified_L_phenylalanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001397`
Super-classes	obo:SO_0001385^c

modified_L_histidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001398`
Super-classes	obo:SO_0001385^c

modified_L_serine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001399`
Super-classes	obo:SO_0001385^c

modified_L_lysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001400`
Super-classes	obo:SO_0001385^c

modified_L_leucine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001401`
Super-classes	obo:SO_0001385^c

modified_L_selenocysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001402`
Super-classes	obo:SO_0001385^c

modified_L_valine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001403`
Super-classes	obo:SO_0001385^c

modified_L_proline^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001404`
Super-classes	obo:SO_0001385^c

modified_L_tyrosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001405`
Super-classes	obo:SO_0001385^c

modified_L_arginine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001406`
Super-classes	obo:SO_0001385^c

peptidyl^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001407`
Super-classes	obo:SO_0000443^c

cleaved_for_gpi_anchor_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001408`
Super-classes	obo:SO_0100011^c

biomaterial_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001409`
Super-classes	obo:SO_0000001^c
Sub-classes	obo:SO_0000695^c obo:SO_0000804^c

experimental_feature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001410`
Super-classes	obo:SO_0000001^c
Sub-classes	obo:SO_0001915^c obo:SO_0001696^c obo:SO_0001248^c obo:SO_0000717^c obo:SO_0001642^c obo:SO_0001457^c obo:SO_0000700^c obo:SO_0000330^c obo:SO_0000994^c obo:SO_0000143^c obo:SO_0002248^c obo:SO_0000343^c obo:SO_0001418^c obo:SO_0001502^c obo:SO_0001005^c obo:SO_0000039^c

biological_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001411`
Super-classes	obo:SO_0000001^c
Sub-classes	obo:SO_0001747^c obo:SO_0001954^c obo:SO_0002300^c obo:SO_0000159^c obo:SO_0000002^c obo:SO_1001275^c obo:SO_0001037^c obo:SO_0002357^c obo:SO_0001985^c obo:SO_0000409^c obo:SO_0005855^c obo:SO_0000609^c obo:SO_0000462^c obo:SO_0000298^c obo:SO_0001237^c obo:SO_0000839^c obo:SO_0001235^c obo:SO_0000610^c obo:SO_0002186^c obo:SO_0000833^c obo:SO_0001236^c obo:SO_0000605^c obo:SO_0001645^c obo:SO_0000657^c obo:SO_0000581^c obo:SO_0000667^c obo:SO_0001872^c obo:SO_0002331^c obo:SO_0002259^c obo:SO_0000336^c obo:SO_0001683^c obo:SO_0000307^c obo:SO_0000704^c obo:SO_0000297^c obo:SO_0000842^c obo:SO_1000036^c obo:SO_0000104^c obo:SO_0000726^c obo:SO_0000018^c obo:SO_0000771^c obo:SO_1000002^c obo:SO_0000296^c obo:SO_0000830^c obo:SO_0000831^c

topologically_defined_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001412`
Super-classes	obo:SO_0000001^c
Sub-classes	obo:SO_0000239^c obo:SO_0000840^c obo:SO_0002304^c

translocation_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001413`
Super-classes	obo:SO_0001021^c

insertion_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001414`
Super-classes	obo:SO_0001021^c

deletion_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001415`
Super-classes	obo:SO_0001021^c

five_prime_flanking_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001416`
Super-classes	obo:SO_0000239^c

three_prime_flanking_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001417`
Super-classes	obo:SO_0000239^c

transcribed_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001418`
Description	Term requested by the MODencode group.
Super-classes	obo:SO_0001410^c

cis_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001419`
Super-classes	obo:SO_0000162^c
Sub-classes	obo:SO_0000998^c obo:SO_0000163^c obo:SO_0000164^c obo:SO_0001993^c

trans_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001420`
Super-classes	obo:SO_0000162^c
Sub-classes	obo:SO_0000706^c obo:SO_0000707^c

splice_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001421`
Super-classes	obo:SO_0000699^c

conformational_switch^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001422`
Description	MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
Super-classes	obo:SO_0100001^c

dye_terminator_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001423`
Super-classes	obo:SO_0000150^c

pyrosequenced_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001424`
Description	An example is a read produced by Roche 454 technology.
Super-classes	obo:SO_0000150^c

ligation_based_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001425`
Description	An example of this kind of read is one produced by ABI SOLiD.
Super-classes	obo:SO_0000150^c

polymerase_synthesis_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001426`
Description	An example is a read produced by Illumina technology.
Super-classes	obo:SO_0000150^c

cis_regulatory_frameshift_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001427`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c

expressed_sequence_assembly^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001428`
Description	From tracker [ 2372385 ] expressed_sequence_assembly.
Super-classes	obo:SO_0000353^c

DNA_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001429`
Super-classes	obo:SO_0001655^c
Sub-classes	obo:SO_0001971^c obo:SO_0100020^c

SO_0001430^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001430`

cryptic_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001431`
Super-classes	obo:SO_0000704^c
Restrictions	so:has_quality^op some obo:SO_0000976^c
Sub-classes	obo:SO_1001196^c

sequence_variant_affecting_polyadenylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001432`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

three_prime_RACE_clone^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001433`
Super-classes	obo:SO_0000317^c

cassette_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001434`
Description	Requested by the Trypanosome community.
Super-classes	obo:SO_0001760^c

alanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001435`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

valine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001436`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

leucine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001437`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

isoleucine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001438`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

proline^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001439`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

tryptophan^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001440`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

phenylalanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001441`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

methionine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001442`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

glycine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001443`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

serine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001444`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

threonine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001445`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

tyrosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001446`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

cysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001447`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

glutamine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001448`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

asparagine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001449`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

lysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001450`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

arginine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001451`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

histidine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001452`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

aspartic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001453`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

glutamic_acid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001454`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

selenocysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001455`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

pyrrolysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001456`
Description	A place holder for a cross product with chebi.
Super-classes	obo:SO_0001237^c

transcribed_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001457`
Description	This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
Super-classes	obo:SO_0001410^c
Restrictions	so:has_part^op some obo:SO_0000695^c
Sub-classes	obo:SO_0001458^c

unigene_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001458`
Description	This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
Super-classes	obo:SO_0001457^c

CRISPR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001459`
Super-classes	obo:SO_0000314^c

insulator_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001460`
Description	See tracker ID 2060908.
Super-classes	obo:SO_0001654^c
Restrictions	so:part_of^op some obo:SO_0000627^c

enhancer_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001461`
Super-classes	obo:SO_0001654^c
Restrictions	so:part_of^op some obo:SO_0000165^c
Sub-classes	obo:SO_0002046^c

contig_collection^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001462`
Description	See tracker ID: 2138359.
Super-classes	obo:SO_0001085^c obo:SO_0001260^c
Restrictions	so:has_part^op some obo:SO_0000149^c

lincRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001463`
Super-classes	obo:SO_0001877^c

UST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001464`
Super-classes	obo:SO_0000345^c
Sub-classes	obo:SO_0001466^c obo:SO_0001465^c

three_prime_UST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001465`
Super-classes	obo:SO_0001464^c

five_prime_UST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001466`
Super-classes	obo:SO_0001464^c

RST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001467`
Super-classes	obo:SO_0000345^c
Sub-classes	obo:SO_0001468^c obo:SO_0001469^c

three_prime_RST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001468`
Super-classes	obo:SO_0001467^c

five_prime_RST^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001469`
Super-classes	obo:SO_0001467^c

UST_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001470`
Super-classes	obo:SO_0000102^c

RST_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001471`
Super-classes	obo:SO_0000102^c

primer_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001472`
Super-classes	obo:SO_0000347^c

miRNA_antiguide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001473`
Super-classes	obo:SO_0001243^c

trans_splice_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001474`
Super-classes	obo:SO_0000699^c

outron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001475`
Super-classes	obo:SO_0000835^c

natural_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001476`
Super-classes	obo:SO_0000155^c obo:SO_0001038^c
Restrictions	so:has_quality^op some obo:SO_0000782^c

gene_trap_construct^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001477`
Super-classes	obo:SO_0000637^c

promoter_trap_construct^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001478`
Super-classes	obo:SO_0000637^c

enhancer_trap_construct^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001479`
Super-classes	obo:SO_0000637^c

PAC_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001480`
Super-classes	obo:SO_0000150^c
Restrictions	so:part_of^op some obo:SO_0000154^c

RAPD^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001481`
Super-classes	obo:SO_0000006^c

shadow_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001482`
Super-classes	obo:SO_0000165^c

SNV^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001483`
Super-classes	obo:SO_1000002^c
Sub-classes	obo:SO_1000009^c obo:SO_0000694^c obo:SO_1000008^c obo:SO_1000017^c

X_element_combinatorial_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001484`
Description	X element combinatorial repeats contain Tbf1p binding sites, and possible functions include a role in telomerase-independent telomere maintenance via recombination or as a barrier against transcriptional silencing. These are usually present as a combination of one or more of several types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
Super-classes	obo:SO_0000657^c
Restrictions	so:part_of^op some obo:SO_0000624^c

Y_prime_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001485`
Description	This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
Super-classes	obo:SO_0000657^c
Restrictions	so:part_of^op some obo:SO_0000624^c

standard_draft^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001486`
Super-classes	obo:SO_0001499^c

high_quality_draft^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001487`
Super-classes	obo:SO_0001499^c

improved_high_quality_draft^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001488`
Super-classes	obo:SO_0001499^c

annotation_directed_improved_draft^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001489`
Super-classes	obo:SO_0001499^c

noncontiguous_finished^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001490`
Super-classes	obo:SO_0001499^c

finished_genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001491`
Super-classes	obo:SO_0001499^c

intronic_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001492`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c
Restrictions	so:part_of^op some obo:SO_0000188^c

centromere_DNA_Element_I^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001493`
Description	This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0001794^c

centromere_DNA_Element_II^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001494`
Description	This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0001794^c

centromere_DNA_Element_III^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001495`
Description	This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0001794^c

telomeric_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001496`
Description	The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
Super-classes	obo:SO_0000657^c
Restrictions	so:part_of^op some obo:SO_0000624^c

X_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001497`
Description	Possible functions include roles in chromosomal segregation, maintenance of chromosome stability, recombinational sequestering, or as a barrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. From Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0000624^c

YAC_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001498`
Super-classes	obo:SO_0000150^c
Restrictions	so:part_of^op some obo:SO_0000152^c

whole_genome_sequence_status^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001499`
Description	This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
Super-classes	obo:SO_0000905^c
Sub-classes	obo:SO_0001490^c obo:SO_0001488^c obo:SO_0001491^c obo:SO_0001487^c obo:SO_0001489^c obo:SO_0001486^c

heritable_phenotypic_marker^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001500`
Super-classes	obo:SO_0001645^c

peptide_collection^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001501`
Description	Term requested via tracker ID: 2910829.
Super-classes	obo:SO_0001260^c
Restrictions	so:has_part^op some obo:SO_0000104^c

high_identity_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001502`
Description	Requested by tracker ID: 2902685.
Super-classes	obo:SO_0001410^c

processed_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001503`
Description	Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
Super-classes	obo:SO_0000673^c
Sub-classes	obo:SO_0002111^c

assortment_derived_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001504`
Super-classes	obo:SO_0000240^c
Sub-classes	obo:SO_0000800^c obo:SO_0000803^c obo:SO_0000801^c obo:SO_0000802^c

reference_genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001505`
Super-classes	obo:SO_0001026^c

variant_genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001506`
Super-classes	obo:SO_0001026^c
Sub-classes	obo:SO_0001524^c

variant_collection^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001507`
Super-classes	obo:SO_0001260^c
Restrictions	so:has_part^op some obo:SO_0001059^c
Sub-classes	obo:SO_0000240^c obo:SO_0001024^c obo:SO_0001028^c obo:SO_0001023^c obo:SO_0001027^c

alteration_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001508`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0001520^c obo:SO_0001523^c obo:SO_0001509^c obo:SO_0001512^c obo:SO_0001517^c

chromosomal_variation_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001509`
Super-classes	obo:SO_0001508^c
Sub-classes	obo:SO_0001511^c obo:SO_0001510^c

intrachromosomal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001510`
Super-classes	obo:SO_0001509^c

interchromosomal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001511`
Super-classes	obo:SO_0001509^c

insertion_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001512`
Super-classes	obo:SO_0001508^c
Sub-classes	obo:SO_0001514^c obo:SO_0001515^c obo:SO_0001513^c

tandem^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001513`
Super-classes	obo:SO_0001512^c

direct^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001514`
Super-classes	obo:SO_0001512^c

inverted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001515`
Super-classes	obo:SO_0001512^c

free^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001516`
Super-classes	obo:SO_0001523^c

inversion_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001517`
Super-classes	obo:SO_0001508^c
Sub-classes	obo:SO_0001518^c obo:SO_0001519^c

pericentric^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001518`
Super-classes	obo:SO_0001517^c

paracentric^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001519`
Super-classes	obo:SO_0001517^c

translocaton_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001520`
Super-classes	obo:SO_0001508^c
Sub-classes	obo:SO_0001521^c obo:SO_0001522^c

reciprocal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001521`
Super-classes	obo:SO_0001520^c

insertional^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001522`
Super-classes	obo:SO_0001520^c

duplication_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001523`
Super-classes	obo:SO_0001508^c
Sub-classes	obo:SO_0001516^c

chromosomally_aberrant_genome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001524`
Super-classes	obo:SO_0001506^c

assembly_error_correction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001525`
Super-classes	obo:SO_0000413^c

base_call_error_correction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001526`
Super-classes	obo:SO_0000413^c

peptide_localization_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001527`
Super-classes	obo:SO_0000839^c
Sub-classes	obo:SO_0001813^c obo:SO_0001531^c obo:SO_0001806^c obo:SO_0000418^c obo:SO_0001530^c obo:SO_0000725^c obo:SO_0001534^c obo:SO_0001808^c obo:SO_0001528^c obo:SO_0001529^c

nuclear_localization_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001528`
Super-classes	obo:SO_0001527^c

endosomal_localization_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001529`
Super-classes	obo:SO_0001527^c

lysosomal_localization_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001530`
Super-classes	obo:SO_0001527^c

nuclear_export_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001531`
Super-classes	obo:SO_0001527^c

recombination_signal_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001532`
Super-classes	obo:SO_0000299^c

cryptic_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001533`
Super-classes	obo:SO_0000162^c

nuclear_rim_localization_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001534`
Super-classes	obo:SO_0001527^c

P_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001535`
Description	Moved from under DNA_transposon (SO:0000182) by Dave Sant as per request from GitHub issue #488 on June 25, 2020
Super-classes	obo:SO_0000208^c

functional_effect_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001536`
Description	Updated after request from Lea Starita, lea.starita@gmail.com from the NCBI.
Super-classes	obo:SO_0001060^c
Sub-classes	obo:SO_0002218^c obo:SO_0002220^c obo:SO_0002318^c obo:SO_0002314^c obo:SO_0002219^c

structural_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001537`
Super-classes	obo:SO_0001060^c
Sub-classes	obo:SO_0001878^c obo:SO_0001882^c obo:SO_0002160^c obo:SO_0001880^c obo:SO_0001879^c obo:SO_0001881^c

transcript_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001538`
Super-classes	obo:SO_0002218^c
Sub-classes	obo:SO_0001543^c obo:SO_0001540^c obo:SO_0001546^c obo:SO_0001549^c

translational_product_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001539`
Super-classes	obo:SO_0002218^c
Sub-classes	obo:SO_0001599^c obo:SO_0001554^c obo:SO_0001602^c obo:SO_0001553^c

level_of_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001540`
Super-classes	obo:SO_0001538^c
Sub-classes	obo:SO_0001542^c obo:SO_0001541^c

decreased_transcript_level_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001541`
Super-classes	obo:SO_0001540^c

increased_transcript_level_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001542`
Super-classes	obo:SO_0001540^c

transcript_processing_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001543`
Super-classes	obo:SO_0001538^c
Sub-classes	obo:SO_0001544^c obo:SO_0001545^c

editing_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001544`
Super-classes	obo:SO_0001543^c

polyadenylation_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001545`
Super-classes	obo:SO_0001543^c
Sub-classes	obo:SO_0001802^c obo:SO_0001803^c

transcript_stability_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001546`
Super-classes	obo:SO_0001538^c
Sub-classes	obo:SO_0001547^c obo:SO_0001548^c

decreased_transcript_stability_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001547`
Super-classes	obo:SO_0001546^c

increased_transcript_stability_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001548`
Super-classes	obo:SO_0001546^c

transcription_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001549`
Super-classes	obo:SO_0001538^c
Sub-classes	obo:SO_0001550^c

rate_of_transcription_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001550`
Super-classes	obo:SO_0001549^c
Sub-classes	obo:SO_0001552^c obo:SO_0001551^c

increased_transcription_rate_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001551`
Super-classes	obo:SO_0001550^c

decreased_transcription_rate_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001552`
Super-classes	obo:SO_0001550^c

translational_product_level_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001553`
Super-classes	obo:SO_0001539^c
Sub-classes	obo:SO_0001556^c obo:SO_0001555^c

polypeptide_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001554`
Super-classes	obo:SO_0001539^c
Sub-classes	obo:SO_0001562^c obo:SO_0001558^c obo:SO_0001559^c obo:SO_0001557^c

decreased_translational_product_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001555`
Super-classes	obo:SO_0001553^c

increased_translational_product_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001556`
Super-classes	obo:SO_0001553^c

polypeptide_gain_of_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001557`
Super-classes	obo:SO_0001554^c

polypeptide_localization_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001558`
Super-classes	obo:SO_0001554^c

polypeptide_loss_of_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001559`
Super-classes	obo:SO_0001554^c
Sub-classes	obo:SO_0001561^c obo:SO_0001560^c

inactive_ligand_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001560`
Super-classes	obo:SO_0001559^c
Sub-classes	obo:SO_0001618^c

polypeptide_partial_loss_of_function^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001561`
Super-classes	obo:SO_0001559^c

polypeptide_post_translational_processing_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001562`
Super-classes	obo:SO_0001554^c

copy_number_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001563`
Super-classes	obo:SO_0002160^c
Sub-classes	obo:SO_0001912^c obo:SO_0001911^c

gene_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001564`
Super-classes	obo:SO_0001878^c
Sub-classes	obo:SO_0002152^c obo:SO_0001598^c obo:SO_0001576^c obo:SO_0001565^c obo:SO_0002153^c

gene_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001565`
Super-classes	obo:SO_0001882^c obo:SO_0001564^c
Sub-classes	obo:SO_0002086^c obo:SO_0002085^c

regulatory_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001566`
Description	EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
Super-classes	obo:SO_0001878^c
Sub-classes	obo:SO_0001782^c

stop_retained_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001567`
Super-classes	obo:SO_0001590^c obo:SO_0001819^c

splicing_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001568`
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001569^c obo:SO_0001630^c obo:SO_0001629^c obo:SO_0001995^c obo:SO_0002169^c obo:SO_0001573^c obo:SO_0001572^c

cryptic_splice_site_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001569`
Super-classes	obo:SO_0001568^c
Sub-classes	obo:SO_0001570^c obo:SO_0001571^c

cryptic_splice_acceptor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001570`
Super-classes	obo:SO_0001569^c

cryptic_splice_donor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001571`
Super-classes	obo:SO_0001569^c

exon_loss_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001572`
Super-classes	obo:SO_0001568^c

intron_gain_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001573`
Super-classes	obo:SO_0001568^c

splice_acceptor_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001574`
Super-classes	obo:SO_0001629^c
Sub-classes	obo:SO_0002328^c obo:SO_0002327^c

splice_donor_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001575`
Super-classes	obo:SO_0001629^c
Sub-classes	obo:SO_0002325^c obo:SO_0002326^c

transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001576`
Super-classes	obo:SO_0001564^c
Sub-classes	obo:SO_0002011^c obo:SO_0001621^c obo:SO_0001968^c obo:SO_0001568^c obo:SO_0002075^c obo:SO_0001627^c obo:SO_0001619^c obo:SO_0001596^c obo:SO_0001577^c obo:SO_0001791^c obo:SO_0002244^c

complex_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001577`
Description	EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
Super-classes	obo:SO_0001576^c

stop_lost^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001578`
Description	EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
Super-classes	obo:SO_0001907^c obo:SO_0001992^c obo:SO_0001590^c

transcript_sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001579`

coding_sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001580`
Super-classes	obo:SO_0001791^c obo:SO_0001968^c
Sub-classes	obo:SO_0001818^c obo:SO_0001590^c obo:SO_0001819^c obo:SO_0001582^c

SO_0001581^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001581`

initiator_codon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001582`
Description	This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
Super-classes	obo:SO_0001580^c
Sub-classes	obo:SO_0002012^c obo:SO_0002019^c

missense_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001583`
Description	EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
Super-classes	obo:SO_0001992^c
Sub-classes	obo:SO_0001585^c obo:SO_0001586^c

SO_0001584^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001584`

conservative_missense_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001585`
Super-classes	obo:SO_0001583^c

non_conservative_missense_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001586`
Super-classes	obo:SO_0001583^c
Sub-classes	obo:SO_0002008^c

stop_gained^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001587`
Description	EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
Super-classes	obo:SO_0001906^c obo:SO_0001992^c
Sub-classes	obo:SO_0002322^c obo:SO_0002321^c

SO_0001588^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001588`

frameshift_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001589`
Description	EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
Super-classes	obo:SO_0001818^c
Sub-classes	obo:SO_0001909^c obo:SO_0001592^c obo:SO_0001910^c obo:SO_0002324^c obo:SO_0001595^c obo:SO_0001594^c obo:SO_0001591^c obo:SO_0001593^c obo:SO_0002323^c

terminator_codon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001590`
Description	The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
Super-classes	obo:SO_0001580^c
Sub-classes	obo:SO_0001567^c obo:SO_0001626^c obo:SO_0001578^c

frame_restoring_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001591`
Super-classes	obo:SO_0001589^c

minus_1_frameshift_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001592`
Super-classes	obo:SO_0001589^c

minus_2_frameshift_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001593`
Super-classes	obo:SO_0001589^c

plus_1_frameshift_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001594`
Super-classes	obo:SO_0001589^c

plus_2_frameshift_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001595`
Super-classes	obo:SO_0001589^c

transcript_secondary_structure_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001596`
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001597^c

compensatory_transcript_secondary_structure_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001597`
Super-classes	obo:SO_0001596^c

translational_product_structure_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001598`
Super-classes	obo:SO_0001564^c
Sub-classes	obo:SO_0001603^c

3D_polypeptide_structure_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001599`
Super-classes	obo:SO_0001539^c
Sub-classes	obo:SO_0002093^c obo:SO_0001601^c obo:SO_0001600^c

complex_3D_structural_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001600`
Super-classes	obo:SO_0001599^c

conformational_change_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001601`
Super-classes	obo:SO_0001599^c

complex_change_of_translational_product_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001602`
Super-classes	obo:SO_0001539^c

polypeptide_sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001603`
Super-classes	obo:SO_0001598^c
Sub-classes	obo:SO_0001606^c obo:SO_0001609^c obo:SO_0001604^c obo:SO_0001605^c obo:SO_0001616^c obo:SO_0001617^c

amino_acid_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001604`
Super-classes	obo:SO_0001603^c

amino_acid_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001605`
Super-classes	obo:SO_0001603^c

amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001606`
Super-classes	obo:SO_0001603^c
Sub-classes	obo:SO_0001607^c obo:SO_0001608^c

conservative_amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001607`
Super-classes	obo:SO_0001606^c

non_conservative_amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001608`
Super-classes	obo:SO_0001606^c

elongated_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001609`
Super-classes	obo:SO_0001603^c
Sub-classes	obo:SO_0001611^c obo:SO_0001610^c

elongated_polypeptide_C_terminal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001610`
Super-classes	obo:SO_0001609^c
Restrictions	so:derives_from^op some obo:SO_0002229^c
Sub-classes	obo:SO_0001612^c obo:SO_0001613^c

elongated_polypeptide_N_terminal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001611`
Super-classes	obo:SO_0001609^c
Restrictions	so:derives_from^op some obo:SO_0002228^c
Sub-classes	obo:SO_0001615^c obo:SO_0001614^c

elongated_in_frame_polypeptide_C_terminal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001612`
Super-classes	obo:SO_0001610^c

elongated_out_of_frame_polypeptide_C_terminal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001613`
Super-classes	obo:SO_0001610^c

elongated_in_frame_polypeptide_N_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001614`
Super-classes	obo:SO_0001611^c

elongated_out_of_frame_polypeptide_N_terminal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001615`
Super-classes	obo:SO_0001611^c

polypeptide_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001616`
Super-classes	obo:SO_0001603^c

polypeptide_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001617`
Super-classes	obo:SO_0001603^c

inactive_catalytic_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001618`
Super-classes	obo:SO_0001560^c

non_coding_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001619`
Description	Within non-coding gene - Located within a gene that does not code for a protein.
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001970^c obo:SO_0001792^c obo:SO_0002088^c obo:SO_0001620^c

mature_miRNA_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001620`
Description	EBI term: Within mature miRNA - Located within a microRNA.
Super-classes	obo:SO_0001619^c

NMD_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001621`
Super-classes	obo:SO_0001576^c

UTR_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001622`
Super-classes	obo:SO_0001968^c obo:SO_0001791^c
Sub-classes	obo:SO_0001623^c obo:SO_0001624^c

5_prime_UTR_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001623`
Description	EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
Super-classes	obo:SO_0001622^c
Sub-classes	obo:SO_0002092^c obo:SO_0002091^c obo:SO_0002013^c obo:SO_0002014^c obo:SO_0001983^c

3_prime_UTR_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001624`
Description	EBI term 3prime UTR variations - In 3prime UTR.
Super-classes	obo:SO_0001622^c
Sub-classes	obo:SO_0002015^c obo:SO_0002090^c obo:SO_0002016^c obo:SO_0002089^c

SO_0001625^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001625`

incomplete_terminal_codon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001626`
Description	EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
Super-classes	obo:SO_0001590^c obo:SO_0001650^c

intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001627`
Description	EBI term: Intronic variations - In intron.
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001970^c obo:SO_0002018^c obo:SO_0001629^c obo:SO_0001969^c

intergenic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001628`
Description	EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
Super-classes	obo:SO_0001878^c
Sub-classes	obo:SO_0001986^c obo:SO_0001631^c obo:SO_0001987^c obo:SO_0002017^c obo:SO_0001632^c obo:SO_0002074^c

splice_site_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001629`
Description	EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
Super-classes	obo:SO_0001568^c obo:SO_0001627^c
Sub-classes	obo:SO_0001787^c obo:SO_0001574^c obo:SO_0001575^c

splice_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001630`
Description	EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
Super-classes	obo:SO_0001568^c
Sub-classes	obo:SO_0002170^c obo:SO_0002084^c obo:SO_0002088^c

upstream_gene_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001631`
Description	Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
Super-classes	obo:SO_0001628^c
Sub-classes	obo:SO_0001635^c obo:SO_0001636^c

downstream_gene_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001632`
Description	Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
Super-classes	obo:SO_0001628^c
Sub-classes	obo:SO_0002083^c obo:SO_0001634^c obo:SO_0001633^c

5KB_downstream_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001633`
Description	EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
Super-classes	obo:SO_0001632^c

500B_downstream_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001634`
Super-classes	obo:SO_0001632^c

5KB_upstream_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001635`
Description	EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
Super-classes	obo:SO_0001631^c

2KB_upstream_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001636`
Super-classes	obo:SO_0001631^c

rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001637`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0001263^c
Sub-classes	obo:SO_0002366^c obo:SO_0002363^c obo:SO_0002360^c obo:SO_0002241^c

piRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001638`
Description	Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514.
Super-classes	obo:SO_0002342^c

RNase_P_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001639`
Description	Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.
Super-classes	obo:SO_0002180^c

RNase_MRP_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001640`
Description	Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533.
Super-classes	obo:SO_0002180^c

lincRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001641`
Super-classes	obo:SO_0002127^c

mathematically_defined_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001642`
Description	Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
Super-classes	obo:SO_0001410^c

telomerase_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001643`
Super-classes	obo:SO_0001263^c

targeting_vector^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001644`
Super-classes	obo:SO_0000440^c obo:SO_0000804^c
Restrictions	so:has_part^op some obo:SO_0000853^c so:has_quality^op some obo:SO_0000783^c

genetic_marker^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001645`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0001500^c obo:SO_0001646^c obo:SO_0002232^c

DArT_marker^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001646`
Super-classes	obo:SO_0001645^c

kozak_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001647`
Super-classes	obo:SO_0000139^c

nested_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001648`
Super-classes	obo:SO_0000101^c

nested_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001649`
Super-classes	obo:SO_0000657^c
Sub-classes	obo:SO_0001658^c

inframe_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001650`
Super-classes	obo:SO_0001818^c
Sub-classes	obo:SO_0001820^c obo:SO_0001626^c obo:SO_0001992^c

SO_0001651^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001651`

SO_0001652^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001652`

retinoic_acid_responsive_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001653`
Super-classes	obo:SO_0000235^c

nucleotide_to_protein_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001654`
Super-classes	obo:SO_0000410^c
Sub-classes	obo:SO_0000235^c obo:SO_0001383^c obo:SO_0001460^c obo:SO_0000059^c obo:SO_0001461^c

nucleotide_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001655`
Description	See GO:0000166 : nucleotide binding.
Super-classes	obo:SO_0000409^c
Sub-classes	obo:SO_0000934^c obo:SO_0005850^c obo:SO_0001429^c

metal_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001656`
Description	See GO:0046872 : metal ion binding.
Super-classes	obo:SO_0000409^c
Sub-classes	obo:SO_0001092^c

ligand_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001657`
Super-classes	obo:SO_0000409^c
Sub-classes	obo:SO_0001105^c

nested_tandem_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001658`
Description	Tracker ID: 3052459.
Super-classes	obo:SO_0001649^c

promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001659`
Description	Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000167^c so:overlaps^op some obo:SO_0000235^c
Sub-classes	obo:SO_0001161^c obo:SO_0001847^c obo:SO_0001861^c obo:SO_0001842^c obo:SO_0001168^c obo:SO_0000173^c obo:SO_0002006^c obo:SO_0001852^c obo:SO_0002044^c obo:SO_0001165^c obo:SO_0001159^c obo:SO_0001157^c obo:SO_0001855^c obo:SO_0001160^c obo:SO_0001858^c obo:SO_0001871^c obo:SO_0002156^c obo:SO_0002216^c obo:SO_0001167^c obo:SO_0001849^c obo:SO_0001845^c obo:SO_0001974^c obo:SO_0001678^c obo:SO_0001843^c obo:SO_0001859^c obo:SO_0002309^c obo:SO_0001846^c obo:SO_0001856^c obo:SO_0001850^c obo:SO_0001857^c obo:SO_0001865^c obo:SO_0002045^c obo:SO_0001839^c obo:SO_0001164^c obo:SO_0001844^c

core_eukaryotic_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001660`
Super-classes	obo:SO_0002309^c
Restrictions	so:part_of^op some obo:SO_0002221^c
Sub-classes	obo:SO_0000174^c obo:SO_0001663^c obo:SO_0000620^c obo:SO_0001901^c obo:SO_0000622^c obo:SO_0001848^c obo:SO_0000619^c obo:SO_0000015^c obo:SO_0001162^c obo:SO_0000014^c obo:SO_0000016^c obo:SO_0001959^c obo:SO_0001664^c obo:SO_0001677^c

RNA_polymerase_II_TATA_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001661`
Super-classes	obo:SO_0000174^c
Restrictions	so:part_of^op some obo:SO_0001669^c

RNA_polymerase_III_TATA_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001662`
Super-classes	obo:SO_0000174^c
Restrictions	so:part_of^op some obo:SO_0000171^c

BREd_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001663`
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

DCE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001664`
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0001669^c

DCE_SI^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001665`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001664^c

DCE_SII^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001666`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001664^c

DCE_SIII^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001667`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001664^c

proximal_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001668`
Super-classes	obo:SO_0001678^c

RNApol_II_core_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001669`
Super-classes	obo:SO_0000170^c

distal_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001670`
Super-classes	obo:SO_0001678^c

bacterial_RNApol_promoter_sigma_70_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001671`
Super-classes	obo:SO_0000613^c

bacterial_RNApol_promoter_sigma54_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001672`
Super-classes	obo:SO_0000613^c

minus_12_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001673`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001672^c

minus_24_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001674`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001672^c

A_box_type_1^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001675`
Description	The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
Super-classes	obo:SO_0000619^c
Restrictions	so:part_of^op some obo:SO_0000617^c

A_box_type_2^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001676`
Description	The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
Super-classes	obo:SO_0000619^c
Restrictions	so:part_of^op some obo:SO_0000618^c

intermediate_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001677`
Super-classes	obo:SO_0001660^c
Restrictions	so:part_of^op some obo:SO_0000617^c

regulatory_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001678`
Super-classes	obo:SO_0001659^c
Sub-classes	obo:SO_0001668^c obo:SO_0001981^c obo:SO_0001670^c obo:SO_0001980^c obo:SO_0001982^c

transcription_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001679`
Description	Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527.

translation_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001680`
Super-classes	obo:SO_0005836^c
Sub-classes	obo:SO_0000140^c

recombination_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001681`
Super-classes	obo:SO_0005836^c
Sub-classes	obo:SO_0002059^c

replication_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001682`
Super-classes	obo:SO_0005836^c

sequence_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001683`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0000714^c

experimental_feature_attribute^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001684`
Super-classes	obo:SO_0000733^c
Sub-classes	obo:SO_0001686^c obo:SO_0001685^c

score^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001685`
Super-classes	obo:SO_0001684^c

quality_value^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001686`
Super-classes	obo:SO_0001684^c

restriction_enzyme_recognition_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001687`
Super-classes	obo:SO_0001954^c
Sub-classes	obo:SO_0001692^c obo:SO_0001691^c

restriction_enzyme_cleavage_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001688`
Super-classes	obo:SO_0002204^c
Sub-classes	obo:SO_0001693^c obo:SO_0001694^c

five_prime_restriction_enzyme_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001689`
Super-classes	obo:SO_0001694^c
Restrictions	so:part_of^op some obo:SO_0001692^c

three_prime_restriction_enzyme_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001690`
Super-classes	obo:SO_0001694^c
Restrictions	so:part_of^op some obo:SO_0001692^c

blunt_end_restriction_enzyme_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001691`
Super-classes	obo:SO_0001687^c

sticky_end_restriction_enzyme_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001692`
Super-classes	obo:SO_0001687^c
Sub-classes	obo:SO_0001976^c obo:SO_0001975^c

blunt_end_restriction_enzyme_cleavage_junction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001693`
Super-classes	obo:SO_0001688^c
Restrictions	so:part_of^op some obo:SO_0001691^c

single_strand_restriction_enzyme_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001694`
Super-classes	obo:SO_0001688^c
Sub-classes	obo:SO_0001689^c obo:SO_0001690^c

restriction_enzyme_single_strand_overhang^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001695`
Super-classes	obo:SO_0001954^c
Restrictions	so:part_of^op some obo:SO_0001692^c
Sub-classes	obo:SO_0001933^c obo:SO_0001932^c

experimentally_defined_binding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001696`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0001697^c

ChIP_seq_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001697`
Super-classes	obo:SO_0001696^c
Restrictions	so:contains^op some obo:SO_0000410^c

ASPE_primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001698`
Super-classes	obo:SO_0000112^c

dCAPS_primer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001699`
Super-classes	obo:SO_0000112^c

histone_modification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001700`
Super-classes	obo:SO_0001089^c obo:SO_0001720^c
Restrictions	so:has_quality^op some obo:SO_0000133^c
Sub-classes	obo:SO_0001737^c obo:SO_0001702^c obo:SO_0001716^c obo:SO_0001701^c

histone_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001701`
Super-classes	obo:SO_0001700^c
Sub-classes	obo:SO_0001935^c obo:SO_0001949^c obo:SO_0001948^c obo:SO_0001732^c obo:SO_0001947^c obo:SO_0001950^c obo:SO_0001736^c obo:SO_0001713^c obo:SO_0001951^c obo:SO_0001733^c obo:SO_0001734^c obo:SO_0001735^c obo:SO_0001714^c

histone_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001702`
Super-classes	obo:SO_0001700^c
Sub-classes	obo:SO_0001973^c obo:SO_0002142^c obo:SO_0001972^c obo:SO_0002143^c

H3K9_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001703`
Super-classes	obo:SO_0001973^c

H3K14_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001704`
Super-classes	obo:SO_0001973^c

H3K4_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001705`
Super-classes	obo:SO_0001734^c

H3K4_trimethylation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001706`
Super-classes	obo:SO_0001734^c

H3K9_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001707`
Super-classes	obo:SO_0001736^c

H3K27_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001708`
Super-classes	obo:SO_0001732^c

H3K27_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001709`
Super-classes	obo:SO_0001732^c

H3K79_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001710`
Super-classes	obo:SO_0001735^c

H3K79_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001711`
Super-classes	obo:SO_0001735^c

H3K79_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001712`
Super-classes	obo:SO_0001735^c

H4K20_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001713`
Super-classes	obo:SO_0001701^c

H2BK5_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001714`
Super-classes	obo:SO_0001701^c

ISRE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001715`
Description	Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.
Super-classes	obo:SO_0000235^c

histone_ubiqitination_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001716`
Super-classes	obo:SO_0001700^c
Sub-classes	obo:SO_0001717^c

H2B_ubiquitination_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001717`
Super-classes	obo:SO_0001716^c

H3K18_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001718`
Super-classes	obo:SO_0001973^c

H3K23_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001719`
Super-classes	obo:SO_0001973^c

epigenetically_modified_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001720`
Description	Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534.
Super-classes	obo:SO_0005836^c
Restrictions	so:has_quality^op some obo:SO_0000133^c
Sub-classes	obo:SO_0000898^c obo:SO_0000305^c obo:SO_0002191^c obo:SO_0002332^c obo:SO_0001700^c

H3K27_acylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001721`

H3K36_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001722`
Super-classes	obo:SO_0001733^c

H3K36_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001723`
Super-classes	obo:SO_0001733^c

H3K36_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001724`
Super-classes	obo:SO_0001733^c

H3K4_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001725`
Super-classes	obo:SO_0001734^c

H3K27_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001726`
Super-classes	obo:SO_0001732^c

H3K9_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001727`
Super-classes	obo:SO_0001736^c

H3K9_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001728`
Super-classes	obo:SO_0001736^c

H4K16_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001729`
Super-classes	obo:SO_0001972^c

H4K5_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001730`
Super-classes	obo:SO_0001972^c

H4K8_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001731`
Super-classes	obo:SO_0001972^c

H3K27_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001732`
Super-classes	obo:SO_0001701^c
Sub-classes	obo:SO_0001709^c obo:SO_0001726^c obo:SO_0001708^c

H3K36_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001733`
Super-classes	obo:SO_0001701^c
Sub-classes	obo:SO_0001722^c obo:SO_0001723^c obo:SO_0001724^c

H3K4_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001734`
Super-classes	obo:SO_0001701^c
Sub-classes	obo:SO_0001706^c obo:SO_0001705^c obo:SO_0001725^c

H3K79_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001735`
Super-classes	obo:SO_0001701^c
Sub-classes	obo:SO_0001712^c obo:SO_0001710^c obo:SO_0001711^c

H3K9_methylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001736`
Super-classes	obo:SO_0001701^c
Sub-classes	obo:SO_0001727^c obo:SO_0001728^c obo:SO_0001707^c

histone_acylation_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001737`
Super-classes	obo:SO_0001700^c
Sub-classes	obo:SO_0001738^c

H4K_acylation_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001738`
Super-classes	obo:SO_0001737^c

gene_with_non_canonical_start_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001739`
Description	Requested by flybase, Dec 2010.
Super-classes	obo:SO_0000704^c
Restrictions	so:contains^op some obo:SO_0000680^c
Sub-classes	obo:SO_0001740^c

gene_with_start_codon_CUG^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001740`
Description	Requested by flybase, Dec 2010.
Super-classes	obo:SO_0001739^c

pseudogenic_gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001741`
Super-classes	obo:SO_3000000^c

copy_number_gain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001742`
Super-classes	obo:SO_0001019^c

copy_number_loss^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001743`
Super-classes	obo:SO_0001019^c

UPD^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001744`
Super-classes	obo:SO_0001059^c
Sub-classes	obo:SO_0001746^c obo:SO_0001745^c

maternal_uniparental_disomy^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001745`
Super-classes	obo:SO_0001744^c

paternal_uniparental_disomy^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001746`
Super-classes	obo:SO_0001744^c

open_chromatin_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001747`
Description	Requested by John Calley 3125900.
Super-classes	obo:SO_0001411^c

SL3_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001748`
Super-classes	obo:SO_0000709^c

SL4_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001749`
Super-classes	obo:SO_0000709^c

SL5_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001750`
Super-classes	obo:SO_0000709^c

SL6_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001751`
Super-classes	obo:SO_0000709^c

SL7_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001752`
Super-classes	obo:SO_0000709^c

SL8_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001753`
Super-classes	obo:SO_0000709^c

SL9_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001754`
Super-classes	obo:SO_0000709^c

SL10_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001755`
Super-classes	obo:SO_0000709^c

SL11_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001756`
Super-classes	obo:SO_0000709^c

SL12_acceptor_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001757`
Super-classes	obo:SO_0000709^c

duplicated_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001758`
Super-classes	obo:SO_0001760^c

unitary_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001759`
Description	This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
Super-classes	obo:SO_0001760^c
Sub-classes	obo:SO_0002108^c obo:SO_0002189^c

non_processed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001760`
Super-classes	obo:SO_0000336^c
Sub-classes	obo:SO_0002107^c obo:SO_0001434^c obo:SO_0001044^c obo:SO_0002106^c obo:SO_0001758^c obo:SO_0001759^c obo:SO_0000044^c

variant_quality^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001761`
Super-classes	obo:SO_0000400^c
Sub-classes	obo:SO_0001762^c obo:SO_0001769^c obo:SO_0001763^c obo:SO_0001814^c

variant_origin^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001762`
Super-classes	obo:SO_0001761^c
Sub-classes	obo:SO_0001779^c obo:SO_0001776^c obo:SO_0001781^c obo:SO_0001777^c obo:SO_0001780^c obo:SO_0001775^c obo:SO_0001778^c

variant_frequency^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001763`
Super-classes	obo:SO_0001761^c
Sub-classes	obo:SO_0001767^c obo:SO_0001768^c obo:SO_0002119^c obo:SO_0001764^c obo:SO_0001765^c obo:SO_0001766^c

unique_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001764`
Super-classes	obo:SO_0001763^c

rare_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001765`
Super-classes	obo:SO_0001763^c

polymorphic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001766`
Super-classes	obo:SO_0001763^c

common_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001767`
Super-classes	obo:SO_0001763^c

fixed_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001768`
Super-classes	obo:SO_0001763^c

variant_phenotype^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001769`
Super-classes	obo:SO_0001761^c
Sub-classes	obo:SO_0001770^c obo:SO_0001771^c obo:SO_0001772^c obo:SO_0001774^c

benign_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001770`
Super-classes	obo:SO_0001769^c

disease_associated_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001771`
Super-classes	obo:SO_0001769^c

disease_causing_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001772`
Super-classes	obo:SO_0001769^c

lethal_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001773`
Super-classes	obo:SO_0002218^c

quantitative_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001774`
Super-classes	obo:SO_0001769^c

maternal_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001775`
Super-classes	obo:SO_0001762^c

paternal_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001776`
Super-classes	obo:SO_0001762^c

somatic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001777`
Super-classes	obo:SO_0001762^c

germline_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001778`
Super-classes	obo:SO_0001762^c

pedigree_specific_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001779`
Super-classes	obo:SO_0001762^c

population_specific_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001780`
Super-classes	obo:SO_0001762^c

de_novo_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001781`
Super-classes	obo:SO_0001762^c

TF_binding_site_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001782`
Super-classes	obo:SO_0001566^c

SO_0001783^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001783`

complex_structural_alteration^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001784`
Super-classes	obo:SO_1000183^c obo:SO_0001785^c
Sub-classes	obo:SO_0002062^c

structural_alteration^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001785`
Super-classes	obo:SO_0001059^c
Sub-classes	obo:SO_0001784^c obo:SO_0001872^c obo:SO_0000199^c

loss_of_heterozygosity^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001786`
Super-classes	obo:SO_0002218^c

splice_donor_5th_base_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001787`
Super-classes	obo:SO_0001629^c

U_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001788`
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0000186^c

mating_type_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001789`
Super-classes	obo:SO_0005855^c

paired_end_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001790`
Super-classes	obo:SO_0000143^c

exon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001791`
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001792^c obo:SO_0001580^c obo:SO_0001622^c

non_coding_transcript_exon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001792`
Super-classes	obo:SO_0001791^c obo:SO_0001619^c

clone_end^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001793`
Super-classes	obo:SO_0000150^c
Restrictions	so:part_of^op some obo:SO_0000151^c

point_centromere^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001794`
Super-classes	obo:SO_0000577^c

regional_centromere^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001795`
Super-classes	obo:SO_0000577^c

regional_centromere_central_core^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001796`
Super-classes	obo:SO_0000330^c
Restrictions	so:part_of^op some obo:SO_0001795^c

centromeric_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001797`
Super-classes	obo:SO_0000657^c
Sub-classes	obo:SO_0001799^c obo:SO_0001899^c obo:SO_0001798^c obo:SO_0001898^c

regional_centromere_inner_repeat_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001798`
Super-classes	obo:SO_0001797^c
Restrictions	so:part_of^op some obo:SO_0001796^c so:part_of^op some obo:SO_0001795^c

regional_centromere_outer_repeat_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001799`
Super-classes	obo:SO_0001797^c
Restrictions	so:part_of^op some obo:SO_0001795^c

tasiRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001800`
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0001801^c

tasiRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001801`
Super-classes	obo:SO_0000483^c

increased_polyadenylation_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001802`
Description	Term requested by M. Dumontier, June 1 2011.
Super-classes	obo:SO_0001545^c

decreased_polyadenylation_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001803`
Description	Term requested by M. Dumontier, June 1 2011.
Super-classes	obo:SO_0001545^c

DDB_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001804`
Description	Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
Super-classes	obo:SO_0001093^c

destruction_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001805`
Super-classes	obo:SO_0100017^c

ER_retention_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001806`
Super-classes	obo:SO_0001527^c

KEN_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001807`
Super-classes	obo:SO_0100017^c

mitochondrial_targeting_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001808`
Super-classes	obo:SO_0001527^c

signal_anchor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001809`
Super-classes	obo:SO_0000418^c

PIP_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001810`
Super-classes	obo:SO_0001093^c

phosphorylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001811`
Super-classes	obo:SO_0001089^c

transmembrane_helix^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001812`
Super-classes	obo:SO_0001114^c
Restrictions	so:part_of^op some obo:SO_0001077^c

vacuolar_sorting_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001813`
Super-classes	obo:SO_0001527^c

coding_variant_quality^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001814`
Super-classes	obo:SO_0001761^c
Sub-classes	obo:SO_0001815^c obo:SO_0001816^c

synonymous^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001815`
Super-classes	obo:SO_0001814^c

non_synonymous^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001816`
Super-classes	obo:SO_0001814^c

inframe^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001817`
Super-classes	obo:SO_0000863^c

protein_altering_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001818`
Super-classes	obo:SO_0001580^c
Sub-classes	obo:SO_0001589^c obo:SO_0001650^c

synonymous_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001819`
Description	EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation). This term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
Super-classes	obo:SO_0001580^c
Sub-classes	obo:SO_0002019^c obo:SO_0001567^c

inframe_indel^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001820`
Super-classes	obo:SO_0001650^c
Sub-classes	obo:SO_0001822^c obo:SO_0001821^c

inframe_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001821`
Super-classes	obo:SO_0001820^c obo:SO_0001908^c
Sub-classes	obo:SO_0001823^c obo:SO_0001824^c

inframe_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001822`
Super-classes	obo:SO_0001820^c obo:SO_0001906^c
Sub-classes	obo:SO_0001826^c obo:SO_0001825^c

conservative_inframe_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001823`
Super-classes	obo:SO_0001821^c

disruptive_inframe_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001824`
Super-classes	obo:SO_0001821^c

conservative_inframe_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001825`
Super-classes	obo:SO_0001822^c

disruptive_inframe_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001826`
Super-classes	obo:SO_0001822^c

mRNA_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001827`
Description	Requested by Bayer Cropscience June, 2011.
Super-classes	obo:SO_0000150^c

genomic_DNA_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001828`
Super-classes	obo:SO_0000150^c

mRNA_contig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001829`
Description	Requested by Bayer Cropscience June, 2011.
Super-classes	obo:SO_0000149^c

AFLP_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001830`
Description	Requested by Bayer Cropscience June, 2011.
Super-classes	obo:SO_0000006^c

protein_hmm_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001831`
Super-classes	obo:SO_0000349^c

immunoglobulin_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001832`
Super-classes	obo:SO_0000839^c
Sub-classes	obo:SO_0001833^c obo:SO_0001834^c

V_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001833`
Super-classes	obo:SO_0001832^c

C_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001834`
Super-classes	obo:SO_0001832^c

N_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001835`
Super-classes	obo:SO_0000301^c

S_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001836`
Super-classes	obo:SO_0000301^c

mobile_element_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001837`
Description	Requested by the EBI.
Super-classes	obo:SO_0000667^c
Restrictions	so:contains^op some obo:SO_0001037^c
Sub-classes	obo:SO_0002064^c obo:SO_0002063^c obo:SO_0002065^c obo:SO_0002187^c

novel_sequence_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001838`
Description	Requested by the NCBI.
Super-classes	obo:SO_0000667^c

CSL_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001839`
Super-classes	obo:SO_0001659^c

GATA_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001840`
Description	Changed to is_a SO:0001055 transcriptional_cis_regulatory_region from core_eukaryotic_promoter_element SO:0001660 after Ruth Lovering from GREEKC initiative pointed out that GATA boxes are frequently in enhancer regions, Dave Sant Aug 2020. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021.
Super-classes	obo:SO_0000235^c
Sub-classes	obo:SO_0001851^c

polymorphic_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001841`
Description	This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated.
Super-classes	obo:SO_0000336^c
Sub-classes	obo:SO_0002110^c

AP_1_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001842`
Super-classes	obo:SO_0001659^c

CRE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001843`
Description	New synonym Atf1/Pcr1 recognition motif added in response to Antonia Lock GitHub Issue Request #437, PMID:15716492
Super-classes	obo:SO_0001659^c

CuRE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001844`
Super-classes	obo:SO_0001659^c

DRE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001845`
Super-classes	obo:SO_0001659^c

FLEX_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001846`
Super-classes	obo:SO_0001659^c

forkhead_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001847`
Super-classes	obo:SO_0001659^c

homol_D_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001848`
Super-classes	obo:SO_0001660^c

homol_E_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001849`
Super-classes	obo:SO_0001659^c

HSE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001850`
Super-classes	obo:SO_0001659^c

iron_repressed_GATA_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001851`
Description	The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
Super-classes	obo:SO_0001840^c

mating_type_M_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001852`
Description	Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
Super-classes	obo:SO_0001659^c

androgen_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001853`
Super-classes	obo:SO_0000713^c

smFISH_probe^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001854`
Super-classes	obo:SO_0000051^c

MCB^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001855`
Super-classes	obo:SO_0001659^c

CCAAT_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001856`
Super-classes	obo:SO_0001659^c

Ace2_UAS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001857`
Super-classes	obo:SO_0001659^c

TR_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001858`
Super-classes	obo:SO_0001659^c

STREP_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001859`
Super-classes	obo:SO_0001659^c

rDNA_intergenic_spacer_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001860`
Description	Page 208 of ISBN:978-0199638901
Super-classes	obo:SO_0000713^c

sterol_regulatory_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001861`
Super-classes	obo:SO_0001659^c

GT_dinucleotide_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001862`
Description	paper:PMID:16043634.
Super-classes	obo:SO_0000290^c

GTT_trinucleotide_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001863`
Super-classes	obo:SO_0000291^c

Sap1_recognition_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001864`
Super-classes	obo:SO_0000713^c

CDRE_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001865`
Super-classes	obo:SO_0001659^c

BAC_read_contig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001866`
Description	Requested by Bayer Cropscience December, 2011.
Super-classes	obo:SO_0000149^c
Restrictions	so:has_origin^op some obo:SO_0000153^c so:part_of^op some obo:SO_0000153^c

candidate_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001867`
Description	Requested by Bayer Cropscience December, 2011.
Super-classes	obo:SO_0000704^c
Sub-classes	obo:SO_0001868^c obo:SO_0001869^c

positional_candidate_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001868`
Description	Requested by Bayer Cropscience December, 2011.
Super-classes	obo:SO_0001867^c

functional_candidate_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001869`
Description	Requested by Bayer Cropscience December, 2011.
Super-classes	obo:SO_0001867^c

enhancerRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001870`
Super-classes	obo:SO_0000655^c
Restrictions	so:transcribed_from^op some obo:SO_0000165^c

PCB^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001871`
Super-classes	obo:SO_0001659^c

rearrangement_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001872`
Description	NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
Super-classes	obo:SO_0001411^c obo:SO_0001785^c

interchromosomal_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001873`
Super-classes	obo:SO_0001021^c

intrachromosomal_breakpoint^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001874`
Super-classes	obo:SO_0001021^c

unassigned_supercontig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001875`
Description	Requested by Bayer Cropscience January, 2012.
Super-classes	obo:SO_0000148^c

partial_genomic_sequence_assembly^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001876`
Description	Requested by Bayer Cropscience January, 2012.
Super-classes	obo:SO_0000353^c
Sub-classes	obo:SO_0000148^c obo:SO_0000719^c

lncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001877`
Super-classes	obo:SO_0000655^c
Sub-classes	obo:SO_0002131^c obo:SO_0001463^c obo:SO_0002132^c obo:SO_0001904^c

feature_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001878`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0001628^c obo:SO_0001017^c obo:SO_0001907^c obo:SO_0001906^c obo:SO_0001564^c obo:SO_0001566^c

feature_ablation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001879`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0001894^c obo:SO_0001893^c

feature_amplification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001880`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0001891^c obo:SO_0001889^c

feature_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001881`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0001884^c obo:SO_0001883^c

feature_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001882`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0001886^c obo:SO_0001565^c obo:SO_0001890^c obo:SO_0001887^c

transcript_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001883`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001881^c

regulatory_region_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001884`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001881^c
Sub-classes	obo:SO_0001885^c

TFBS_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001885`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001884^c

transcript_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001886`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001882^c

regulatory_region_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001887`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001882^c
Sub-classes	obo:SO_0001888^c

TFBS_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001888`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001887^c

transcript_amplification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001889`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001880^c

transcript_regulatory_region_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001890`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001882^c

regulatory_region_amplification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001891`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001880^c
Sub-classes	obo:SO_0001892^c

TFBS_amplification^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001892`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001891^c

transcript_ablation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001893`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001879^c

regulatory_region_ablation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001894`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001879^c
Sub-classes	obo:SO_0001895^c

TFBS_ablation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001895`
Description	Created in conjunction with the EBI.
Super-classes	obo:SO_0001894^c

transposable_element_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001896`
Super-classes	obo:SO_0000316^c
Restrictions	so:part_of^op some obo:SO_0000101^c

transposable_element_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001897`
Super-classes	obo:SO_0000336^c
Restrictions	so:part_of^op some obo:SO_0000101^c

dg_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001898`
Description	For the S. pombe project - requested by Val Wood.
Super-classes	obo:SO_0001797^c
Restrictions	so:part_of^op some obo:SO_0001799^c

dh_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001899`
Description	For the S. pombe project - requested by Val Wood.
Super-classes	obo:SO_0001797^c
Restrictions	so:part_of^op some obo:SO_0001799^c

SO_0001900^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001900`

AACCCT_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001901`
Super-classes	obo:SO_0001660^c

splice_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001902`
Super-classes	obo:SO_0000835^c
Restrictions	so:part_of^op some obo:SO_0000185^c

SO_0001903^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001903`

antisense_lncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001904`
Description	Relationship is_a SO:0000644 antisense_RNA added 23 April 2021. See GitHub Issue #443
Super-classes	obo:SO_0000644^c obo:SO_0001877^c

regional_centromere_outer_repeat_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001905`
Super-classes	obo:SO_0000185^c
Restrictions	so:derives_from^op some obo:SO_0001799^c

feature_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001906`
Super-classes	obo:SO_0001878^c
Sub-classes	obo:SO_0001587^c obo:SO_0001910^c obo:SO_0001822^c

feature_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001907`
Super-classes	obo:SO_0001878^c
Sub-classes	obo:SO_0001578^c obo:SO_0001908^c

internal_feature_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001908`
Super-classes	obo:SO_0001907^c
Sub-classes	obo:SO_0001821^c obo:SO_0001909^c

frameshift_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001909`
Super-classes	obo:SO_0001589^c obo:SO_0001908^c

frameshift_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001910`
Super-classes	obo:SO_0001589^c obo:SO_0001906^c

copy_number_increase^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001911`
Super-classes	obo:SO_0001563^c

copy_number_decrease^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001912`
Super-classes	obo:SO_0001563^c

bacterial_RNApol_promoter_sigma_ecf_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001913`
Description	Requested by Kevin Clancy - invitrogen -May 2012.
Super-classes	obo:SO_0000613^c

rDNA_replication_fork_barrier^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001914`
Description	Requested by Midori - June 2012.
Super-classes	obo:SO_0000713^c

transcription_start_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001915`
Super-classes	obo:SO_0001410^c
Sub-classes	obo:SO_0001917^c

CAGE_tag^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001916`
Super-classes	obo:SO_0000324^c

CAGE_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001917`
Super-classes	obo:SO_0001915^c

5_methylcytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001918`
Super-classes	obo:SO_0000114^c

4_methylcytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001919`
Super-classes	obo:SO_0000114^c

N6_methyladenine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001920`
Super-classes	obo:SO_0000161^c

mitochondrial_contig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001921`
Description	Requested by Bayer Cropscience, October, 2012.
Super-classes	obo:SO_0000149^c
Restrictions	so:has_origin^op some obo:SO_0000737^c

mitochondrial_supercontig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001922`
Super-classes	obo:SO_0000148^c

TERRA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001923`
Description	Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
Super-classes	obo:SO_0001927^c

ARRET^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001924`
Description	Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
Super-classes	obo:SO_0001927^c

ARIA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001925`
Description	Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
Super-classes	obo:SO_0001927^c

anti_ARRET^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001926`
Description	Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
Super-classes	obo:SO_0001927^c

telomeric_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001927`
Super-classes	obo:SO_0000655^c
Sub-classes	obo:SO_0001925^c obo:SO_0001924^c obo:SO_0001923^c obo:SO_0001926^c

distal_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001928`
Description	This term is used by Complete Genomics in the structural variant analysis files.
Super-classes	obo:SO_1000035^c

mitochondrial_DNA_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001929`
Description	Requested by Bayer Cropscience, October, 2012.
Super-classes	obo:SO_0000150^c
Restrictions	so:has_origin^op some obo:SO_0001032^c

chloroplast_DNA_read^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001930`
Description	Requested by Bayer Cropscience, October, 2012.
Super-classes	obo:SO_0000150^c
Restrictions	so:has_origin^op some obo:SO_0001033^c

consensus_gDNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001931`
Description	Requested by Bayer Cropscience November, 2012.
Super-classes	obo:SO_0000994^c

restriction_enzyme_five_prime_single_strand_overhang^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001932`
Super-classes	obo:SO_0001695^c

restriction_enzyme_three_prime_single_strand_overhang^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001933`
Super-classes	obo:SO_0001695^c

monomeric_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001934`
Super-classes	obo:SO_0000705^c

H3K20_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001935`
Super-classes	obo:SO_0001701^c

H3K36_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001936`
Super-classes	obo:SO_0001973^c

H2BK12_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001937`
Super-classes	obo:SO_0002143^c

H2AK5_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001938`
Super-classes	obo:SO_0002142^c

H4K12_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001939`
Super-classes	obo:SO_0001972^c

H2BK120_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001940`
Super-classes	obo:SO_0002143^c

H4K91_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001941`
Super-classes	obo:SO_0001972^c

H2BK20_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001942`
Super-classes	obo:SO_0002143^c

H3K4_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001943`
Super-classes	obo:SO_0001973^c

H2AK9_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001944`
Super-classes	obo:SO_0002142^c

H3K56_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001945`
Super-classes	obo:SO_0001973^c

H2BK15_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001946`
Super-classes	obo:SO_0002143^c

H3R2_monomethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001947`
Super-classes	obo:SO_0001701^c

H3R2_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001948`
Super-classes	obo:SO_0001701^c

H4R3_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001949`
Super-classes	obo:SO_0001701^c

H4K4_trimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001950`
Super-classes	obo:SO_0001701^c

H3K23_dimethylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001951`
Super-classes	obo:SO_0001701^c

promoter_flanking_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001952`
Super-classes	obo:SO_0001055^c

restriction_enzyme_assembly_scar^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001953`
Super-classes	obo:SO_0001954^c

restriction_enzyme_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001954`
Description	Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0001695^c obo:SO_0001953^c obo:SO_0001687^c

protein_stability_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001955`
Super-classes	obo:SO_0000839^c

protease_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001956`
Super-classes	obo:SO_0000839^c

RNA_stability_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001957`

lariat_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001958`
Description	Requested by PomBase 3604508.
Super-classes	obo:SO_0000188^c

TCT_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001959`
Super-classes	obo:SO_0001660^c

5_hydroxymethylcytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001960`
Super-classes	obo:SO_0000114^c

5_formylcytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001961`
Super-classes	obo:SO_0001963^c

modified_adenine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001962`
Super-classes	obo:SO_0000305^c
Sub-classes	obo:SO_0000161^c obo:SO_0001967^c

modified_cytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001963`
Super-classes	obo:SO_0000305^c
Sub-classes	obo:SO_0001961^c obo:SO_0000114^c obo:SO_0001966^c

modified_guanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001964`
Super-classes	obo:SO_0000305^c
Sub-classes	obo:SO_0001965^c

8_oxoguanine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001965`
Super-classes	obo:SO_0001964^c

5_carboxylcytosine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001966`
Super-classes	obo:SO_0001963^c

8_oxoadenine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001967`
Super-classes	obo:SO_0001962^c

coding_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001968`
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0001969^c obo:SO_0001580^c obo:SO_0001622^c

coding_transcript_intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001969`
Super-classes	obo:SO_0001968^c obo:SO_0001627^c
Sub-classes	obo:SO_0002091^c obo:SO_0002090^c

non_coding_transcript_intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001970`
Super-classes	obo:SO_0001627^c obo:SO_0001619^c

zinc_finger_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001971`
Super-classes	obo:SO_0001429^c

histone_4_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001972`
Super-classes	obo:SO_0001702^c
Sub-classes	obo:SO_0001939^c obo:SO_0001731^c obo:SO_0001941^c obo:SO_0001729^c obo:SO_0001730^c

histone_3_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001973`
Super-classes	obo:SO_0001702^c
Sub-classes	obo:SO_0001704^c obo:SO_0002049^c obo:SO_0001936^c obo:SO_0001719^c obo:SO_0001945^c obo:SO_0001943^c obo:SO_0001703^c obo:SO_0001718^c

CTCF_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001974`
Super-classes	obo:SO_0001659^c

five_prime_sticky_end_restriction_enzyme_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001975`
Description	Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
Super-classes	obo:SO_0001692^c

three_prime_sticky_end_restriction_enzyme_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001976`
Description	Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
Super-classes	obo:SO_0001692^c

ribonuclease_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001977`
Super-classes	obo:SO_0000833^c

signature^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001978`
Description	Requested by Jackie Quinn for use in synthetic biology.
Super-classes	obo:SO_0000804^c

RNA_stability_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001979`
Super-classes	obo:SO_0000715^c
Sub-classes	obo:SO_0002207^c

G_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001980`
Description	A plant specific region.
Super-classes	obo:SO_0001678^c

L_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001981`
Super-classes	obo:SO_0001678^c

I-box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001982`
Super-classes	obo:SO_0001678^c

5_prime_UTR_premature_start_codon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001983`
Description	Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
Super-classes	obo:SO_0001623^c
Sub-classes	obo:SO_0001988^c obo:SO_0001990^c obo:SO_0001989^c

silent_mating_type_cassette_array^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001984`
Super-classes	obo:SO_0005854^c
Sub-classes	obo:SO_0002158^c obo:SO_0002157^c

Okazaki_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001985`
Description	Requested by Midori Harris, 2013.
Super-classes	obo:SO_0001411^c

upstream_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001986`
Description	Requested by Graham Ritchie, EBI/Sanger.
Super-classes	obo:SO_0001628^c

downstream_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001987`
Description	Requested by Graham Ritchie, EBI/Sanger.
Super-classes	obo:SO_0001628^c

5_prime_UTR_premature_start_codon_gain_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001988`
Super-classes	obo:SO_0001983^c

5_prime_UTR_premature_start_codon_loss_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001989`
Super-classes	obo:SO_0001983^c

five_prime_UTR_premature_start_codon_location_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001990`
Super-classes	obo:SO_0001983^c

consensus_AFLP_fragment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001991`
Description	Requested by Bayer Cropscience September, 2013.
Super-classes	obo:SO_0000994^c

nonsynonymous_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001992`
Super-classes	obo:SO_0001650^c
Sub-classes	obo:SO_0001587^c obo:SO_0001578^c obo:SO_0001583^c obo:SO_0002214^c obo:SO_0002012^c

extended_cis_splice_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001993`
Description	Added by Andy Menzies (Sanger).
Super-classes	obo:SO_0001419^c

intron_base_5^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001994`
Super-classes	obo:SO_0001014^c
Restrictions	so:part_of^op some obo:SO_0001993^c

extended_intronic_splice_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001995`
Description	Added by Andy Menzies (Sanger).
Super-classes	obo:SO_0001568^c

extended_intronic_splice_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001996`
Super-classes	obo:SO_0001014^c

subtelomere^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001997`
Super-classes	obo:SO_0000628^c

sgRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001998`
Super-classes	obo:SO_0000696^c

mating_type_region_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0001999`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0001789^c
Sub-classes	obo:SO_0002003^c obo:SO_0002024^c obo:SO_0002030^c obo:SO_0002001^c obo:SO_0002002^c

SO_0002000^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002000`

Y_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002001`
Description	Requested by Janos Demeter, SGD.
Super-classes	obo:SO_0001999^c

Z1_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002002`
Description	Requested by Janos Demeter, SGD.
Super-classes	obo:SO_0001999^c

Z2_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002003`
Description	Requested by Janos Demeter, SGD.
Super-classes	obo:SO_0001999^c

ARS_consensus_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002004`
Super-classes	obo:SO_0000713^c
Restrictions	so:part_of^op some obo:SO_0000436^c

DSR_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002005`
Description	Requested by Antonia Locke, (Pombe).
Super-classes	obo:SO_0000713^c

zinc_repressed_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002006`
Description	This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
Super-classes	obo:SO_0001659^c
Sub-classes	obo:SO_0002225^c

MNV^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002007`
Super-classes	obo:SO_1000002^c
Sub-classes	obo:SO_0001013^c

rare_amino_acid_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002008`
Description	Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
Super-classes	obo:SO_0001586^c
Sub-classes	obo:SO_0002010^c obo:SO_0002009^c

selenocysteine_loss^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002009`
Description	Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
Super-classes	obo:SO_0002008^c

pyrrolysine_loss^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002010`
Description	Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
Super-classes	obo:SO_0002008^c

intragenic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002011`
Description	Requested by Pablo Cingolani, for use in SnpEff.
Super-classes	obo:SO_0001576^c

start_lost^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002012`
Description	Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
Super-classes	obo:SO_0001582^c obo:SO_0001992^c

5_prime_UTR_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002013`
Super-classes	obo:SO_0001623^c

5_prime_UTR_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002014`
Super-classes	obo:SO_0001623^c

3_prime_UTR_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002015`
Super-classes	obo:SO_0001624^c

3_prime_UTR_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002016`
Super-classes	obo:SO_0001624^c

conserved_intergenic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002017`
Description	Requested by Uma Paila (UVA) for snpEff.
Super-classes	obo:SO_0001628^c

conserved_intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002018`
Description	Requested by Uma Paila (UVA) for snpEff.
Super-classes	obo:SO_0001627^c

start_retained_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002019`
Description	Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
Super-classes	obo:SO_0001819^c obo:SO_0001582^c

boundary_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002020`
Description	Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).
Super-classes	obo:SO_0000627^c

mating_type_region_replication_fork_barrier^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002021`
Description	Requested by Midori Harris.
Super-classes	obo:SO_0000713^c

priRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002022`
Super-classes	obo:SO_0000655^c

multiplexing_sequence_identifier^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002023`
Super-classes	obo:SO_0000324^c

W_region^c # Classes

URI http://purl.obolibrary.org/obo/SO_0002024

Description

MERGED COMMENT: TARGET COMMENT: Requested by Janos Demeter, SGD.

SOURCE COMMENT: Requested by Janos Demeter, SGD.

Super-classes obo:SO_0001999^c

cis_acting_homologous_chromosome_pairing_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002025`
Description	Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
Super-classes	obo:SO_0000713^c

intein_encoding_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002026`
Description	Requested by Janos Demeter 2014.
Super-classes	obo:SO_0000842^c

uORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002027`
Super-classes	obo:SO_0000236^c
Sub-classes	obo:SO_0002150^c obo:SO_0002151^c

sORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002028`
Super-classes	obo:SO_0000236^c

tnaORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002029`
Super-classes	obo:SO_0000236^c

X_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002030`
Super-classes	obo:SO_0001999^c

shRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002031`
Super-classes	obo:SO_0000655^c

moR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002032`
Description	MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. Requested by Thomas Desvignes, Jan 2015.
Super-classes	obo:SO_0000370^c
Restrictions	so:part_of^op some obo:SO_0001244^c

loR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002033`
Description	MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do. Requested by Thomas Desvignes, Jan 2015.
Super-classes	obo:SO_0000370^c
Restrictions	so:part_of^op some obo:SO_0001244^c

miR_encoding_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002034`
Super-classes	obo:SO_0000232^c
Restrictions	so:has_part^op some obo:SO_0001244^c

lncRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002035`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0002036^c obo:SO_0002113^c

miR_encoding_lncRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002036`
Super-classes	obo:SO_0002035^c
Restrictions	so:has_part^op some obo:SO_0001244^c

miR_encoding_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002037`
Super-classes	obo:SO_0000210^c
Restrictions	so:has_part^op some obo:SO_0001244^c

shRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002038`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0002039^c

miR_encoding_shRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002039`
Super-classes	obo:SO_0002038^c
Restrictions	so:has_part^op some obo:SO_0001244^c

vaultRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002040`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0002041^c

miR_encoding_vaultRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002041`
Super-classes	obo:SO_0002040^c
Restrictions	so:has_part^op some obo:SO_0001244^c

Y_RNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002042`
Super-classes	obo:SO_0000483^c
Sub-classes	obo:SO_0002043^c

miR_encoding_Y_RNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002043`
Super-classes	obo:SO_0002042^c
Restrictions	so:has_part^op some obo:SO_0001244^c

TCS_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002044`
Description	Requested by Rama - SGD.
Super-classes	obo:SO_0001659^c

pheromone_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002045`
Description	Requested by Rama, SGD.
Super-classes	obo:SO_0001659^c obo:SO_0000235^c

FRE^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002046`
Description	Requested by Rama, SGD.
Super-classes	obo:SO_0001461^c

transcription_pause_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002047`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c

disabled_reading_frame^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002048`
Super-classes	obo:SO_0000717^c

H3K27_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002049`
Description	Requested by: Sagar Jain, Richard Scheuermann.
Super-classes	obo:SO_0001973^c

constitutive_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002050`
Super-classes	obo:SO_0000167^c

inducible_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002051`
Super-classes	obo:SO_0000167^c

dominant_negative_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002052`
Description	Requested by Deanna Church.
Super-classes	obo:SO_0002218^c

gain_of_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002053`
Super-classes	obo:SO_0002218^c

loss_of_function_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002054`
Super-classes	obo:SO_0002218^c

null_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002055`
Super-classes	obo:SO_0002218^c
Sub-classes	obo:SO_0002317^c

intronic_splicing_silencer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002056`
Description	Requested by Javier Diez Perez.
Super-classes	obo:SO_0000625^c
Restrictions	so:part_of^op some obo:SO_0000188^c

intronic_splicing_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002057`

exonic_splicing_silencer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002058`
Description	Requested by Javier Diez Perez.
Super-classes	obo:SO_0000625^c obo:SO_0000852^c

recombination_enhancer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002059`
Super-classes	obo:SO_0001681^c

interchromosomal_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002060`
Super-classes	obo:SO_1000044^c
Sub-classes	obo:SO_1000150^c

intrachromosomal_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002061`
Super-classes	obo:SO_1000044^c

complex_chromosomal_rearrangement^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002062`
Super-classes	obo:SO_0001784^c

Alu_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002063`
Super-classes	obo:SO_0001837^c

LINE1_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002064`
Super-classes	obo:SO_0001837^c
Restrictions	so:derives_from^op some obo:SO_0002272^c

SVA_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002065`
Super-classes	obo:SO_0001837^c

mobile_element_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002066`
Super-classes	obo:SO_0000159^c
Sub-classes	obo:SO_0002070^c obo:SO_0002067^c obo:SO_0002068^c obo:SO_0002069^c

HERV_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002067`
Super-classes	obo:SO_0002066^c
Restrictions	so:derives_from^op some obo:SO_0002268^c

SVA_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002068`
Super-classes	obo:SO_0002066^c

LINE1_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002069`
Super-classes	obo:SO_0002066^c
Restrictions	so:derives_from^op some obo:SO_0002272^c

Alu_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002070`
Super-classes	obo:SO_0002066^c

CDS_supported_by_peptide_spectrum_match^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002071`
Super-classes	obo:SO_1001251^c

sequence_comparison^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002072`
Super-classes	obo:SO_0000110^c
Sub-classes	obo:SO_0002073^c obo:SO_0001059^c

no_sequence_alteration^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002073`
Description	This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly.
Super-classes	obo:SO_0002072^c

intergenic_1kb_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002074`
Description	This term is added to map to the Annovar annotation 'upstream,downstream' .
Super-classes	obo:SO_0001628^c

incomplete_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002075`
Description	This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation. It is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems.
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0002076^c obo:SO_0002080^c obo:SO_0002078^c obo:SO_0002077^c obo:SO_0002081^c obo:SO_0002079^c

incomplete_transcript_3UTR_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002076`
Super-classes	obo:SO_0002075^c

incomplete_transcript_5UTR_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002077`
Super-classes	obo:SO_0002075^c

incomplete_transcript_intronic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002078`
Super-classes	obo:SO_0002075^c

incomplete_transcript_splice_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002079`
Super-classes	obo:SO_0002075^c
Sub-classes	obo:SO_0002082^c

incomplete_transcript_exonic_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002080`
Super-classes	obo:SO_0002075^c

incomplete_transcript_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002081`
Super-classes	obo:SO_0002075^c

incomplete_transcript_coding_splice_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002082`
Super-classes	obo:SO_0002079^c

2KB_downstream_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002083`
Super-classes	obo:SO_0001632^c

exonic_splice_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002084`
Super-classes	obo:SO_0001630^c

unidirectional_gene_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002085`
Description	Requested by SNPEFF team. Feb 2016.
Super-classes	obo:SO_0001565^c

bidirectional_gene_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002086`
Description	Requested by SNPEFF team. Feb 2016.
Super-classes	obo:SO_0001565^c

pseudogenic_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002087`
Super-classes	obo:SO_0000462^c
Restrictions	so:part_of^op some obo:SO_0000516^c

non_coding_transcript_splice_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002088`
Super-classes	obo:SO_0001619^c obo:SO_0001630^c

3_prime_UTR_exon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002089`
Description	Requested by visze github tracker ID 346.
Super-classes	obo:SO_0001624^c

3_prime_UTR_intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002090`
Description	Requested by visze github tracker ID 346.
Super-classes	obo:SO_0001624^c obo:SO_0001969^c

5_prime_UTR_intron_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002091`
Description	Requested by visze github tracker ID 346.
Super-classes	obo:SO_0001623^c obo:SO_0001969^c

5_prime_UTR_exon_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002092`
Description	Requested by visze github tracker ID 346.
Super-classes	obo:SO_0001623^c

structural_interaction_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002093`
Description	Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be "interacting" and thus important for protein structure.
Super-classes	obo:SO_0001599^c

non_allelic_homologous_recombination_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002094`
Super-classes	obo:SO_0000339^c

scaRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002095`
Description	Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509.
Super-classes	obo:SO_0000275^c
Sub-classes	obo:SO_0002370^c obo:SO_0002371^c obo:SO_0002369^c

short_tandem_repeat_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002096`
Super-classes	obo:SO_0000248^c

vertebrate_immune_system_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002097`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0000336^c
Sub-classes	obo:SO_0002099^c obo:SO_0002098^c

immunoglobulin_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002098`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002097^c
Sub-classes	obo:SO_0002102^c obo:SO_0002100^c obo:SO_0002101^c

T_cell_receptor_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002099`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002097^c
Sub-classes	obo:SO_0002103^c obo:SO_0002104^c

IG_C_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002100`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002098^c

IG_J_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002101`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002098^c

IG_V_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002102`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002098^c

TR_V_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002103`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002099^c

TR_J_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002104`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002099^c

translated_processed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002105`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0000043^c

translated_unprocessed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002106`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0001760^c

transcribed_unprocessed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002107`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0001760^c

transcribed_unitary_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002108`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0001759^c

transcribed_processed_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002109`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0000043^c

polymorphic_pseudogene_with_retained_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002110`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0001841^c

pseudogene_processed_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002111`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0001503^c
Sub-classes	obo:SO_0002116^c

coding_transcript_with_retained_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002112`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0000120^c

lncRNA_with_retained_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002113`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0002035^c

NMD_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002114`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0000120^c
Sub-classes	obo:SO_0002118^c

pseudogenic_transcript_with_retained_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002115`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
Super-classes	obo:SO_0000185^c

polymorphic_pseudogene_processed_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002116`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0002111^c

^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002117`

NMD_polymorphic_pseudogene_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002118`
Description	Term added as part of collaboration with Gencode, adding biotypes used in annotation.
Super-classes	obo:SO_0002114^c

allelic_frequency^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002119`
Description	Requested by HL7 clinical genomics group.
Super-classes	obo:SO_0001763^c

three_prime_overlapping_ncrna^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002120`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
Super-classes	obo:SO_0000655^c

vertebrate_immune_system_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002121`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0000704^c
Sub-classes	obo:SO_0002122^c obo:SO_0002133^c

immunoglobulin_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002122`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002121^c
Sub-classes	obo:SO_0002125^c obo:SO_0002126^c obo:SO_0002123^c obo:SO_0002124^c

IG_C_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002123`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002122^c

IG_D_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002124`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002122^c

IG_J_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002125`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002122^c

IG_V_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002126`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002122^c

lncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002127`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes.
Super-classes	obo:SO_0001263^c
Sub-classes	obo:SO_0002182^c obo:SO_0002184^c obo:SO_0001641^c obo:SO_0002183^c obo:SO_0002185^c

mt_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002128`
Description	Updated definition to be consistent with format of other rRNA definitions on 10 June 2021. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000252^c
Sub-classes	obo:SO_0002344^c obo:SO_0002345^c

mt_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002129`
Super-classes	obo:SO_0000253^c

NSD_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002130`
Super-classes	obo:SO_0000234^c

sense_intronic_ncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002131`
Super-classes	obo:SO_0001877^c

sense_overlap_ncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002132`
Super-classes	obo:SO_0001877^c

T_cell_receptor_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002133`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002121^c
Sub-classes	obo:SO_0002134^c obo:SO_0002137^c obo:SO_0002135^c obo:SO_0002136^c

TR_C_Gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002134`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002133^c

TR_D_Gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002135`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002133^c

TR_J_Gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002136`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002133^c

TR_V_Gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002137`
Description	These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT.
Super-classes	obo:SO_0002133^c

predicted_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002138`
Super-classes	obo:SO_0000673^c
Sub-classes	obo:SO_0002139^c

unconfirmed_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002139`
Super-classes	obo:SO_0002138^c

early_origin_of_replication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002140`
Super-classes	obo:SO_0000296^c

late_origin_of_replication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002141`
Super-classes	obo:SO_0000296^c

histone_2A_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002142`
Super-classes	obo:SO_0001702^c
Sub-classes	obo:SO_0002144^c obo:SO_0001938^c obo:SO_0001944^c

histone_2B_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002143`
Super-classes	obo:SO_0001702^c
Sub-classes	obo:SO_0001937^c obo:SO_0002164^c obo:SO_0001940^c obo:SO_0001946^c obo:SO_0001942^c

histone_2AZ_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002144`
Super-classes	obo:SO_0002142^c
Sub-classes	obo:SO_0002149^c obo:SO_0002148^c obo:SO_0002145^c obo:SO_0002146^c obo:SO_0002147^c

H2AZK4_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002145`
Super-classes	obo:SO_0002144^c

H2AZK7_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002146`
Super-classes	obo:SO_0002144^c

H2AZK11_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002147`
Super-classes	obo:SO_0002144^c

H2AZK13_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002148`
Super-classes	obo:SO_0002144^c

H2AZK15_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002149`
Super-classes	obo:SO_0002144^c

AUG_initiated_uORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002150`
Super-classes	obo:SO_0002027^c

non_AUG_initiated_uORF^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002151`
Super-classes	obo:SO_0002027^c

genic_downstream_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002152`
Super-classes	obo:SO_0001564^c

genic_upstream_transcript_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002153`
Super-classes	obo:SO_0001564^c

mitotic_recombination_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002154`
Super-classes	obo:SO_0000298^c

meiotic_recombination_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002155`
Super-classes	obo:SO_0000298^c

CArG_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002156`
Description	Requested by Antonia Lock
Super-classes	obo:SO_0001659^c

Mat2P^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002157`
Super-classes	obo:SO_0001984^c

Mat3M^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002158`
Super-classes	obo:SO_0001984^c

SHP_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002159`
Super-classes	obo:SO_0100017^c

sequence_length_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002160`
Super-classes	obo:SO_0001537^c
Sub-classes	obo:SO_0002161^c obo:SO_0001563^c

short_tandem_repeat_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002161`
Super-classes	obo:SO_0002160^c
Sub-classes	obo:SO_0002163^c obo:SO_0002162^c

short_tandem_repeat_expansion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002162`
Super-classes	obo:SO_0002161^c
Sub-classes	obo:SO_0002165^c

short_tandem_repeat_contraction^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002163`
Super-classes	obo:SO_0002161^c

H2BK5_acetylation_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002164`
Super-classes	obo:SO_0002143^c

trinucleotide_repeat_expansion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002165`
Super-classes	obo:SO_0002162^c

ref_miRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002166`
Super-classes	obo:SO_0000276^c

isomiR^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002167`
Super-classes	obo:SO_0000276^c

RNA_thermometer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002168`
Super-classes	obo:SO_0000836^c
Restrictions	so:part_of^op some obo:SO_0000234^c

splice_polypyrimidine_tract_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002169`
Super-classes	obo:SO_0001568^c

splice_donor_region_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002170`
Super-classes	obo:SO_0001630^c

telomeric_D_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002171`
Description	This definition is from GO:0061820 telomeric D-loop disassembly.
Super-classes	obo:SO_0000296^c

sequence_alteration_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002172`
Super-classes	obo:SO_0000413^c
Sub-classes	obo:SO_0002174^c obo:SO_0002175^c obo:SO_0002176^c obo:SO_0002173^c

indel_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002173`
Super-classes	obo:SO_0002172^c

deletion_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002174`
Super-classes	obo:SO_0002172^c

insertion_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002175`
Super-classes	obo:SO_0002172^c
Sub-classes	obo:SO_0002177^c

substitution_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002176`
Super-classes	obo:SO_0002172^c
Sub-classes	obo:SO_0002179^c obo:SO_0002178^c

duplication_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002177`
Super-classes	obo:SO_0002175^c

SNV_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002178`
Super-classes	obo:SO_0002176^c

MNV_artifact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002179`
Super-classes	obo:SO_0002176^c

enzymatic_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002180`
Super-classes	obo:SO_0001263^c
Sub-classes	obo:SO_0001640^c obo:SO_0002181^c obo:SO_0001639^c

ribozyme_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002181`
Super-classes	obo:SO_0002180^c

antisense_lncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002182`
Super-classes	obo:SO_0002127^c

sense_overlap_ncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002183`
Super-classes	obo:SO_0002127^c

sense_intronic_ncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002184`
Super-classes	obo:SO_0002127^c

bidirectional_promoter_lncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002185`
Description	This is a gencode term. See GitHub Issue #408. Synonyms "bidirectional promoter lncRNA gene" and "bidirectional_promoter_lncRNA_gene" added 23 April 2021 by David Sant. See GitHub Issue #506.
Super-classes	obo:SO_0002127^c

mutational_hotspot^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002186`
Super-classes	obo:SO_0001411^c

HERV_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002187`
Super-classes	obo:SO_0001837^c
Restrictions	so:derives_from^op some obo:SO_0002268^c

functional_gene_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002188`
Description	A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors.
Super-classes	obo:SO_0000831^c

allelic_pseudogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002189`
Super-classes	obo:SO_0001759^c

enhancer_blocking_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002190`
Description	Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf).
Super-classes	obo:SO_0000627^c

imprinting_control_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002191`
Description	Moved from is_a regulatory_region (SO:0005836) to is_a epigenetically_modified_region (SO:0001720) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530.
Super-classes	obo:SO_0001720^c

flanking_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002192`
Super-classes	obo:SO_0000657^c

processed_pseudogenic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002193`
Super-classes	obo:SO_0000777^c

unprocessed_pseudogenic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002194`
Super-classes	obo:SO_0000777^c

unitary_pseudogenic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002195`
Super-classes	obo:SO_0000777^c

allelic_pseudogenic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002196`
Super-classes	obo:SO_0000777^c

processed_pseudogenic_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002197`
Super-classes	obo:SO_0000778^c

unprocessed_pseudogenic_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002198`
Super-classes	obo:SO_0000778^c

unitary_pseudogenic_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002199`
Super-classes	obo:SO_0000778^c

allelic_pseudogenic_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002200`
Super-classes	obo:SO_0000778^c

terminal_repeat^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002201`
Super-classes	obo:SO_0000657^c

repeat_instability_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002202`
Super-classes	obo:SO_0000705^c

replication_start_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002203`
Super-classes	obo:SO_0000296^c

nucleotide_cleavage_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002204`
Super-classes	obo:SO_0000699^c
Sub-classes	obo:SO_0001688^c

response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002205`
Description	Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c

sequence_source^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002206`
Description	Terms such as genomic_DNA or mRNA can be used to describe a sequence source.
Super-classes	obo:SO_0000400^c

UNAAAC_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002207`
Super-classes	obo:SO_0001979^c

long_terminal_repeat_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002208`
Super-classes	obo:SO_0000673^c

genomic_DNA_contig^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002209`
Description	Requested by Bayer Crop Science, March 2018
Super-classes	obo:SO_0000149^c

presence_absence_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002210`
Description	Requested by Bayer Crop Science, March 2018
Super-classes	obo:SO_0001019^c

circular_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002211`
Super-classes	obo:SO_0000155^c

linear_plasmid^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002212`
Super-classes	obo:SO_0000155^c

transcription_termination_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002213`
Super-classes	obo:SO_0000951^c

redundant_inserted_stop_gained^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002214`
Super-classes	obo:SO_0001992^c

Zas1_recognition_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002215`
Super-classes	obo:SO_0000713^c

Pho7_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002216`
Super-classes	obo:SO_0001659^c

unspecified_indel^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002217`
Description	This term is used when there is a change that is either an insertion or a deletion but it is unknown which event occurred.
Super-classes	obo:SO_0001059^c

functionally_abnormal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002218`
Description	Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
Super-classes	obo:SO_0001536^c
Sub-classes	obo:SO_0001539^c obo:SO_0001786^c obo:SO_0001538^c obo:SO_0002052^c obo:SO_0002054^c obo:SO_0002320^c obo:SO_0002319^c obo:SO_0002053^c obo:SO_0002055^c obo:SO_0001773^c

functionally_normal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002219`
Description	Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
Super-classes	obo:SO_0001536^c

function_uncertain_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002220`
Description	Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019.
Super-classes	obo:SO_0001536^c

eukaryotic_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002221`
Super-classes	obo:SO_0000167^c
Sub-classes	obo:SO_0000169^c obo:SO_0000171^c obo:SO_0000170^c

prokaryotic_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002222`
Super-classes	obo:SO_0000167^c
Sub-classes	obo:SO_0000613^c

inert_DNA_spacer^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002223`
Description	Updated by Evan Christensen on May 27, 2021 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/494
Super-classes	obo:SO_0005836^c

2A_self_cleaving_peptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002224`
Description	Added by Dave Sant on October 21, 2019 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/475
Super-classes	obo:SO_0000839^c

LOZ1_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002225`
Description	Added on October 30, 2019 as per request of Val Wood request on GitHub Issue# 476 https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/476
Super-classes	obo:SO_0002006^c

group_IIC_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002226`
Super-classes	obo:SO_0000603^c

CDS_extension^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002227`
Description	Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
Super-classes	obo:SO_0000316^c
Sub-classes	obo:SO_0002229^c obo:SO_0002228^c

CDS_five_prime_extension^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002228`
Description	Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
Super-classes	obo:SO_0002227^c

CDS_three_prime_extension^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002229`
Description	Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)
Super-classes	obo:SO_0002227^c

CAAX_box^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002230`
Description	Added as per request by Val Wood GitHub issue #479 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/479)
Super-classes	obo:SO_0100017^c

self_cleaving_ribozyme^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002231`
Description	Added as per request by John T. Sexton GitHub issue #470 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470)
Super-classes	obo:SO_0000374^c
Restrictions	so:has_quality^op some obo:SO_0001977^c

selection_marker^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002232`
Description	Added as per request by Bryan Bartley GitHub issue #468 and #402 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/468)
Super-classes	obo:SO_0001645^c

homologous_chromosome_recognition_and_pairing_locus^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002233`
Description	Added as per request by Val Wood GitHub issue #483 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/483)
Super-classes	obo:SO_0000409^c
Restrictions	so:member_of^op some obo:SO_0000830^c

pumilio_response_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002234`
Description	Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455)
Super-classes	obo:SO_0000837^c
Restrictions	so:part_of^op some obo:SO_0000205^c

SUMO_interaction_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002235`
Description	Added as per request GitHub issue #434 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/434)
Super-classes	obo:SO_0001093^c

cytosolic_rRNA_18S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002236`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002362^c
Restrictions	so:derives_from^op some obo:SO_0000407^c

cytosolic_rRNA_16S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002237`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002362^c
Restrictions	so:derives_from^op some obo:SO_0001000^c

cytosolic_rRNA_5S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002238`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c
Restrictions	so:derives_from^op some obo:SO_0000652^c

cytosolic_rRNA_28S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002239`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c
Restrictions	so:derives_from^op some obo:SO_0000653^c

cytosolic_rRNA_5_8S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002240`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c
Restrictions	so:derives_from^op some obo:SO_0000375^c

rRNA_21S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002241`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472) Removed relationship derives_from SO:0001171 on 10 June 2021 when SO:0001171 rRNA_21S was obsoleted into SO:0002345 mt_LSU_rRNA. See GitHub Issue #493.
Super-classes	obo:SO_0001637^c

cytosolic_rRNA_25S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002242`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c
Restrictions	so:derives_from^op some obo:SO_0001002^c

cytosolic_rRNA_23S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002243`
Description	Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c
Restrictions	so:derives_from^op some obo:SO_0001001^c

partially_duplicated_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002244`
Description	Added as per request from the Illumina group
Super-classes	obo:SO_0001576^c
Sub-classes	obo:SO_0002246^c obo:SO_0002245^c

five_prime_duplicated_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002245`
Description	Added as per request from the Illumina group
Super-classes	obo:SO_0002244^c

three_prime_duplicated_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002246`
Description	Added as per request from the Illumina group
Super-classes	obo:SO_0002244^c

sncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002247`
Description	Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)
Super-classes	obo:SO_0000655^c
Sub-classes	obo:SO_0000253^c obo:SO_0000275^c obo:SO_0000370^c obo:SO_0000274^c

spurious_protein^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002248`
Description	Added as per request from GitHub Issue #478 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/478)
Super-classes	obo:SO_0001410^c

mature_protein_region_of_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002249`
Description	Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
Super-classes	obo:SO_0000851^c

propeptide_region_of_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002250`
Description	Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
Super-classes	obo:SO_0000851^c

signal_peptide_region_of_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002251`
Description	Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
Super-classes	obo:SO_0000851^c

transit_peptide_region_of_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002252`
Description	Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)
Super-classes	obo:SO_0000851^c

stem_loop_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002253`
Description	Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
Super-classes	obo:SO_0000122^c
Restrictions	so:part_of^op some obo:SO_0000313^c
Sub-classes	obo:SO_0002254^c obo:SO_0002255^c

loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002254`
Description	Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
Super-classes	obo:SO_0002253^c

stem^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002255`
Description	Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
Super-classes	obo:SO_0002253^c
Sub-classes	obo:SO_0002256^c

non_complimentary_stem^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002256`
Description	Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)
Super-classes	obo:SO_0002255^c

knob^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002257`
Description	Added as per request from GitHub Issue #487 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/487)
Super-classes	obo:SO_0000657^c

teb1_recognition_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002258`
Description	Requested by Antonia Locke, (Pombe) as per GitHub Issue Request #439 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/439)
Super-classes	obo:SO_0000713^c

polyA_site_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002259`
Description	Added as per GitHub Issue Request #450 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/450)
Super-classes	obo:SO_0001411^c
Restrictions	so:has_part^op some obo:SO_0000553^c so:part_of^op some obo:SO_0000205^c

LARD^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002260`
Description	Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)
Super-classes	obo:SO_0000186^c

TRIM^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002261`
Description	Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)
Super-classes	obo:SO_0000186^c

Watson_strand^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002262`
Description	Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)
Super-classes	obo:SO_0000830^c

Crick_strand^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002263`
Description	Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)
Super-classes	obo:SO_0000830^c

Copia_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002264`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000186^c

Gypsy_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002265`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000186^c

Bel_Pao_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002266`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000186^c

Retrovirus_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002267`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000186^c

Endogenous_Retrovirus_LTR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002268`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000186^c

R2_LINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002269`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000194^c

RTE_LINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002270`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000194^c

Jockey_LINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002271`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000194^c

L1_LINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002272`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000194^c

I_LINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002273`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000194^c

tRNA_SINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002274`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000206^c

7SL_SINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002275`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000206^c

5S_SINE_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002276`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000206^c

Crypton_YR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002277`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000182^c

Tc1_Mariner_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002278`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

hAT_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002279`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

Mutator_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002280`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

Merlin_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002281`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

Transib_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002282`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

piggyBac_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002283`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

PIF_Harbinger_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002284`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

CACTA_TIR_transposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002285`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000208^c

YR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002286`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000189^c
Sub-classes	obo:SO_0002287^c obo:SO_0002289^c obo:SO_0002288^c

DIRS_YR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002287`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0002286^c

Ngaro_YR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002288`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0002286^c

Viper_YR_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002289`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0002286^c

Penelope_retrotransposon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002290`
Description	Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)
Super-classes	obo:SO_0000189^c

circular_ncRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002291`
Description	Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)
Super-classes	obo:SO_0000655^c

circular_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002292`
Description	Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)
Super-classes	obo:SO_0000234^c

mitochondrial_control_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002293`
Description	Added as per GitHub Issue Request #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) from INSDC
Super-classes	obo:SO_0000296^c
Restrictions	so:has_origin^op some obo:SO_0000737^c
Sub-classes	obo:SO_0002294^c

mitochondrial_D_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002294`
Description	Added as per request by Terence Murphy (INSDC) for GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)
Super-classes	obo:SO_0000297^c obo:SO_0002293^c

transcription_factor_regulatory_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002295`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_0000235^c

TFRS_module^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002296`
Description	Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c
Restrictions	so:has_part^op some obo:SO_0002295^c

TFRS_collection^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002297`
Description	Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527.
Super-classes	obo:SO_0001055^c
Restrictions	so:has_part^op some obo:SO_0002295^c

simple_operon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002298`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_0000178^c

complex_operon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002299`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_0000178^c

unit_of_gene_expression^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002300`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0002301^c

transcription_unit^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002301`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_0002300^c

simple_regulon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002302`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_1001284^c

complex_regulon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002303`
Description	Added as per Mejia-Almonte et.al PMID:32665585
Super-classes	obo:SO_1001284^c

topologically_associated_domain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002304`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
Super-classes	obo:SO_0001412^c

topologically_associated_domain_boundary^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002305`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
Super-classes	obo:SO_0000699^c
Restrictions	so:part_of^op some obo:SO_0002304^c

chromatin_regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002306`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
Super-classes	obo:SO_0000830^c

DNA_loop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002307`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
Super-classes	obo:SO_0000830^c
Restrictions	so:overlaps^op some obo:SO_0002304^c

DNA_loop_anchor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002308`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
Super-classes	obo:SO_0000727^c
Restrictions	so:part_of^op some obo:SO_0002307^c

core_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002309`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
Super-classes	obo:SO_0001659^c
Restrictions	so:part_of^op some obo:SO_0000167^c
Sub-classes	obo:SO_0001660^c obo:SO_0000315^c obo:SO_0002312^c obo:SO_0002313^c

cryptic_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002310`
Description	Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
Super-classes	obo:SO_0000167^c
Restrictions	so:part_of^op some obo:SO_0001431^c

viral_promoter^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002311`
Super-classes	obo:SO_0000167^c
Sub-classes	obo:SO_0001204^c

core_prokaryotic_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002312`
Super-classes	obo:SO_0002309^c
Restrictions	so:part_of^op some obo:SO_0002222^c

core_viral_promoter_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002313`
Super-classes	obo:SO_0002309^c
Restrictions	so:part_of^op some obo:SO_0002311^c

altered_gene_product_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002314`
Description	Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
Super-classes	obo:SO_0001536^c
Sub-classes	obo:SO_0002316^c obo:SO_0002315^c

increased_gene_product_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002315`
Description	Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
Super-classes	obo:SO_0002314^c

decreased_gene_product_level^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002316`
Description	Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
Super-classes	obo:SO_0002314^c
Sub-classes	obo:SO_0002317^c

absent_gene_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002317`
Description	Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
Super-classes	obo:SO_0002055^c obo:SO_0002316^c

altered_gene_product_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002318`
Description	Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)
Super-classes	obo:SO_0001536^c

NMD_triggering_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002319`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0002218^c
Sub-classes	obo:SO_0002321^c obo:SO_0002323^c obo:SO_0002327^c obo:SO_0002325^c

NMD_escaping_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002320`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0002218^c
Sub-classes	obo:SO_0002326^c obo:SO_0002322^c obo:SO_0002328^c obo:SO_0002324^c

stop_gained_NMD_triggering^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002321`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0002319^c obo:SO_0001587^c

stop_gained_NMD_escaping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002322`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0001587^c obo:SO_0002320^c

frameshift_variant_NMD_triggering^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002323`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0002319^c obo:SO_0001589^c

frameshift_variant_NMD_escaping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002324`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0001589^c obo:SO_0002320^c

splice_donor_variant_NMD_triggering^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002325`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0001575^c obo:SO_0002319^c

splice_donor_variant_NMD_escaping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002326`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0002320^c obo:SO_0001575^c

splice_acceptor_variant_NMD_triggering^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002327`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0001574^c obo:SO_0002319^c

splice_acceptor_variant_NMD_escaping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002328`
Description	Added as per request from Ang Roberts as part of GenCC November 2020.
Super-classes	obo:SO_0001574^c obo:SO_0002320^c

minus_1_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002329`
Description	Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522.
Super-classes	obo:SO_0001210^c

minus_2_translational_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002330`
Description	Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522.
Super-classes	obo:SO_0001210^c

accessible_DNA_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002331`
Description	Added as part of GREEKC terms. See GitHub Issues #531 & #534.
Super-classes	obo:SO_0001411^c
Restrictions	so:overlaps^op some obo:SO_0001720^c
Sub-classes	obo:SO_0000322^c

epigenomically_modified_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002332`
Description	Added as part of GREEKC terms to differentiate between inherited and not inherited epigenetic changes. See GitHub Issue #532.
Super-classes	obo:SO_0001720^c
Restrictions	so:has_quality^op some obo:SO_0000133^c

amber_stop_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002333`
Description	Added as per GitHub request #537.
Super-classes	obo:SO_0000319^c

ochre_stop_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002334`
Description	Added as per GitHub request #537.
Super-classes	obo:SO_0000319^c

opal_stop_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002335`
Description	Added as per GitHub request #537.
Super-classes	obo:SO_0000319^c

cytosolic_rRNA_2S_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002336`
Description	Added as a request from FlyBase. See GitHub Issue #507. Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002361^c

cytosolic_2S_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002337`
Description	Added as a request from FlyBase. See GitHub Issue #507. Renamed from rRNA_2S to cytosolic_2S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493.
Super-classes	obo:SO_0000651^c

U7_snRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002338`
Description	Added as a request from FlyBase. See GitHub Issue #508
Super-classes	obo:SO_0000274^c

scaRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002339`
Description	Added as a request from FlyBase. See GitHub Issue #510
Super-classes	obo:SO_0001267^c
Sub-classes	obo:SO_0002373^c obo:SO_0002372^c obo:SO_0002374^c

RNA_7SK^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002340`
Description	Added as a request from FlyBase. See GitHub Issue #512
Super-classes	obo:SO_0000655^c

RNA_7SK_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002341`
Description	Added as a request from FlyBase. See GitHub Issue #512
Super-classes	obo:SO_0001263^c

sncRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002342`
Description	Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514
Super-classes	obo:SO_0001263^c
Sub-classes	obo:SO_0001267^c obo:SO_0001272^c obo:SO_0001638^c obo:SO_0001265^c obo:SO_0001271^c obo:SO_0001268^c

cytosolic_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002343`
Description	Added as a request from EBI. See GitHub Issue #493
Super-classes	obo:SO_0000252^c
Sub-classes	obo:SO_0000651^c obo:SO_0000650^c

mt_SSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002344`
Description	Added as a request from EMBL. See GitHub Issue #493
Super-classes	obo:SO_0002128^c

mt_LSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002345`
Description	Added as a request from EMBL. See GitHub Issue #493
Super-classes	obo:SO_0002128^c

plastid_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002346`
Description	Added as a request from EMBL. See GitHub Issue #493
Super-classes	obo:SO_0000252^c
Sub-classes	obo:SO_0002347^c obo:SO_0002348^c

plastid_SSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002347`
Description	Added as a request from EMBL. See GitHub Issue #493
Super-classes	obo:SO_0002346^c

plastid_LSU_rRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002348`
Description	Added as a request from EMBL. See GitHub Issue #493
Super-classes	obo:SO_0002346^c

fragile_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002349`
Description	See GitHub Issue #301.
Super-classes	obo:SO_0001021^c
Sub-classes	obo:SO_0002350^c obo:SO_0002351^c

common_fragile_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002350`
Description	See GitHub Issue #301.
Super-classes	obo:SO_0002349^c

rare_fragile_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002351`
Description	See GitHub Issue #301.
Super-classes	obo:SO_0002349^c

sisRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002352`
Description	See GitHub Issue #515.
Super-classes	obo:SO_0000655^c

sbRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002353`
Description	See GitHub Issue #516.
Super-classes	obo:SO_0001263^c

sbRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002354`
Description	See GitHub Issue #516.
Super-classes	obo:SO_0000655^c

hpRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002355`
Description	See GitHub Issue #518.
Super-classes	obo:SO_0001263^c

hpRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002356`
Description	See GitHub Issue #518.
Super-classes	obo:SO_0000655^c

biosynthetic_gene_cluster^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002357`
Description	See GitHub Issue #558.
Super-classes	obo:SO_0001411^c

vault_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002358`
Description	As of 11 November 2021 the HNGC lists 4 genes as RNA, vault. These are HGNC IDs: 12654, 12655, 12656, 37054.
Super-classes	obo:SO_0001263^c

Y_RNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002359`
Description	There are four genes from HGNC that are annotated this way. HGNC IDs: 10242, 10243, 10244, and 10248.
Super-classes	obo:SO_0001263^c

cytosolic_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002360`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0001637^c
Sub-classes	obo:SO_0002361^c obo:SO_0002362^c

cytosolic_LSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002361`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002360^c
Sub-classes	obo:SO_0002242^c obo:SO_0002238^c obo:SO_0002243^c obo:SO_0002240^c obo:SO_0002239^c obo:SO_0002336^c

cytosolic_SSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002362`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002360^c
Sub-classes	obo:SO_0002237^c obo:SO_0002236^c

mt_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002363`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0001637^c
Sub-classes	obo:SO_0002364^c obo:SO_0002365^c

mt_LSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002364`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002363^c

mt_SSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002365`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002363^c

plastid_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002366`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0001637^c
Sub-classes	obo:SO_0002368^c obo:SO_0002367^c

plastid_LSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002367`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002366^c

plastid_SSU_rRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002368`
Description	Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513).
Super-classes	obo:SO_0002366^c

C_D_box_scaRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002369`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002095^c

H_ACA_box_scaRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002370`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002095^c

C-D_H_ACA_box_scaRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002371`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002095^c

C_D_box_scaRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002372`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002339^c

H_ACA_box_scaRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002373`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002339^c

C-D_H_ACA_box_scaRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002374`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002339^c

C_D_box_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002375`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565.
Super-classes	obo:SO_0001267^c
Sub-classes	obo:SO_0002377^c obo:SO_0002379^c obo:SO_0002378^c

H_ACA_box_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002376`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565.
Super-classes	obo:SO_0001267^c
Sub-classes	obo:SO_0002380^c

U14_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002377`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002375^c

U3_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002378`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002375^c

methylation_guide_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002379`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002375^c

pseudouridylation_guide_snoRNA_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0002380`
Description	Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519).
Super-classes	obo:SO_0002376^c

regulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005836`
Super-classes	obo:SO_0000831^c
Sub-classes	obo:SO_0001720^c obo:SO_0001680^c obo:SO_0001682^c obo:SO_0002223^c obo:SO_0001055^c obo:SO_0001681^c

U14_snoRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005837`
Super-classes	obo:SO_0000232^c

SO_0005839^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005839`

methylation_guide_snoRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005841`
Description	Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
Super-classes	obo:SO_0000593^c
Restrictions	so:derives_from^op some obo:SO_0000580^c

rRNA_cleavage_RNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005843`
Super-classes	obo:SO_0000655^c
Restrictions	so:derives_from^op some obo:SO_0000582^c

exon_of_single_exon_gene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005845`
Super-classes	obo:SO_0000147^c

cassette_array_member^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005847`
Super-classes	obo:SO_0005848^c

gene_cassette_member^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005848`
Super-classes	obo:SO_0000081^c
Sub-classes	obo:SO_0005847^c

gene_subarray_member^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005849`
Super-classes	obo:SO_0000081^c

primer_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005850`
Super-classes	obo:SO_0001655^c
Restrictions	so:part_of^op some obo:SO_0000186^c

gene_array^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005851`
Description	This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
Super-classes	obo:SO_0005855^c

gene_subarray^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005852`
Description	This would include, for example, a cluster of genes encoding different histones.
Super-classes	obo:SO_0005855^c

gene_cassette^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005853`
Description	This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
Super-classes	obo:SO_0000704^c

gene_cassette_array^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005854`
Description	This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
Super-classes	obo:SO_0005855^c
Restrictions	so:has_part^op some obo:SO_0005853^c
Sub-classes	obo:SO_0001984^c

gene_group^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005855`
Super-classes	obo:SO_0001411^c
Sub-classes	obo:SO_0005854^c obo:SO_0000178^c obo:SO_0005852^c obo:SO_1001284^c obo:SO_0001789^c obo:SO_0005851^c

selenocysteine_tRNA_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005856`
Super-classes	obo:SO_0000210^c

selenocysteinyl_tRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005857`
Super-classes	obo:SO_0000253^c
Restrictions	so:derives_from^op some obo:SO_0005856^c

syntenic_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0005858`
Super-classes	obo:SO_0000330^c
Restrictions	so:has_quality^op some obo:SO_0000860^c

biochemical_region_of_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100001`
Description	Range.
Super-classes	obo:SO_0001067^c
Sub-classes	obo:SO_0001422^c obo:SO_0100002^c obo:SO_0100018^c obo:SO_0100019^c obo:SO_0001089^c

molecular_contact_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100002`
Description	Range.
Super-classes	obo:SO_0100001^c
Sub-classes	obo:SO_0001105^c obo:SO_0001093^c obo:SO_0100020^c obo:SO_0001092^c

intrinsically_unstructured_polypeptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100003`
Super-classes	obo:SO_0001070^c

catmat_left_handed_three^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100004`
Super-classes	obo:SO_0001078^c

catmat_left_handed_four^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100005`
Super-classes	obo:SO_0001078^c

catmat_right_handed_three^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100006`
Super-classes	obo:SO_0001078^c

catmat_right_handed_four^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100007`
Super-classes	obo:SO_0001078^c

alpha_beta_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100008`
Super-classes	obo:SO_0001078^c

lipoprotein_signal_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100009`
Super-classes	obo:SO_0100011^c

no_output^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100010`
Super-classes	obo:SO_0000703^c

cleaved_peptide_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100011`
Description	Range.
Super-classes	obo:SO_0000839^c
Restrictions	so:part_of^op some obo:SO_0001063^c
Sub-classes	obo:SO_0000691^c obo:SO_0001062^c obo:SO_0100014^c obo:SO_0001061^c obo:SO_0100016^c obo:SO_0100009^c obo:SO_0100015^c obo:SO_0000728^c obo:SO_0001408^c

peptide_coil^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100012`
Super-classes	obo:SO_0001078^c

hydrophobic_region_of_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100013`
Description	Range.
Super-classes	obo:SO_0000839^c

n_terminal_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100014`
Super-classes	obo:SO_0100011^c
Restrictions	so:part_of^op some obo:SO_0000418^c

c_terminal_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100015`
Super-classes	obo:SO_0100011^c
Restrictions	so:part_of^op some obo:SO_0000418^c

central_hydrophobic_region_of_signal_peptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100016`
Super-classes	obo:SO_0100011^c
Restrictions	so:part_of^op some obo:SO_0000418^c

polypeptide_conserved_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100017`
Super-classes	obo:SO_0001067^c
Sub-classes	obo:SO_0001805^c obo:SO_0002159^c obo:SO_0001807^c obo:SO_0002230^c

polypeptide_binding_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100018`
Super-classes	obo:SO_0100001^c

polypeptide_catalytic_motif^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100019`
Super-classes	obo:SO_0100001^c

polypeptide_DNA_contact^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100020`
Super-classes	obo:SO_0100002^c obo:SO_0001429^c

polypeptide_conserved_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100021`
Super-classes	obo:SO_0000839^c
Sub-classes	obo:SO_0001067^c obo:SO_0001068^c obo:SO_0000417^c

SO_0100042^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_0100042`

substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000002`
Super-classes	obo:SO_0001059^c obo:SO_0001411^c
Sub-classes	obo:SO_1000005^c obo:SO_0002007^c obo:SO_0001483^c

SO_1000004^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000004`

complex_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000005`
Super-classes	obo:SO_1000002^c

SO_1000007^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000007`

point_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000008`
Super-classes	obo:SO_0001483^c

transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000009`
Super-classes	obo:SO_0001483^c
Sub-classes	obo:SO_1000010^c obo:SO_1000014^c

pyrimidine_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000010`
Super-classes	obo:SO_1000009^c
Sub-classes	obo:SO_1000011^c obo:SO_1000013^c

C_to_T_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000011`
Super-classes	obo:SO_1000010^c
Sub-classes	obo:SO_1000012^c

C_to_T_transition_at_pCpG_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000012`
Super-classes	obo:SO_1000011^c

T_to_C_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000013`
Super-classes	obo:SO_1000010^c

purine_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000014`
Super-classes	obo:SO_1000009^c
Sub-classes	obo:SO_1000016^c obo:SO_1000015^c

A_to_G_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000015`
Super-classes	obo:SO_1000014^c

G_to_A_transition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000016`
Super-classes	obo:SO_1000014^c

transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000017`
Super-classes	obo:SO_0001483^c
Sub-classes	obo:SO_1000018^c obo:SO_1000023^c

pyrimidine_to_purine_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000018`
Super-classes	obo:SO_1000017^c
Sub-classes	obo:SO_1000020^c obo:SO_1000022^c obo:SO_1000019^c obo:SO_1000021^c

C_to_A_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000019`
Super-classes	obo:SO_1000018^c

C_to_G_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000020`
Super-classes	obo:SO_1000018^c

T_to_A_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000021`
Super-classes	obo:SO_1000018^c

T_to_G_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000022`
Super-classes	obo:SO_1000018^c

purine_to_pyrimidine_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000023`
Super-classes	obo:SO_1000017^c
Sub-classes	obo:SO_1000025^c obo:SO_1000024^c obo:SO_1000027^c obo:SO_1000026^c

A_to_C_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000024`
Super-classes	obo:SO_1000023^c

A_to_T_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000025`
Super-classes	obo:SO_1000023^c

G_to_C_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000026`
Super-classes	obo:SO_1000023^c

G_to_T_transversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000027`
Super-classes	obo:SO_1000023^c

intrachromosomal_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000028`
Super-classes	obo:SO_1000183^c
Restrictions	so:has_quality^op some obo:SO_0001510^c
Sub-classes	obo:SO_1000045^c obo:SO_1000030^c obo:SO_1000038^c obo:SO_1000029^c obo:SO_1000141^c

chromosomal_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000029`
Super-classes	obo:SO_1000028^c
Restrictions	so:has_part^op some obo:SO_0000159^c
Sub-classes	obo:SO_0000062^c obo:SO_0000461^c obo:SO_1000147^c obo:SO_1000171^c obo:SO_0000512^c obo:SO_0000465^c

chromosomal_inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000030`
Super-classes	obo:SO_1000028^c
Restrictions	so:has_part^op some obo:SO_1000036^c
Sub-classes	obo:SO_0000439^c obo:SO_1000046^c obo:SO_1000148^c obo:SO_1000171^c obo:SO_1000047^c obo:SO_1000151^c

interchromosomal_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000031`
Super-classes	obo:SO_1000183^c
Restrictions	so:has_quality^op some obo:SO_0001511^c
Sub-classes	obo:SO_1000044^c obo:SO_1000149^c obo:SO_1000155^c

delins^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000032`
Description	Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion.
Super-classes	obo:SO_0001059^c

SO_1000033^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000033`

SO_1000034^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000034`

duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000035`
Super-classes	obo:SO_0000667^c
Sub-classes	obo:SO_1000173^c obo:SO_0001928^c

inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000036`
Super-classes	obo:SO_0001059^c obo:SO_0001411^c

chromosomal_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000037`
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_1000154^c obo:SO_0000457^c obo:SO_1000038^c obo:SO_1000144^c

intrachromosomal_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000038`
Super-classes	obo:SO_1000037^c obo:SO_1000028^c
Restrictions	so:has_part^op some obo:SO_1000035^c
Sub-classes	obo:SO_1000149^c obo:SO_1000041^c obo:SO_0000547^c obo:SO_0000549^c obo:SO_0000465^c

direct_tandem_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000039`
Super-classes	obo:SO_1000173^c

inverted_tandem_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000040`
Super-classes	obo:SO_1000173^c

intrachromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000041`
Super-classes	obo:SO_1000038^c obo:SO_0000453^c
Restrictions	so:has_part^op some obo:SO_0000199^c so:has_part^op some obo:SO_1000035^c
Sub-classes	obo:SO_0000062^c obo:SO_1000159^c obo:SO_1000162^c

compound_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000042`
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_1000140^c obo:SO_0000060^c obo:SO_1000138^c

Robertsonian_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000043`
Super-classes	obo:SO_1000044^c

chromosomal_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000044`
Super-classes	obo:SO_1000031^c obo:SO_0000199^c
Sub-classes	obo:SO_1000147^c obo:SO_0002060^c obo:SO_0000686^c obo:SO_1000148^c obo:SO_1000043^c obo:SO_0002061^c obo:SO_1000048^c

ring_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000045`
Super-classes	obo:SO_1000028^c
Restrictions	so:has_quality^op some obo:SO_0000988^c
Sub-classes	obo:SO_1000145^c obo:SO_0000439^c

pericentric_inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000046`
Super-classes	obo:SO_1000030^c
Restrictions	so:has_quality^op some obo:SO_0001518^c

paracentric_inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000047`
Super-classes	obo:SO_1000030^c
Restrictions	so:has_quality^op some obo:SO_0001519^c

reciprocal_chromosomal_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000048`
Super-classes	obo:SO_1000044^c

sequence_variation_affecting_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000049`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_no_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000050`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.

sequence_variation_affecting_coding_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000054`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_initiator_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000055`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_coding_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000056`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_synonymous_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000057`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_non_synonymous_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000058`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_missense_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000059`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conservative_missense_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000060`
Description	The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.

sequence_variant_causing_nonconservative_missense_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000061`
Description	The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.

sequence_variant_causing_nonsense_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000062`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_terminator_codon_change_in_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000063`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_reading_frame^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000064`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

frameshift_sequence_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000065`

sequence_variant_causing_plus_1_frameshift_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000066`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_minus_1_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000067`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_plus_2_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000068`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_minus_2_frameshift^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000069`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcript_processing^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000070`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splicing^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000071`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splice_donor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000072`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_splice_acceptor^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000073`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_cryptic_splice_activation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000074`
Description	A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.

sequence_variant_affecting_editing^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000075`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcription^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000076`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_rate_of_transcription^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000078`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_transcript_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000079`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_increasing_rate_of_transcription^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000080`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_rate_of_transcription^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000081`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence variant_affecting_transcript_stability^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000082`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_increasing_transcript_stability^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000083`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_transcript_stability^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000084`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_affecting_level_of_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000085`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_decreasing_level_of_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000086`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variation_increasing_level_of_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000087`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_translational_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000088`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_no_change_of_translational_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000089`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.

SO_1000090^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000090`

SO_1000091^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000091`

sequence_variant_causing_complex_change_of_translational_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000092`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000093`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conservative_amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000094`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_nonconservative_amino_acid_substitution^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000095`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_insertion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000096`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_amino_acid_deletion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000097`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_truncation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000098`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000099`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_polypeptide_N_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000100`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_polypeptide_C_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000101`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_level_of_translational_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000102`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_decreasing_level_of_translation_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000103`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_increasing_level_of_translation_product^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000104`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_polypeptide_amino_acid_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000105`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_inframe_polypeptide_N_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000106`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutation_causing_out_of_frame_polypeptide_N_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000107`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

mutaton_causing_inframe_polypeptide_C_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000108`

mutation_causing_out_of_frame_polypeptide_C_terminal_elongation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000109`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

frame_restoring_sequence_variant^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000110`

sequence_variant_affecting_3D_structure_of_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000111`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_no_3D_structural_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000112`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.

SO_1000113^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000113`

SO_1000114^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000114`

sequence_variant_causing_complex_3D_structural_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000115`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_conformational_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000116`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_polypeptide_function^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000117`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_loss_of_function_of_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000118`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_inactive_ligand_binding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000119`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_inactive_catalytic_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000120`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_localization_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000121`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_polypeptide_post_translational_processing_change^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000122`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

polypeptide_post_translational_processing_affected^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000123`

sequence_variant_causing_partial_loss_of_function_of_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000124`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_gain_of_function_of_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000125`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_affecting_transcript_secondary_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000126`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_compensatory_transcript_secondary_structure_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000127`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_effect^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000132`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Updated after discussion with Peter Taschner - Feb 09.

sequence_variant_causing_polypeptide_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000134`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

autosynaptic_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000136`
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_1000142^c obo:SO_1000143^c

homo_compound_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000138`
Super-classes	obo:SO_1000042^c

hetero_compound_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000140`
Super-classes	obo:SO_1000042^c

chromosome_fission^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000141`
Super-classes	obo:SO_1000028^c

dextrosynaptic_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000142`
Description	Corrected spelling from dexstrosynaptic_chromosome to dextrosynaptic_chromosome on April 14, 2020 in response to GitHub request #447
Super-classes	obo:SO_1000136^c

laevosynaptic_chromosome^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000143`
Super-classes	obo:SO_1000136^c

free_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000144`
Super-classes	obo:SO_1000037^c
Sub-classes	obo:SO_1000145^c

free_ring_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000145`
Super-classes	obo:SO_1000045^c obo:SO_1000144^c
Restrictions	so:has_quality^op some obo:SO_0001516^c

SO_1000146^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000146`

deficient_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000147`
Super-classes	obo:SO_1000044^c obo:SO_1000029^c
Restrictions	so:has_part^op some obo:SO_0000159^c

inversion_cum_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000148`
Super-classes	obo:SO_1000030^c obo:SO_1000044^c
Restrictions	so:has_part^op some obo:SO_1000036^c
Sub-classes	obo:SO_1000158^c

bipartite_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000149`
Super-classes	obo:SO_1000038^c obo:SO_1000031^c

cyclic_translocation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000150`
Super-classes	obo:SO_0002060^c

bipartite_inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000151`
Super-classes	obo:SO_1000030^c

uninverted_insertional_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000152`
Super-classes	obo:SO_1000154^c

inverted_insertional_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000153`
Super-classes	obo:SO_1000154^c

insertional_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000154`
Super-classes	obo:SO_1000037^c
Sub-classes	obo:SO_1000153^c obo:SO_1000160^c obo:SO_1000152^c

interchromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000155`
Super-classes	obo:SO_0000453^c obo:SO_1000031^c
Sub-classes	obo:SO_1000157^c obo:SO_1000161^c obo:SO_0000063^c obo:SO_1000156^c

inverted_interchromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000156`
Super-classes	obo:SO_1000155^c

uninverted_interchromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000157`
Super-classes	obo:SO_1000155^c

inverted_intrachromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000158`
Super-classes	obo:SO_1000148^c
Restrictions	so:has_part^op some obo:SO_1000036^c

uninverted_intrachromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000159`
Super-classes	obo:SO_1000041^c
Restrictions	so:has_part^op some obo:SO_0001514^c

unoriented_insertional_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000160`
Description	Flag - unknown in the definition.
Super-classes	obo:SO_1000154^c

unoriented_interchromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000161`
Description	FLAG - term describes an unknown.
Super-classes	obo:SO_1000155^c

unoriented_intrachromosomal_transposition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000162`
Description	FLAG - definition describes an unknown.
Super-classes	obo:SO_1000041^c

uncharacterized_chromosomal_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000170`
Super-classes	obo:SO_1000183^c
Sub-classes	obo:SO_1000175^c

deficient_inversion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000171`
Super-classes	obo:SO_1000029^c obo:SO_1000030^c
Restrictions	so:has_part^op some obo:SO_0000159^c so:has_part^op some obo:SO_1000036^c

tandem_duplication^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000173`
Super-classes	obo:SO_1000035^c
Sub-classes	obo:SO_1000039^c obo:SO_1000040^c

partially_characterized_chromosomal_mutation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000175`
Super-classes	obo:SO_1000170^c

SO_1000177^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000177`

SO_1000179^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000179`

sequence_variant_affecting_gene_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000180`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_gene_fusion^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000181`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

chromosome_number_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000182`
Super-classes	obo:SO_0000240^c
Sub-classes	obo:SO_0000054^c obo:SO_0001254^c

chromosome_structure_variation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000183`
Super-classes	obo:SO_0000240^c
Sub-classes	obo:SO_1000042^c obo:SO_0000065^c obo:SO_1000028^c obo:SO_1000037^c obo:SO_0000550^c obo:SO_0001784^c obo:SO_0000453^c obo:SO_1000136^c obo:SO_1000031^c obo:SO_1000170^c

sequence_variant_causes_exon_loss^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000184`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causes_intron_gain^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000185`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_cryptic_splice_donor_activation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1000186`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

sequence_variant_causing_cryptic_splice_acceptor_activation^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001186`
Description	OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.

alternatively_spliced_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001187`
Super-classes	obo:SO_0000673^c
Restrictions	so:has_quality^op some obo:SO_0000877^c

encodes_1_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001188`
Super-classes	obo:SO_0000463^c

encodes_greater_than_1_polypeptide^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001189`
Super-classes	obo:SO_0000463^c
Sub-classes	obo:SO_1001195^c obo:SO_1001192^c

encodes_different_polypeptides_different_stop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001190`
Super-classes	obo:SO_1001195^c

encodes_overlapping_peptides_different_start^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001191`
Super-classes	obo:SO_1001195^c

encodes_disjoint_polypeptides^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001192`
Super-classes	obo:SO_1001189^c

encodes_overlapping_polypeptides_different_start_and_stop^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001193`
Super-classes	obo:SO_1001195^c

alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001194`

encodes_overlapping_peptides^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001195`
Super-classes	obo:SO_1001189^c
Sub-classes	obo:SO_1001190^c obo:SO_1001193^c obo:SO_1001191^c

cryptogene^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001196`
Super-classes	obo:SO_0000654^c obo:SO_0001431^c
Restrictions	so:has_quality^op some obo:SO_0000976^c

dicistronic_primary_transcript^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001197`
Super-classes	obo:SO_0000631^c obo:SO_0000079^c
Restrictions	so:has_quality^op some obo:SO_0000879^c

member_of_regulon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001217`
Super-classes	obo:SO_0000081^c

alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001244`

CDS_independently_known^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001246`
Super-classes	obo:SO_0000316^c
Restrictions	so:has_quality^op some obo:SO_0000906^c

orphan_CDS^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001247`
Super-classes	obo:SO_1001254^c
Restrictions	so:has_origin^op some obo:SO_0000910^c

CDS_supported_by_domain_match_data^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001249`
Super-classes	obo:SO_1001251^c
Restrictions	so:has_quality^op some obo:SO_0000908^c

CDS_supported_by_sequence_similarity_data^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001251`
Super-classes	obo:SO_1001254^c
Restrictions	so:has_quality^op some obo:SO_0000907^c
Sub-classes	obo:SO_1001249^c obo:SO_1001259^c obo:SO_0002071^c

CDS_predicted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001254`
Super-classes	obo:SO_0000316^c
Restrictions	so:has_quality^op some obo:SO_0000732^c
Sub-classes	obo:SO_1001251^c obo:SO_1001247^c

status_of_coding_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001255`

CDS_supported_by_EST_or_cDNA_data^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001259`
Super-classes	obo:SO_1001251^c
Restrictions	so:has_quality^op some obo:SO_0000909^c

internal_Shine_Dalgarno_sequence^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001260`
Super-classes	obo:SO_1001268^c obo:SO_0000243^c

recoded_mRNA^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001261`
Super-classes	obo:SO_0000234^c
Restrictions	so:has_quality^op some obo:SO_0000881^c
Sub-classes	obo:SO_1001264^c obo:SO_1001265^c

minus_1_translationally_frameshifted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001262`
Super-classes	obo:SO_0000887^c

plus_1_translationally_frameshifted^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001263`
Super-classes	obo:SO_0000887^c

mRNA_recoded_by_translational_bypass^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001264`
Super-classes	obo:SO_1001261^c
Restrictions	so:has_quality^op some obo:SO_0000886^c

mRNA_recoded_by_codon_redefinition^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001265`
Super-classes	obo:SO_1001261^c
Restrictions	so:has_quality^op some obo:SO_0000882^c

stop_codon_redefinition_as_selenocysteine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001266`

stop_codon_readthrough^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001267`

recoding_stimulatory_region^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001268`
Super-classes	obo:SO_0000836^c
Sub-classes	obo:SO_1001280^c obo:SO_1001260^c obo:SO_1001277^c obo:SO_1001288^c obo:SO_1001274^c

four_bp_start_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001269`
Super-classes	obo:SO_0000680^c

stop_codon_redefinition_as_pyrrolysine^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001270`

archaeal_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001271`
Description	Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
Super-classes	obo:SO_0001216^c

tRNA_intron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001272`
Description	Could be a cross product with Gene ontology, GO:0006388.
Super-classes	obo:SO_0001216^c

CTG_start_codon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001273`
Super-classes	obo:SO_0000680^c

SECIS_element^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001274`
Super-classes	obo:SO_1001268^c

retron^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001275`
Super-classes	obo:SO_0001411^c

three_prime_recoding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001277`
Super-classes	obo:SO_1001268^c
Sub-classes	obo:SO_1001281^c obo:SO_1001287^c obo:SO_1001286^c obo:SO_1001279^c

three_prime_stem_loop_structure^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001279`
Super-classes	obo:SO_1001277^c

five_prime_recoding_site^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001280`
Super-classes	obo:SO_1001268^c

flanking_three_prime_quadruplet_recoding_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001281`
Super-classes	obo:SO_1001277^c

UAG_stop_codon_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001282`
Super-classes	obo:SO_1001288^c

UAA_stop_codon_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001283`
Super-classes	obo:SO_1001288^c

regulon^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001284`
Description	Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300
Super-classes	obo:SO_0005855^c
Restrictions	so:has_part^op some obo:SO_0002300^c
Sub-classes	obo:SO_0002302^c obo:SO_0002303^c

UGA_stop_codon_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001285`
Super-classes	obo:SO_1001288^c

three_prime_repeat_recoding_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001286`
Super-classes	obo:SO_1001277^c

distant_three_prime_recoding_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001287`
Super-classes	obo:SO_1001277^c

stop_codon_signal^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_1001288`
Description	This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
Super-classes	obo:SO_1001268^c
Sub-classes	obo:SO_1001283^c obo:SO_1001285^c obo:SO_1001282^c

databank_entry^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_2000061`
Super-classes	obo:SO_0000695^c

gene_segment^c # Classes

URI	`http://purl.obolibrary.org/obo/SO_3000000`
Description	Requested by tracker 2021594, July 2008, by Alex.
Super-classes	obo:SO_0000842^c
Sub-classes	obo:SO_0001741^c

URI	`http://purl.obolibrary.org/obo/so#associated_with`
Description	This relationship is vague and up for discussion.

URI	`http://purl.obolibrary.org/obo/so#complete_evidence_for_feature`
Description	If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
Super-properties	so:evidence_for_feature^op

URI	`http://purl.obolibrary.org/obo/so#connects_on`
Description	Example: A splice_junction connects_on exon, exon, mature_transcript.

URI	`http://purl.obolibrary.org/obo/so#contained_by`
Description	The inverse is contains. Example: intein contained_by immature_peptide_region.

URI	`http://purl.obolibrary.org/obo/so#contains`
Description	Example: pre_miRNA contains miRNA_loop.

URI	`http://purl.obolibrary.org/obo/so#evidence_for_feature`
Description	This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.

URI	`http://purl.obolibrary.org/obo/so#exemplar_of`
Description	Tracker id: 2594157.

URI	`http://purl.obolibrary.org/obo/so#finished_by`
Description	Example CDS finished_by stop_codon.

URI	`http://purl.obolibrary.org/obo/so#finishes`
Description	Example: stop_codon finishes CDS.

URI	`http://purl.obolibrary.org/obo/so#gained`
Description	A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may gain a stop codon not present in the reference sequence.

URI	`http://purl.obolibrary.org/obo/so#has_integral_part`
Description	Example: mRNA has_integral_part CDS.
Super-properties	so:has_part^op

URI	`http://purl.obolibrary.org/obo/so#has_part`
Description	Example: operon has_part gene.

URI	`http://purl.obolibrary.org/obo/so#has_quality`
Description	The relationship between a feature and an attribute.

URI	`http://purl.obolibrary.org/obo/so#homologous_to`
Super-properties	so:similar_to^op

URI	`http://purl.obolibrary.org/obo/so#integral_part_of`
Description	Example: exon integral_part_of transcript.
Super-properties	so:part_of^op

URI	`http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of`
Description	Example: region is consecutive_sequence of base.

URI	`http://purl.obolibrary.org/obo/so#lost`
Description	A relation with which to annotate the changes in a variant sequence with respect to a reference. For example a variant transcript may have lost a stop codon present in the reference sequence.

URI	`http://purl.obolibrary.org/obo/so#maximally_overlaps`
Description	Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.

URI	`http://purl.obolibrary.org/obo/so#member_of`
Description	A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
Super-properties	so:part_of^op

URI	`http://purl.obolibrary.org/obo/so#non_functional_homolog_of`
Super-properties	so:homologous_to^op

{no title found}

Metadata

Table of Contents

Overview

Classes ↑

BS_00003c # Classes

BS_0000338c # Classes

BS_0000339c # Classes

BS_0000340c # Classes

BS_0000341c # Classes

BS_00012c # Classes

BS_00026c # Classes

BS_00027c # Classes

BS_00028c # Classes

BS_00029c # Classes

BS_00032c # Classes

BS_00033c # Classes

BS_00036c # Classes

BS_00040c # Classes

BS_00041c # Classes

BS_00042c # Classes

BS_00052c # Classes

BS_00055c # Classes

BS_00063c # Classes

BS_00067c # Classes

BS_00068c # Classes

BS_00069c # Classes

BS_00070c # Classes

BS_00071c # Classes

BS_00072c # Classes

BS_00073c # Classes

BS_00076c # Classes

BS_00077c # Classes

BS_00124c # Classes

BS_00125c # Classes

BS_00128c # Classes

BS_00129c # Classes

BS_00131c # Classes

BS_00134c # Classes

BS_00136c # Classes

BS_00137c # Classes

BS_00140c # Classes

BS_00141c # Classes

BS_00142c # Classes

BS_00143c # Classes

BS_00144c # Classes

BS_00145c # Classes

BS_00146c # Classes

BS_00147c # Classes

BS_00148c # Classes

BS_00149c # Classes

BS_00151c # Classes

BS_00152c # Classes

BS_00153c # Classes

BS_00154c # Classes

BS_00155c # Classes

BS_00156c # Classes

BS_00157c # Classes

BS_00158c # Classes

BS_00159c # Classes

BS_00178c # Classes

BS_00181c # Classes

BS_00182c # Classes

BS_00185c # Classes

BS_00186c # Classes

BS_00187c # Classes

BS_00202c # Classes

BS_00203c # Classes

BS_00204c # Classes

BS_00205c # Classes

BS_00206c # Classes

BS_00207c # Classes

BS_00208c # Classes

BS_00209c # Classes

BS_00210c # Classes

BS_00211c # Classes

BS_00212c # Classes

BS_00213c # Classes

BS_00214c # Classes

BS_00215c # Classes

BS_00003^c # Classes

BS_0000338^c # Classes

BS_0000339^c # Classes

BS_0000340^c # Classes

BS_0000341^c # Classes

BS_00012^c # Classes

BS_00026^c # Classes

BS_00027^c # Classes

BS_00028^c # Classes

BS_00029^c # Classes

BS_00032^c # Classes

BS_00033^c # Classes

BS_00036^c # Classes

BS_00040^c # Classes

BS_00041^c # Classes

BS_00042^c # Classes

BS_00052^c # Classes

BS_00055^c # Classes

BS_00063^c # Classes

BS_00067^c # Classes

BS_00068^c # Classes

BS_00069^c # Classes

BS_00070^c # Classes

BS_00071^c # Classes

BS_00072^c # Classes

BS_00073^c # Classes

BS_00076^c # Classes

BS_00077^c # Classes

BS_00124^c # Classes

BS_00125^c # Classes

BS_00128^c # Classes

BS_00129^c # Classes

BS_00131^c # Classes

BS_00134^c # Classes

BS_00136^c # Classes

BS_00137^c # Classes

BS_00140^c # Classes

BS_00141^c # Classes

BS_00142^c # Classes

BS_00143^c # Classes

BS_00144^c # Classes

BS_00145^c # Classes

BS_00146^c # Classes

BS_00147^c # Classes

BS_00148^c # Classes

BS_00149^c # Classes

BS_00151^c # Classes

BS_00152^c # Classes

BS_00153^c # Classes

BS_00154^c # Classes

BS_00155^c # Classes

BS_00156^c # Classes

BS_00157^c # Classes

BS_00158^c # Classes

BS_00159^c # Classes

BS_00178^c # Classes

BS_00181^c # Classes

BS_00182^c # Classes

BS_00185^c # Classes

BS_00186^c # Classes

BS_00187^c # Classes

BS_00202^c # Classes

BS_00203^c # Classes

BS_00204^c # Classes

BS_00205^c # Classes

BS_00206^c # Classes

BS_00207^c # Classes

BS_00208^c # Classes

BS_00209^c # Classes

BS_00210^c # Classes

BS_00211^c # Classes

BS_00212^c # Classes

BS_00213^c # Classes

BS_00214^c # Classes

BS_00215^c # Classes

BS_00216^c # Classes

BS_00219^c # Classes

BS_00220^c # Classes

BS_00221^c # Classes

BS_00222^c # Classes

URI	`http://purl.obolibrary.org/obo/so#orthologous_to`
Super-properties	so:homologous_to^op

URI	`http://purl.obolibrary.org/obo/so#overlaps`
Description	Example: coding_exon overlaps CDS.

URI	`http://purl.obolibrary.org/obo/so#paralogous_to`
Super-properties	so:homologous_to^op

URI	`http://purl.obolibrary.org/obo/so#part_of`
Description	Example: amino_acid part_of polypeptide.

URI	`http://purl.obolibrary.org/obo/so#partial_evidence_for_feature`
Super-properties	so:evidence_for_feature^op

URI	`http://purl.obolibrary.org/obo/so#processed_from`
Description	Example: miRNA processed_from miRNA_primary_transcript.

URI	`http://purl.obolibrary.org/obo/so#processed_into`
Description	Example: miRNA_primary_transcript processed into miRNA.

URI	`http://purl.obolibrary.org/obo/so#started_by`
Description	Example: CDS started_by start_codon.

URI	`http://purl.obolibrary.org/obo/so#starts`
Description	Example: start_codon starts CDS.

URI	`http://purl.obolibrary.org/obo/so#transcribed_from`
Description	Example: primary_transcript transcribed_from gene.