Sequence Ontology (SO)

Name: Sequence Ontology (SO)
Published: 2026-11-13T13:52:25.298104Z

Selected English labels and exact synonyms from the Sequence Ontology (SO), release 2026-08-07, with source identifiers and spelling preserved. Licensed CC BY 4.0; full attribution is listed under Sources. Under semantic review; not endorsed by the ontology's maintainers.

Curator: Chloe Harris

Languages shown reflect this page; source translations may cover only some concepts.

English
catmat-3lUnrated catmat_left_handed_threeUnrated
functionally_normalUnrated function retained variantUnrated
INSDC_qualifier:unprocessedUnrated non_processed_pseudogeneUnrated unprocessed pseudogeneUnrated unprocessed_pseudogeneUnrated
late originUnrated late origin of replicationUnrated late_origin_of_replicationUnrated late replication originUnrated
imG2Unrated isowyosineUnrated
histone binding siteUnrated histone_binding_siteUnrated
CsrB RsmB RNAUnrated CsrB-RsmB RNAUnrated CsrB_RsmB_RNAUnrated
V D DJ C clusterUnrated V_D_DJ_C_clusterUnrated V-D-(DJ)-C-CLUSTERUnrated
TFBS binding site translocationUnrated TFBS_translocationUnrated transcription factor binding site translocationUnrated
INSDC_qualifier:nestedUnrated nested repeatUnrated nested_repeatUnrated
exonUnrated INSDC_feature:exonUnrated
regulatory region fusionUnrated regulatory_region_fusionUnrated
m2,7GmUnrated N2,7,2'-O-trimethylguanosineUnrated N2 7 2prirme O trimethylguanosineUnrated N2_7_2prirme_O_trimethylguanosineUnrated
sense intronic lncRNA geneUnrated sense_intronic_lncRNA_geneUnrated sense intronic ncRNA geneUnrated
codon redefinedUnrated codon_redefinedUnrated
ribozymicUnrated
inversion derived bipartite duplicationUnrated inversion_derived_bipartite_duplicationUnrated
DNA constraintUnrated DNA constraint sequenceUnrated DNA_constraint_sequenceUnrated
conservative increase in CDS lengthUnrated conservative inframe insertionUnrated conservative_inframe_insertionUnrated
Hairpin RNA geneUnrated hpRNA_geneUnrated
phosphorylation siteUnrated phosphorylation_siteUnrated
translationally frameshiftedUnrated translationally_frameshiftedUnrated
floxed geneUnrated floxed_geneUnrated
propeptide cleavage siteUnrated propeptide_cleavage_siteUnrated
D J C clusterUnrated D_J_C_clusterUnrated D-J-C-CLUSTERUnrated
RNA chromosomeUnrated RNA_chromosomeUnrated
selenocysteine lossUnrated selenocysteine_lossUnrated
attC siteUnrated attC_siteUnrated
gene with non canonical start codonUnrated gene_with_non_canonical_start_codonUnrated
H4K91acUnrated H4K91 acetylation siteUnrated H4K91_acetylation_siteUnrated
INSDC_feature:stem_loopUnrated RNA_hairpin_loopUnrated stem loopUnrated stem-loopUnrated stem_loopUnrated
INSDC_qualifier:replication_regulatory_regionUnrated replication regulatory regionUnrated replication_regulatory_regionUnrated
YAC endUnrated YAC_endUnrated
immunoglobulin pseudogeneUnrated immunoglobulin_pseudogeneUnrated
five_prime_UTR_premature_start_codon_location_variantUnrated
EUnrated GluUnrated glutamic acidUnrated glutamic_acidUnrated
ANNOVAR:stopgainUnrated Jannovar:stop_gainedUnrated nonsenseUnrated nonsense codonUnrated Seattleseq:stop-gainedUnrated snpEff:STOP_GAINEDUnrated stop gainedUnrated stop_gainedUnrated VAAST:stop_gainedUnrated VAT:prematureStopUnrated VEP:stop_gainedUnrated
insulator_binding_siteUnrated
5-methylaminomethyl-2-selenouridineUnrated five methylaminomethyl two selenouridineUnrated five_methylaminomethyl_two_selenouridineUnrated mnm5se2UUnrated
engineered foreign transposable element geneUnrated engineered_foreign_transposable_element_geneUnrated
SAGE tagUnrated SAGE_tagUnrated
elongated_out_of_frame_polypeptide_C_terminalUnrated elongated polypeptide out of frame C terminalUnrated
U3 3' long terminal repeat regionUnrated U3 three prime LTR regionUnrated U3_three_prime_LTR_regionUnrated
PNAUnrated
DNA loop anchorUnrated DNA_loop_anchorUnrated
inside intron antiparallelUnrated inside_intron_antiparallelUnrated
coiled coilUnrated coiled_coilUnrated
HERV deletionUnrated HERV_deletionUnrated
natural_variant_siteUnrated
tryptophanyl-transfer ribonucleic acidUnrated tryptophanyl-transfer RNAUnrated tryptophanyl tRNAUnrated tryptophanyl_tRNAUnrated
splice acceptor variant-NMD triggeringUnrated splice_acceptor_variant_NMD_triggeringUnrated splice acceptor variant-nonsense-mediated decay triggeringUnrated
H3R2 dimethylation siteUnrated H3R2_dimethylation_siteUnrated H3R2me2Unrated
insertion breakpointUnrated insertion_breakpointUnrated
ModGluUnrated modified L glutamic acidUnrated modified L-glutamic acidUnrated modified_L_glutamic_acidUnrated
HUnrated HisUnrated histidineUnrated
transgenicUnrated
D geneUnrated D-GENEUnrated D_gene_segmentUnrated INSDC_feature:D_segmentUnrated
duplicationUnrated nucleotide duplicationUnrated
possible base call errorUnrated possible_base_call_errorUnrated
chromosome variationUnrated chromosome_variationUnrated
transcription pause siteUnrated transcription_pause_siteUnrated
engineered transposable elementUnrated engineered_transposable_elementUnrated
TECUnrated to_be_experimentally_confirmed_transcriptUnrated unconfirmed_transcriptUnrated
INSDC_qualifier:SRP_RNAUnrated SRP RNAUnrated SRP_RNAUnrated
translated processed pseudogeneUnrated translated_processed_pseudogeneUnrated
small nucleolar RNA U3Unrated snoRNA U3Unrated U3 small nucleolar RNAUnrated U3 snoRNAUnrated U3_snoRNAUnrated
uninverted intrachromosomal transpositionUnrated uninverted_intrachromosomal_transpositionUnrated
SRP RNA primary transcriptUnrated SRP_RNA_primary_transcriptUnrated
silenced by histone deacetylationUnrated silenced_by_histone_deacetylationUnrated
purine to pyrimidine transversionUnrated purine_to_pyrimidine_transversionUnrated
tRNA primary transcriptUnrated tRNA_primary_transcriptUnrated
tasiRNA primary transcriptUnrated tasiRNA_primary_transcriptUnrated
rate of transcription variantUnrated rate_of_transcription_variantUnrated
complex chromosomal rearrangementUnrated complex_chromosomal_rearrangementUnrated
NMD triggering variantUnrated NMD_triggering_variantUnrated nonsense-mediated decay triggering variantUnrated
pre-miRNAUnrated pre_miRNAUnrated
decreased_transcript_stability_variantUnrated decrease transcript stability variantUnrated
inframeUnrated
cassette pseudogeneUnrated cassette_pseudogeneUnrated
coding-synonUnrated Jannovar:synonymous_variantUnrated Seattleseq:synonymousUnrated snpEff:SYNONYMOUS_CODINGUnrated synonymous_codingUnrated synonymous codonUnrated synonymous_codonUnrated synonymous_variantUnrated VAAST:synonymous_codonUnrated VAAST:synonymous_variantUnrated VAT:synonymousUnrated VEP:synonymous_variantUnrated
T3 RNA Polymerase PromoterUnrated T3_RNA_Polymerase_PromoterUnrated
TFRS collectionUnrated TFRS_collectionUnrated transcription factor regulatory site collectionUnrated
VUnrated ValUnrated valineUnrated
3' restriction enzyme junctionUnrated three_prime_restriction_enzyme_junctionUnrated
silenced by DNA modificationUnrated silenced_by_DNA_modificationUnrated
PRE binding RNAUnrated pumilio response elementUnrated pumilio_response_elementUnrated
intramembrane polypeptide regionUnrated intramembrane_polypeptide_regionUnrated
proplastid geneUnrated proplastid_geneUnrated
inverted ring chromosomeUnrated inverted_ring_chromosomeUnrated
vertebrate immune system gene recombination spacerUnrated vertebrate_immune_system_gene_recombination_spacerUnrated
coding region of exonUnrated coding_region_of_exonUnrated
deficient interchromosomal transpositionUnrated deficient_interchromosomal_transpositionUnrated
5_prime_UTR_premature_start_codon_loss_variantUnrated
modified amino acid featureUnrated modified_amino_acid_featureUnrated
J nonamerUnrated J_nonamerUnrated J-NONAMERUnrated
antisense_lncRNAUnrated natural antisense transcriptUnrated
five_prime_RSTUnrated
encodes alternate transcription start sitesUnrated encodes_alternate_transcription_start_sitesUnrated
LINE1_insertionUnrated
unoriented insertional duplicationUnrated unoriented_insertional_duplicationUnrated

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