| created from: /Users/kareneilbeck/cvs/SO/ontology/so-xp.obo |
| format-version: 1.2 |
| date: 14:08:2006 16:22 |
| saved-by: kareneilbeck |
| default-namespace: sequence |
| remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ |
C_D_box_snoRNA_encoding |
SO:0000585 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: C_D_box_snoRNA_encoding is_a snoRNA_encoding |
Child relationships: |
DNA |
SO:0000352 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: DNA is_a nucleic_acid |
Child relationships: |
FRT_flanked |
SO:0000361 |
| Definition: An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: FRT_flanked is_a flanked |
Child relationships: |
H_ACA_box_snoRNA_encoding |
SO:0000608 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: H_ACA_box_snoRNA_encoding is_a snoRNA_encoding |
Child relationships: |
RNA |
SO:0000356 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: RNA is_a nucleic_acid |
Child relationships: |
SRP_RNA_encoding |
SO:0000642 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: SRP_RNA_encoding is_a non_protein_coding |
Child relationships: |
allelically_excluded |
SO:0000137 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: allelically_excluded is_a epigenetically_modified |
Child relationships: |
alternatively_spliced |
SO:0000877 |
| Definition: An attribute describing a situation where a gene may encode for more than 1 transcript. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: alternatively_spliced is_a transcript_attribute |
Child relationships: |
antisense |
SO:0000077 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: antisense is_a overlapping |
Child relationships: |
apicoplast_sequence |
SO:0000743 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: apicoplast_sequence is_a plastid_sequence |
Child relationships: |
archeal_intron |
SO:1001271 |
| Definition: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism. | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: archeal_intron is_a intron_attribute |
Child relationships: |
autoregulated |
SO:0000471 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: autoregulated is_a transcriptionally_regulated |
Child relationships: negatively_autoregulated is_a autoregulated positively_autoregulated is_a autoregulated |
bound_by_factor |
SO:0000277 |
| Definition: An attribute describing a sequence that is bound by another molecule. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: bound_by_factor is_a feature_attribute |
Child relationships: bound_by_protein is_a bound_by_factor bound_by_nucleic_acid is_a bound_by_factor |
bound_by_nucleic_acid |
SO:0000876 |
| Definition: An attribute describing a sequence that is bound by a nucleic acid. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: bound_by_nucleic_acid is_a bound_by_factor |
Child relationships: |
bound_by_protein |
SO:0000875 |
| Definition: An attribute describing a sequence that is bound by a protein. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: bound_by_protein is_a bound_by_factor |
Child relationships: |
cDNA |
SO:0000756 |
| Definition: DNA synthesized by reverse transcriptase using RNA as a template | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cDNA is_a nucleic_acid |
Child relationships: double_stranded_cDNA is_a cDNA single_stranded_cDNA is_a cDNA |
capped |
SO:0000146 |
| Definition: An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: capped is_a transcript_attribute |
Child relationships: |
cassette_array_member |
SO:0005847 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cassette_array_member is_a gene_cassette_member |
Child relationships: |
chloroplast_sequence |
SO:0000745 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: chloroplast_sequence is_a plastid_sequence |
Child relationships: |
chromoplast_sequence |
SO:0000744 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: chromoplast_sequence is_a plastid_sequence |
Child relationships: |
cloned |
SO:0000788 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cloned is_a reagent_attribute |
Child relationships: cloned_cDNA is_a cloned cloned_genomic is_a cloned |
cloned_cDNA |
SO:0000792 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cloned_cDNA is_a cloned |
Child relationships: |
cloned_genomic |
SO:0000791 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cloned_genomic is_a cloned |
Child relationships: |
codon_redefined |
SO:0000882 |
| Definition: An attribute describing the alteration of codon meaning. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: codon_redefined is_a recoded |
Child relationships: stop_codon_read_through is_a codon_redefined |
conserved |
SO:0000856 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: conserved is_a feature_attribute |
Child relationships: homologous is_a conserved syntenic is_a conserved |
cryptogene |
SO:1001196 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cryptogene is_a non_protein_coding |
Child relationships: |
cyanelle_sequence |
SO:0000746 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: cyanelle_sequence is_a plastid_sequence |
Child relationships: |
designed_sequence |
SO:0000546 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: designed_sequence is_a synthetic_sequence |
Child relationships: |
dicistronic |
SO:0000879 |
| Definition: An attribute describing a sequence that contains the code for two gene products. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: dicistronic is_a polycistronic |
Child relationships: |
double_stranded_cDNA |
SO:0000758 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: double_stranded_cDNA is_a cDNA |
Child relationships: |
edited |
SO:0000116 |
| Definition: An attribute describing a sequence that is modified by editing | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: edited is_a transcript_attribute |
Child relationships: |
encodes_1_polypeptide |
SO:1001188 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_1_polypeptide is_a encodes_alternately_spliced_transcripts |
Child relationships: |
encodes_alternately_spliced_transcripts |
SO:0000463 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_alternately_spliced_transcripts is_a gene_attribute |
Child relationships: encodes_1_polypeptide is_a encodes_alternately_spliced_transcripts encodes_greater_than_1_polypeptide is_a encodes_alternately_spliced_transcripts |
encodes_different_polypeptides_different_stop |
SO:1001190 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_different_polypeptides_different_stop is_a encodes_overlapping_peptides |
Child relationships: |
encodes_disjoint_polypeptides |
SO:1001192 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_disjoint_polypeptides is_a encodes_greater_than_1_polypeptide |
Child relationships: |
encodes_greater_than_1_polypeptide |
SO:1001189 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_greater_than_1_polypeptide is_a encodes_alternately_spliced_transcripts |
Child relationships: encodes_disjoint_polypeptides is_a encodes_greater_than_1_polypeptide encodes_overlapping_peptides is_a encodes_greater_than_1_polypeptide |
encodes_overlapping_peptides |
SO:1001195 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_overlapping_peptides is_a encodes_greater_than_1_polypeptide |
Child relationships: encodes_overlapping_polypeptides_different_start_and_stop is_a encodes_overlapping_peptides encodes_overlapping_peptides_different_start is_a encodes_overlapping_peptides encodes_different_polypeptides_different_stop is_a encodes_overlapping_peptides |
encodes_overlapping_peptides_different_start |
SO:1001191 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_overlapping_peptides_different_start is_a encodes_overlapping_peptides |
Child relationships: |
encodes_overlapping_polypeptides_different_start_and_stop |
SO:1001193 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: encodes_overlapping_polypeptides_different_start_and_stop is_a encodes_overlapping_peptides |
Child relationships: |
endogenous_retroviral_sequence |
SO:0000903 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: endogenous_retroviral_sequence is_a proviral_sequence |
Child relationships: |
engineered |
SO:0000783 |
| Definition: An attribute to describe a region that was modified in vitro. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: engineered is_a feature_attribute |
Child relationships: |
epigenetically_modified |
SO:0000133 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: epigenetically_modified is_a gene_attribute |
Child relationships: allelically_excluded is_a epigenetically_modified rearranged_at_DNA_level is_a epigenetically_modified imprinted is_a epigenetically_modified |
exemplar |
SO:0000864 |
| Definition: An attribute describing a sequence is reprsentative of a class of similar sequences. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: exemplar is_a mRNA_attribute |
Child relationships: |
experimentally_determined |
SO:0000312 |
| Definition: Attribute to describe a feature that has been experiemntally verified. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: experimentally_determined is_a validated |
Child relationships: |
feature_attribute |
SO:0000733 |
| Definition: An attribute describing a located_sequence_feature. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: feature_attribute is_a sequence_attribute |
Child relationships: gene_attribute is_a feature_attribute transcript_attribute is_a feature_attribute pseudogene_attribute is_a feature_attribute foreign is_a feature_attribute intermediate is_a feature_attribute wild_type is_a feature_attribute flanked is_a feature_attribute transgenic is_a feature_attribute engineered is_a feature_attribute conserved is_a feature_attribute intron_attribute is_a feature_attribute reagent_attribute is_a feature_attribute recombinationally_rearranged is_a feature_attribute bound_by_factor is_a feature_attribute fusion is_a feature_attribute status is_a feature_attribute natural is_a feature_attribute rescue is_a feature_attribute |
five_prime_five_prime_overlap |
SO:0000074 |
| Definition: An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: five_prime_five_prime_overlap is_a overlapping |
Child relationships: |
five_prime_three_prime_overlap |
SO:0000073 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: five_prime_three_prime_overlap is_a overlapping |
Child relationships: |
flanked |
SO:0000357 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: flanked is_a feature_attribute |
Child relationships: FRT_flanked is_a flanked floxed is_a flanked |
floxed |
SO:0000359 |
| Definition: An attribute describing sequence that is flanked by Lox-P sites. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: floxed is_a flanked |
Child relationships: |
foreign |
SO:0000784 |
| Definition: An atrribute to describe a region from another species. | |
| DBxref:SO:ke | |
| Synonyms: [foreign_transposable_element] | |
| Aspect: sequence_attribute | |
| Parent relationships: foreign is_a feature_attribute |
Child relationships: |
fragment |
SO:0000731 |
| Definition: An attribute to describe a feature that is incomplete. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: fragment is_a status |
Child relationships: |
frameshift |
SO:0000865 |
| Definition: An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: frameshift is_a mRNA_attribute |
Child relationships: minus_1_frameshift is_a frameshift plus_1_frameshift is_a frameshift minus_2_frameshift is_a frameshift plus_2_framshift is_a frameshift |
fusion |
SO:0000806 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: fusion is_a feature_attribute |
Child relationships: |
gene_array_member |
SO:0000081 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: [gene_array_member] | |
| Aspect: sequence_attribute | |
| Parent relationships: gene_array_member is_a gene_attribute |
Child relationships: gene_subarray_member is_a gene_array_member gene_cassette_member is_a gene_array_member operon_member is_a gene_array_member member_of_regulon is_a gene_array_member |
gene_attribute |
SO:0000401 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: gene_attribute is_a feature_attribute |
Child relationships: gene_to_gene_feature is_a gene_attribute gene_array_member is_a gene_attribute regulated is_a gene_attribute non_protein_coding is_a gene_attribute protein_coding is_a gene_attribute epigenetically_modified is_a gene_attribute encodes_alternately_spliced_transcripts is_a gene_attribute |
gene_cassette_member |
SO:0005848 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: gene_cassette_member is_a gene_array_member |
Child relationships: cassette_array_member is_a gene_cassette_member |
gene_subarray_member |
SO:0005849 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: gene_subarray_member is_a gene_array_member |
Child relationships: |
gene_to_gene_feature |
SO:0000067 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: gene_to_gene_feature is_a gene_attribute |
Child relationships: overlapping is_a gene_to_gene_feature |
homologous |
SO:0000857 |
| Definition: Similarity due to common ancestry. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: homologous is_a conserved |
Child relationships: paralogous is_a homologous orthologous is_a homologous |
imprinted |
SO:0000134 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: imprinted is_a regulated imprinted is_a epigenetically_modified |
Child relationships: paternally_imprinted is_a imprinted maternally_imprinted is_a imprinted |
independently_known |
SO:0000906 |
| Definition: Attribute to describe a feature that is independently_known - not predicted. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: independently_known is_a status |
Child relationships: |
inside_intron |
SO:0000069 |
| Definition: An attribute to describe a gene when it is located within the intron of another gene. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: inside_intron is_a overlapping |
Child relationships: inside_intron_antiparallel is_a inside_intron inside_intron_parallel is_a inside_intron |
inside_intron_antiparallel |
SO:0000070 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: inside_intron_antiparallel is_a inside_intron |
Child relationships: |
inside_intron_parallel |
SO:0000071 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: inside_intron_parallel is_a inside_intron |
Child relationships: |
intein_containing |
SO:0000729 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: intein_containing is_a protein_coding |
Child relationships: |
intermediate |
SO:0000933 |
| Definition: An attribute to describe a feature between stages of processing. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: intermediate is_a feature_attribute |
Child relationships: |
intron_attribute |
SO:0000661 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: intron_attribute is_a feature_attribute |
Child relationships: archeal_intron is_a intron_attribute mobile_intron is_a intron_attribute tRNA_intron is_a intron_attribute |
invalidated |
SO:0000790 |
| Definition: An attribute describing a feature that is invalidated. | |
| DBxref:SO:ke | |
| Synonyms: [invalidated_clone] | |
| Aspect: sequence_attribute | |
| Parent relationships: invalidated is_a status |
Child relationships: invalidated_by_genomic_polyA_primed_cDNA is_a invalidated invalidated_by_chimeric_cDNA is_a invalidated invalidated_by_partial_processing is_a invalidated invalidated_by_genomic_contamination is_a invalidated |
invalidated_by_chimeric_cDNA |
SO:0000362 |
| Definition: A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: invalidated_by_chimeric_cDNA is_a invalidated |
Child relationships: |
invalidated_by_genomic_contamination |
SO:0000414 |
| Definition: An attribue to describe a feature that is invalidated due to genomic contamination. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: invalidated_by_genomic_contamination is_a invalidated |
Child relationships: |
invalidated_by_genomic_polyA_primed_cDNA |
SO:0000415 |
| Definition: An attribue to describe a feature that is invalidated due to polyA priming. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: invalidated_by_genomic_polyA_primed_cDNA is_a invalidated |
Child relationships: |
invalidated_by_partial_processing |
SO:0000416 |
| Definition: An attribue to describe a feature that is invalidated due to partial processing. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: invalidated_by_partial_processing is_a invalidated |
Child relationships: |
kinetoplast_sequence |
SO:0000741 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: kinetoplast_sequence is_a mitochondrial_sequence |
Child relationships: |
leucoplast_sequence |
SO:0000747 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: leucoplast_sequence is_a plastid_sequence |
Child relationships: |
mRNA_attribute |
SO:0000863 |
| Definition: An attribute describing an mRNA feature. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: mRNA_attribute is_a transcript_attribute |
Child relationships: exemplar is_a mRNA_attribute frameshift is_a mRNA_attribute recoded is_a mRNA_attribute polyadenylated is_a mRNA_attribute |
macronuclear_sequence |
SO:0000083 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: macronuclear_sequence is_a organelle_location |
Child relationships: |
maternally_imprinted |
SO:0000135 |
| Definition: An attribute to describe genes that are regulated by maternal imprinting. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: maternally_imprinted is_a imprinted |
Child relationships: |
maxicircle_sequence |
SO:0000742 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: maxicircle_sequence is_a mitochondrial_sequence |
Child relationships: |
member_of_regulon |
SO:1001217 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: member_of_regulon is_a gene_array_member |
Child relationships: |
miRNA_encoding |
SO:0000571 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: miRNA_encoding is_a non_protein_coding |
Child relationships: |
micronuclear_sequence |
SO:0000084 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: micronuclear_sequence is_a organelle_location |
Child relationships: |
minus_1_frameshift |
SO:0000866 |
| Definition: A frameshift caused by deleting one base | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: minus_1_frameshift is_a frameshift |
Child relationships: |
minus_1_translational_frameshift |
SO:1001262 |
| Definition: An attribute describing a translational frameshift of -1. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: minus_1_translational_frameshift is_a translational_frameshift |
Child relationships: |
minus_2_frameshift |
SO:0000867 |
| Definition: A frameshift caused by deleting two bases | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: minus_2_frameshift is_a frameshift |
Child relationships: |
mitochondrial_sequence |
SO:0000737 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: mitochondrial_sequence is_a organelle_location |
Child relationships: maxicircle_sequence is_a mitochondrial_sequence kinetoplast_sequence is_a mitochondrial_sequence |
mobile_intron |
SO:0000666 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: mobile_intron is_a intron_attribute |
Child relationships: |
monocistronic |
SO:0000878 |
| Definition: An attribute describing a sequence that contains the code for one gene product. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: monocistronic is_a transcript_attribute |
Child relationships: |
natural |
SO:0000782 |
| Definition: An attribute describing a feature that occurs in nature. | |
| DBxref:SO:ke | |
| Synonyms: [natural_transposable_element] | |
| Aspect: sequence_attribute | |
| Parent relationships: natural is_a feature_attribute |
Child relationships: |
negatively_autoregulated |
SO:0000473 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: negatively_autoregulated is_a transcriptionally_repressed negatively_autoregulated is_a autoregulated |
Child relationships: |
non_protein_coding |
SO:0000011 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: non_protein_coding is_a gene_attribute |
Child relationships: miRNA_encoding is_a non_protein_coding cryptogene is_a non_protein_coding tmRNA_encoding is_a non_protein_coding snRNA_encoding is_a non_protein_coding snoRNA_encoding is_a non_protein_coding scRNA_encoding is_a non_protein_coding stRNA_encoding is_a non_protein_coding SRP_RNA_encoding is_a non_protein_coding tRNA_encoding is_a non_protein_coding rRNA_encoding is_a non_protein_coding |
nuclear_mitochondrial |
SO:0000899 |
| Definition: An attribute describing a nuclear pseudogene of a mitochndrial gene. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: nuclear_mitochondrial is_a pseudogene_attribute |
Child relationships: |
nuclear_sequence |
SO:0000738 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: nuclear_sequence is_a organelle_location |
Child relationships: |
nucleic_acid |
SO:0000348 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: nucleic_acid is_a polymer_type |
Child relationships: cDNA is_a nucleic_acid RNA is_a nucleic_acid DNA is_a nucleic_acid |
nucleomorphic_sequence |
SO:0000739 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: nucleomorphic_sequence is_a organelle_location |
Child relationships: |
operon_member |
SO:0000080 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: operon_member is_a gene_array_member |
Child relationships: |
organelle_location |
SO:0000736 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: organelle_location is_a sequence_location |
Child relationships: nucleomorphic_sequence is_a organelle_location nuclear_sequence is_a organelle_location micronuclear_sequence is_a organelle_location macronuclear_sequence is_a organelle_location plastid_sequence is_a organelle_location mitochondrial_sequence is_a organelle_location |
orphan |
SO:0000910 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: orphan is_a predicted |
Child relationships: |
orthologous |
SO:0000858 |
| Definition: A kind of homology where divergence occured after a speciation event. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: orthologous is_a homologous |
Child relationships: |
overlapping |
SO:0000068 |
| Definition: An attribute describing a gene that has sequence that overlaps the sequence of another gene. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: overlapping is_a gene_to_gene_feature |
Child relationships: three_prime_three_prime_overlap is_a overlapping inside_intron is_a overlapping five_prime_three_prime_overlap is_a overlapping three_prime_five_prime_overlap is_a overlapping antisense is_a overlapping five_prime_five_prime_overlap is_a overlapping |
paralogous |
SO:0000859 |
| Definition: A kind of homology where divergence occured after a duplication event. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: paralogous is_a homologous |
Child relationships: |
paternally_imprinted |
SO:0000136 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: paternally_imprinted is_a imprinted |
Child relationships: |
plasmid_sequence |
SO:0000749 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: plasmid_sequence is_a sequence_location |
Child relationships: |
plastid_sequence |
SO:0000740 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: plastid_sequence is_a organelle_location |
Child relationships: apicoplast_sequence is_a plastid_sequence leucoplast_sequence is_a plastid_sequence cyanelle_sequence is_a plastid_sequence chromoplast_sequence is_a plastid_sequence proplastid_sequence is_a plastid_sequence chloroplast_sequence is_a plastid_sequence |
plus_1_frameshift |
SO:0000868 |
| Definition: A frameshift caused by inserting one base | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: plus_1_frameshift is_a frameshift |
Child relationships: |
plus_1_translational_frameshift |
SO:1001263 |
| Definition: An attribute describing a translational frameshift of +1. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: plus_1_translational_frameshift is_a translational_frameshift |
Child relationships: |
plus_2_framshift |
SO:0000869 |
| Definition: A frameshift caused by inserting two bases | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: plus_2_framshift is_a frameshift |
Child relationships: |
polyadenylated |
SO:0000246 |
| Definition: A attribute describing the additon of a poly A tail to the 3' end of a mRNA molecule. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: polyadenylated is_a mRNA_attribute |
Child relationships: |
polycistronic |
SO:0000880 |
| Definition: An attribute describing a sequence that contains the code for more than one gene product. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: polycistronic is_a transcript_attribute |
Child relationships: dicistronic is_a polycistronic |
polymer_type |
SO:0000443 |
| Definition: An attribute to describe the kind of biological sequence. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: polymer_type is_a sequence_attribute |
Child relationships: nucleic_acid is_a polymer_type protein is_a polymer_type synthetic_sequence is_a polymer_type |
positively_autoregulated |
SO:0000475 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: positively_autoregulated is_a transcriptionally_induced positively_autoregulated is_a autoregulated |
Child relationships: |
post_translationally_regulated |
SO:0000130 |
| Definition: An attribute describing a gene that is regulated after it has been translated. | |
| DBxref:SO:ke | |
| Synonyms: [post-translationally_regulated] | |
| Aspect: sequence_attribute | |
| Parent relationships: post_translationally_regulated is_a regulated |
Child relationships: post_translationally_regulated_by_protein_modification is_a post_translationally_regulated post_translationally_regulated_by_protein_stability is_a post_translationally_regulated |
post_translationally_regulated_by_protein_modification |
SO:0000469 |
| Definition: An attribute describing a gene sequence where the resulting protein is modified to regulate it. | |
| DBxref:SO:ke | |
| Synonyms: [post-translationally_regulated_by_protein_modification] | |
| Aspect: sequence_attribute | |
| Parent relationships: post_translationally_regulated_by_protein_modification is_a post_translationally_regulated |
Child relationships: |
post_translationally_regulated_by_protein_stability |
SO:0000467 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: [post-translationally_regulated_by_protein_stability] | |
| Aspect: sequence_attribute | |
| Parent relationships: post_translationally_regulated_by_protein_stability is_a post_translationally_regulated |
Child relationships: |
predicted |
SO:0000732 |
| Definition: An attribute describing an unverified region | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: predicted is_a status |
Child relationships: supported_by_sequence_similarity is_a predicted orphan is_a predicted predicted_by_ab_initio_computation is_a predicted |
predicted_by_ab_initio_computation |
SO:0000911 |
| Definition: An attribute describng a feaure that is predticted by a computer program that did not rely on sequence similarity. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: predicted_by_ab_initio_computation is_a predicted |
Child relationships: |
processed |
SO:0000900 |
| Definition: An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed bak inot the genome, lacking introns and promotors, but often including a polyA tail. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: processed is_a pseudogene_attribute |
Child relationships: |
proplastid_sequence |
SO:0000748 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: proplastid_sequence is_a plastid_sequence |
Child relationships: |
protein |
SO:0000358 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: protein is_a polymer_type |
Child relationships: |
protein_coding |
SO:0000010 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: protein_coding is_a gene_attribute |
Child relationships: retrotransposed is_a protein_coding intein_containing is_a protein_coding |
proviral_sequence |
SO:0000751 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: proviral_sequence is_a sequence_location |
Child relationships: endogenous_retroviral_sequence is_a proviral_sequence |
pseudogene_attribute |
SO:0000042 |
| Definition: An attribute of a pseudogene (SO:0000336). | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: pseudogene_attribute is_a feature_attribute |
Child relationships: processed is_a pseudogene_attribute retrotransposed is_a pseudogene_attribute nuclear_mitochondrial is_a pseudogene_attribute unequally_crossed_over is_a pseudogene_attribute |
rRNA_encoding |
SO:0000573 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: rRNA_encoding is_a non_protein_coding |
Child relationships: |
random_sequence |
SO:0000449 |
| Definition: A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequencyof these components. | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: random_sequence is_a synthetic_sequence |
Child relationships: |
reagent_attribute |
SO:0000786 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: reagent_attribute is_a feature_attribute |
Child relationships: cloned is_a reagent_attribute |
rearranged_at_DNA_level |
SO:0000904 |
| Definition: An attribute to describe the sequence of a feature, where the DNA is rearranged. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: rearranged_at_DNA_level is_a epigenetically_modified |
Child relationships: |
recoded |
SO:0000881 |
| Definition: An atribute describing am mRNA sequences that has been reprogrammed at translation, causing localized alterations. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: recoded is_a mRNA_attribute |
Child relationships: codon_redefined is_a recoded recoded_by_translational_bypass is_a recoded translational_frameshift is_a recoded |
recoded_by_translational_bypass |
SO:0000886 |
| Definition: Rcoding mRNA where a block of nucleotides is not translated. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: recoded_by_translational_bypass is_a recoded |
Child relationships: |
recombinationally_rearranged |
SO:0000940 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: recombinationally_rearranged is_a feature_attribute |
Child relationships: |
regulated |
SO:0000119 |
| Definition: An attribute to describe a sequence that is regulated. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: regulated is_a gene_attribute |
Child relationships: translationally_regulated is_a regulated transcriptionally_regulated is_a regulated imprinted is_a regulated post_translationally_regulated is_a regulated |
rescue |
SO:0000814 |
| Definition: An attribute describing a regions ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: rescue is_a feature_attribute |
Child relationships: |
retrotransposed |
SO:0000569 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: [captured_pseudogene] [SO:0100042] | |
| Aspect: sequence_attribute | |
| Parent relationships: retrotransposed is_a protein_coding retrotransposed is_a pseudogene_attribute |
Child relationships: |
scRNA_encoding |
SO:0000575 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: scRNA_encoding is_a non_protein_coding |
Child relationships: |
sequence_location |
SO:0000735 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: sequence_location is_a sequence_attribute |
Child relationships: plasmid_sequence is_a sequence_location proviral_sequence is_a sequence_location organelle_location is_a sequence_location |
silenced |
SO:0000893 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: silenced is_a transcriptionally_repressed |
Child relationships: silenced_by_DNA_modification is_a silenced |
silenced_by_DNA_methylation |
SO:0000895 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: silenced_by_DNA_methylation is_a silenced_by_DNA_modification |
Child relationships: |
silenced_by_DNA_modification |
SO:0000894 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: silenced_by_DNA_modification is_a silenced |
Child relationships: silenced_by_DNA_methylation is_a silenced_by_DNA_modification |
single_stranded_cDNA |
SO:0000757 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: single_stranded_cDNA is_a cDNA |
Child relationships: |
snRNA_encoding |
SO:0000623 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: snRNA_encoding is_a non_protein_coding |
Child relationships: |
snoRNA_encoding |
SO:0000578 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: snoRNA_encoding is_a non_protein_coding |
Child relationships: H_ACA_box_snoRNA_encoding is_a snoRNA_encoding C_D_box_snoRNA_encoding is_a snoRNA_encoding |
stRNA_encoding |
SO:0000656 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: stRNA_encoding is_a non_protein_coding |
Child relationships: |
status |
SO:0000905 |
| Definition: An attribute describing the status of a feature, based on the available evidence. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: status is_a feature_attribute |
Child relationships: validated is_a status fragment is_a status invalidated is_a status independently_known is_a status predicted is_a status |
stop_codon_read_through |
SO:0000883 |
| Definition: A stop codon redefined to be a new amino acid | |
| DBxref:SO:ke | |
| Synonyms: [stop codon readthrough] | |
| Aspect: sequence_attribute | |
| Parent relationships: stop_codon_read_through is_a codon_redefined |
Child relationships: stop_codon_redefined_as_pyrrolysine is_a stop_codon_read_through stop_codon_redefined_as_selenocysteine is_a stop_codon_read_through |
stop_codon_redefined_as_pyrrolysine |
SO:0000884 |
| Definition: A stop codon redefined to be the new amino acid, pyrrolysine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: stop_codon_redefined_as_pyrrolysine is_a stop_codon_read_through |
Child relationships: |
stop_codon_redefined_as_selenocysteine |
SO:0000885 |
| Definition: A stop codon redefined to be the new amino acid, selenocysteine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: stop_codon_redefined_as_selenocysteine is_a stop_codon_read_through |
Child relationships: |
supported_by_EST_or_cDNA |
SO:0000909 |
| Definition: An attribute to describe a feature that has been predicted using sequence smilarity to EST or cDNA data. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: supported_by_EST_or_cDNA is_a supported_by_sequence_similarity |
Child relationships: |
supported_by_domain_match |
SO:0000908 |
| Definition: An attribute to describe a feature that has been predicted using sequence smilarity of a known domain. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: supported_by_domain_match is_a supported_by_sequence_similarity |
Child relationships: |
supported_by_sequence_similarity |
SO:0000907 |
| Definition: An attribute to describe a feature that has been predicted using sequence smilarity techniques. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: supported_by_sequence_similarity is_a predicted |
Child relationships: supported_by_domain_match is_a supported_by_sequence_similarity supported_by_EST_or_cDNA is_a supported_by_sequence_similarity |
syntenic |
SO:0000860 |
| Definition: Attribute describing sequence regions occurring in same order on chromosome of different species. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: syntenic is_a conserved |
Child relationships: |
synthetic_sequence |
SO:0000351 |
| Definition: A sequence of nucleotides or amino acids that has been designed by an experimentor and which may, or may not, correspond with any natural sequence. | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: synthetic_sequence is_a polymer_type |
Child relationships: random_sequence is_a synthetic_sequence designed_sequence is_a synthetic_sequence |
tRNA_encoding |
SO:0000663 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: tRNA_encoding is_a non_protein_coding |
Child relationships: |
tRNA_intron |
SO:1001272 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: tRNA_intron is_a intron_attribute |
Child relationships: |
three_prime_five_prime_overlap |
SO:0000076 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: three_prime_five_prime_overlap is_a overlapping |
Child relationships: |
three_prime_three_prime_overlap |
SO:0000075 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: three_prime_three_prime_overlap is_a overlapping |
Child relationships: |
tmRNA_encoding |
SO:0000659 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: tmRNA_encoding is_a non_protein_coding |
Child relationships: |
trans_spliced |
SO:0000870 |
| Definition: An attribute describing transcript sequence that is created by splicing exons from diferent genes. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: trans_spliced is_a transcript_attribute |
Child relationships: |
transcript_attribute |
SO:0000237 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transcript_attribute is_a feature_attribute |
Child relationships: alternatively_spliced is_a transcript_attribute capped is_a transcript_attribute edited is_a transcript_attribute monocistronic is_a transcript_attribute trans_spliced is_a transcript_attribute polycistronic is_a transcript_attribute mRNA_attribute is_a transcript_attribute |
transcriptionally_constitutive |
SO:0000124 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transcriptionally_constitutive is_a transcriptionally_regulated |
Child relationships: |
transcriptionally_induced |
SO:0000125 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transcriptionally_induced is_a transcriptionally_regulated |
Child relationships: positively_autoregulated is_a transcriptionally_induced |
transcriptionally_regulated |
SO:0000123 |
| Definition: . | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transcriptionally_regulated is_a regulated |
Child relationships: transcriptionally_induced is_a transcriptionally_regulated transcriptionally_repressed is_a transcriptionally_regulated autoregulated is_a transcriptionally_regulated transcriptionally_constitutive is_a transcriptionally_regulated |
transcriptionally_repressed |
SO:0000126 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transcriptionally_repressed is_a transcriptionally_regulated |
Child relationships: negatively_autoregulated is_a transcriptionally_repressed silenced is_a transcriptionally_repressed |
transgenic |
SO:0000781 |
| Definition: Attribute describing sequence that has been integrated with foreign sequence. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: transgenic is_a feature_attribute |
Child relationships: |
translational_frameshift |
SO:0000887 |
| Definition: Recoding by frameshifting a particular site. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: translational_frameshift is_a recoded |
Child relationships: minus_1_translational_frameshift is_a translational_frameshift plus_1_translational_frameshift is_a translational_frameshift |
translationally_regulated |
SO:0000131 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: translationally_regulated is_a regulated |
Child relationships: |
unequally_crossed_over |
SO:0000901 |
| Definition: An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: unequally_crossed_over is_a pseudogene_attribute |
Child relationships: |
validated |
SO:0000789 |
| Definition: An attribute to describe a feature that has been proven. | |
| DBxref:SO:ke | |
| Synonyms: [validated_clone] | |
| Aspect: sequence_attribute | |
| Parent relationships: validated is_a status |
Child relationships: experimentally_determined is_a validated |
wild_type |
SO:0000817 |
| Definition: An attribute describing sequence with the genotype found in nature/or standard laboratory stock | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: sequence_attribute | |
| Parent relationships: wild_type is_a feature_attribute |
Child relationships: |
ARS |
SO:0000436 |
| Definition: A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. | |
| DBxref:SO:ma | |
| Synonyms: [autonomously_replicating_sequence] | |
| Aspect: located_sequence_feature | |
| Parent relationships: ARS is_a region |
Child relationships: |
A_box |
SO:0000619 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: A_box is_a RNApol_III_promotor_type_2_region |
Child relationships: |
A_minor_RNA_motif |
SO:0000022 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: A_minor_RNA_motif is_a asymmetric_RNA_internal_loop |
Child relationships: |
A_to_C_transversion |
SO:1000024 |
| Definition: A transversion from adenine to cytidine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: A_to_C_transversion is_a purine_to_pyrimidine_transversion |
Child relationships: |
A_to_G_transition |
SO:1000015 |
| Definition: A transition of an adenine to a guanine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: A_to_G_transition is_a purine_transition |
Child relationships: |
A_to_T_transversion |
SO:1000025 |
| Definition: A transversion from adenine to thymine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: A_to_T_transversion is_a purine_to_pyrimidine_transversion |
Child relationships: |
BAC |
SO:0000153 |
| Definition: Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. | |
| DBxref:SO:ma | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: BAC is_a vector |
Child relationships: |
BRE_motif |
SO:0000016 |
| Definition: A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. | |
| DBxref:PMID:12651739 | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: BRE_motif is_a RNA_II_promotor_region |
Child relationships: |
B_box |
SO:0000620 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: B_box is_a RNApol_III_promotor_type_2_region |
Child relationships: |
CAAT_signal |
SO:0000172 |
| Definition: Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: CAAT_signal is_a RNA_II_promotor_region |
Child relationships: |
CDS |
SO:0000316 |
| Definition: A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. | |
| DBxref:SO:ma | |
| Synonyms: [coding_sequence] | |
| Aspect: located_sequence_feature | |
| Parent relationships: CDS is_a mRNA_region |
Child relationships: polypeptide derives_from CDS CDS_region part_of CDS |
CDS_region |
SO:0000851 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: CDS_region is_a mRNA_region CDS_region part_of CDS |
Child relationships: coding_end is_a CDS_region coding_start is_a CDS_region |
CTG_start_codon |
SO:1001273 |
| Definition: A non-canonical start codon of sequence CTG. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: CTG_start_codon is_a non_canonical_start_codon |
Child relationships: |
C_D_box_snoRNA |
SO:0000593 |
| Definition: Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. | |
| DBxref:external reference [http:////www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] | |
| Synonyms: [C/D_box_snoRNA] | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_D_box_snoRNA is_a snoRNA |
Child relationships: |
C_D_box_snoRNA_primary_transcript |
SO:0000595 |
| Definition: A primary transcript encoding a small nucleolar RNA of the box C/D family. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_D_box_snoRNA_primary_transcript is_a snoRNA_primary_transcript |
Child relationships: |
C_box |
SO:0000622 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_box is_a RNApol_III_promotor_type_1_region |
Child relationships: |
C_cluster |
SO:0000558 |
| Definition: Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. | |
| DBxref: | |
| Synonyms: [C-CLUSTER] | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_cluster is_a vertebrate_immunoglobulin_T_cell_receptor_gene_cluster |
Child relationships: C_gene part_of C_cluster |
C_gene |
SO:0000478 |
| Definition: Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). | |
| DBxref: | |
| Synonyms: [C_GENE] [constant_gene] | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_gene part_of VJ_J_C_cluster C_gene part_of V_D_DJ_C_cluster C_gene part_of V_VJ_J_C_cluster C_gene part_of VDJ_C_cluster C_gene part_of V_D_J_C_cluster C_gene part_of V_D_DJ_J_C_cluster C_gene part_of D_DJ_C_cluster C_gene part_of V_J_C_cluster C_gene part_of V_DJ_C_cluster C_gene part_of V_VDJ_C_cluster C_gene part_of V_VJ_C_cluster C_gene part_of V_VDJ_J_C_cluster C_gene is_a vertebrate_immunoglobulin_T_cell_receptor_segment C_gene part_of D_DJ_J_C_cluster C_gene part_of VJ_C_cluster C_gene part_of DJ_J_C_cluster C_gene part_of D_J_C_cluster C_gene part_of J_C_cluster C_gene part_of DJ_C_cluster C_gene part_of V_DJ_J_C_cluster C_gene part_of VDJ_J_C_cluster C_gene part_of C_cluster |
Child relationships: |
C_to_A_transversion |
SO:1000019 |
| Definition: A transversion from cytidine to adenine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_to_A_transversion is_a pyrimidine_to_purine_transversion |
Child relationships: |
C_to_G_transversion |
SO:1000020 |
| Definition: undefined | |
| DBxref: | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_to_G_transversion is_a pyrimidine_to_purine_transversion |
Child relationships: |
C_to_T_transition |
SO:1000011 |
| Definition: A transition of a cytidine to a thymine. | |
| DBxref:SO:ke | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_to_T_transition is_a pyrimidine_transition |
Child relationships: C_to_T_transition_at_pCpG_site is_a C_to_T_transition |
C_to_T_transition_at_pCpG_site |
SO:1000012 |
| Definition: The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. | |
| DBxref:external reference [http:////www.ebi.ac.uk/mutations/recommendations/mutevent.html] | |
| Synonyms: | |
| Aspect: located_sequence_feature | |
| Parent relationships: C_to_T_transition_at_pCpG_site is_a C_to_T_transition |
Child relationships: |
CpG_island |
SO:0000307 |
| Definition: Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. | |
| DBxref:SO:rd | |
| Synonyms: [CG_island] | |
| Aspect: located_sequence_feature | |
| Parent relationships: CpG_island is_a region |
Child relationships: |