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
AUnrated AlaUnrated alanineUnrated
DNA spacer replication fork barrierUnrated rDNA replication fork barrierUnrated rDNA_replication_fork_barrierUnrated RFBUnrated RTS1 barrierUnrated RTS1 elementUnrated
polyadenylatedUnrated
gDNA contigUnrated gDNA_contigUnrated genomic DNA contigUnrated genomic_DNA_contigUnrated
dye_terminator_readUnrated
metal_binding_siteUnrated
T_cell_receptor_pseudogeneUnrated
oncogenic_variantUnrated
IGSUnrated internal guide sequenceUnrated internal_guide_sequenceUnrated
H3K4 di-methylation siteUnrated H3K4_dimethylation_siteUnrated
U2 intronUnrated U2_intronUnrated
episomeUnrated
silenced geneUnrated silenced_geneUnrated
shRNA primary transcriptUnrated shRNA_primary_transcriptUnrated
INSDC_qualifier:non_allelic_homologousUnrated INSDC_qualifier:non_allelic_homologous_recombinationUnrated NAHRRUnrated non allelic homologous recombination regionUnrated non_allelic_homologous_recombination_regionUnrated
CAGE tagUnrated CAGE_tagUnrated
bound by factorUnrated bound_by_factorUnrated
INSDC_qualifier:unprocessedUnrated unprocessed pseudogenic tRNAUnrated unprocessed_pseudogenic_tRNAUnrated
5-carboxymethyluridineUnrated cm5UUnrated five carboxymethyluridineUnrated five_carboxymethyluridineUnrated
structural interaction variantUnrated structural_interaction_variantUnrated
pseudouridylation guide snoRNAUnrated pseudouridylation_guide_snoRNAUnrated
J gene recombination featureUnrated J_gene_recombination_featureUnrated J-RSUnrated
lincRNA geneUnrated lincRNA_geneUnrated
AFLPUnrated AFLP fragmentUnrated AFLP_fragmentUnrated AFLP-PCRUnrated amplified fragment length polymorphismUnrated amplified fragment length polymorphism PCRUnrated
allelic_frequencyUnrated
anchor binding siteUnrated anchor_binding_siteUnrated
Mat2PUnrated
Penelope retrotransposonUnrated Penelope_retrotransposonUnrated RPP retrotransposonUnrated
D-boxUnrated destruction boxUnrated destruction_boxUnrated
wild type rescue geneUnrated wild_type_rescue_geneUnrated
U3 long terminal repeat regionUnrated U3 LTR regionUnrated U3_LTR_regionUnrated
three_prime_gene_fusionUnrated
minus 2 frameshiftUnrated minus_2_frameshiftUnrated
assemblyUnrated
SL5 acceptor siteUnrated SL5_acceptor_siteUnrated
small nuclear RNA geneUnrated snRNA geneUnrated snRNA_geneUnrated
centric-fusion translocationsUnrated Robertsonian fusionUnrated Robertsonian_fusionUnrated whole-arm translocationsUnrated
noncoding exonUnrated noncoding_exonUnrated
geneUnrated INSDC_feature:geneUnrated
upstream transcript variantUnrated upstream_transcript_variantUnrated
duplication_attributeUnrated
complex substitutionUnrated complex_substitutionUnrated
stemUnrated stem portion of stem loopUnrated
H3K4 mono-methylation siteUnrated H3K4_monomethylation_siteUnrated
peptide_helixUnrated
open chromatin regionUnrated open_chromatin_regionUnrated
Bel Pao LTR retrotransposonUnrated Bel-Pao LTR retrotransposonUnrated Bel_Pao_LTR_retrotransposonUnrated RLB retrotransposonUnrated
modified L prolineUnrated modified L-proline Unrated modified_L_prolineUnrated ModProUnrated
predicted geneUnrated predicted_geneUnrated
CDS supported by domain match dataUnrated CDS_supported_by_domain_match_dataUnrated
polypeptide catalytic motifUnrated polypeptide_catalytic_motifUnrated
functional gene regionUnrated functional_gene_regionUnrated
chromoplast sequenceUnrated chromoplast_sequenceUnrated
classical pseudoknotUnrated hairpin-type pseudoknotUnrated H pseudoknotUnrated H-pseudoknotUnrated H_pseudoknotUnrated H-type pseudoknotUnrated
kinetoplast geneUnrated kinetoplast_geneUnrated
mitochondrial large subunit rRNAUnrated mitochondrial LSU rRNAUnrated mt_LSU_rRNAUnrated MT LSU rRNAUnrated
4-demethylwyosineUnrated four demethylwyosineUnrated four_demethylwyosineUnrated imG-14Unrated
H3K4 methylation siteUnrated H3K4_methylation_siteUnrated
overlapping EST setUnrated overlapping_EST_setUnrated
SVA deletionUnrated SVA_deletionUnrated
blunt_end_restriction_enzyme_cleavage_junctionUnrated
methylation guide snoRNA geneUnrated methylation_guide_snoRNA_geneUnrated
transcriptionally constitutiveUnrated transcriptionally_constitutiveUnrated
wild typeUnrated wild_typeUnrated
pathogenic islandUnrated pathogenic_islandUnrated
crypticUnrated
protein altering variantUnrated protein_altering_variantUnrated VEP:protein_altering_variantUnrated
complex change in transcriptUnrated complex_indelUnrated complex transcript variantUnrated complex_transcript_variantUnrated
disruptive decrease in CDS lengthUnrated disruptive inframe deletionUnrated disruptive_inframe_deletionUnrated Jannovar:disruptive_inframe_deletionUnrated snpEff:CODON_CHANGE_PLUS_CODON_DELETIONUnrated
monocistronicUnrated
2S rRNA geneUnrated cytosolic_rRNA_2S_geneUnrated rRNA 2S geneUnrated
ARSUnrated autonomously replicating sequenceUnrated
sticky_end_restriction_enzyme_cleavage_siteUnrated
dif siteUnrated dif_siteUnrated
V DJ C clusterUnrated V_DJ_C_clusterUnrated V-(DJ)-C-CLUSTERUnrated
complex change of translational product variantUnrated complex_change_of_translational_product_variantUnrated
independently knownUnrated independently_knownUnrated
translation regulatory regionUnrated translation_regulatory_regionUnrated
ANNOVAR:stoplossUnrated Jannovar:stop_lostUnrated Seattleseq:stop-lostUnrated snpEff:STOP_LOSTUnrated stop codon lostUnrated stop lostUnrated stop_lostUnrated VAAST:stop_lostUnrated VAT:removedStopUnrated VEP:stop_lostUnrated
enzymatic RNAUnrated enzymatic_RNAUnrated
acceptor splice siteUnrated splice acceptor siteUnrated three_prime_cis_splice_siteUnrated three prime splice siteUnrated
gene trap constructUnrated gene_trap_constructUnrated
polycistronicUnrated
cis regulatory moduleUnrated cis_regulatory_moduleUnrated CRMUnrated TF moduleUnrated transcription factor moduleUnrated
gene with stop codon redefined as pyrrolysineUnrated gene_with_stop_codon_redefined_as_pyrrolysineUnrated
V J C clusterUnrated V_J_C_clusterUnrated V-J-C-CLUSTERUnrated
copy number increaseUnrated copy_number_increaseUnrated
5' intronUnrated 5' intron sequenceUnrated five prime intronUnrated five_prime_intronUnrated
vertebrate immunoglobulin T cell receptor rearranged gene clusterUnrated vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_clusterUnrated
three prime repeat recoding signalUnrated three_prime_repeat_recoding_signalUnrated
statusUnrated
7-aminomethyl-7-deazaguanosineUnrated preQ1Unrated seven aminomethyl seven deazaguanosineUnrated seven_aminomethyl_seven_deazaguanosineUnrated
terminal inverted repeatUnrated terminal_inverted_repeatUnrated TIRUnrated
INSDC_feature:protein_bindUnrated protein binding siteUnrated protein_binding_siteUnrated
multiplexing sequence identifierUnrated multiplexing_sequence_identifierUnrated
T to G transversionUnrated T_to_G_transversionUnrated
translocation breakpointUnrated translocation_breakpointUnrated
snRNA encodingUnrated snRNA_encodingUnrated
direct repeatUnrated direct_repeatUnrated INSDC_qualifier:directUnrated
lambda vectorUnrated lambda_vectorUnrated

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