The feature keys used and recommended for DDBJ submissions are as follows.
For further information of INSDC feature keys, read Feature Table Definition: 7.2 Appendix II: Feature keys reference.
Feature/Qualifier Usage Matrix
The chart below explains recommended combinations of feature and qualifier keys for DDBJ submissions.
Feature/Qualifier usage matrix (November 9, 2016)
For more detail of available combinations of feature and qualifier keys in INSDC entries, read: Feature Table Definition: 7.2 Appendix II: Feature keys reference.
Definition of Feature key
- assembly_gapFeature Table Definition
- gap between two components of a genome or transcriptome assembly
- C_regionFeature Table Definition
- Constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.
Includes one or more exons depending on the particular chain.
- CDSFeature Table Definition
- coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon).
See also the page about CDS feature.
- centromereFeature Table Definition
- region of biological interest identified as a centromere and which has been experimentally characterized
- D-loopFeature Table Definition
- displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region;
also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein
- D_segmentFeature Table Definition
- Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain.
- exonFeature Table Definition
- region of genome that codes for portion of spliced mRNA, rRNA and tRNA
- gapFeature Table Definition
- gap in the sequence; sequencing gap other than assembly_gap
- intronFeature Table Definition
- a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it
- J_segmentFeature Table Definition
- Joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.
- mat_peptideFeature Table Definition
- mature peptide or protein coding sequence; coding sequence for the mature or final peptide or protein product following post-translational modification.
The location does not include the stop codon (unlike the corresponding CDS)
- misc_bindingFeature Table Definition
- site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other binding key (primer_bind or protein_bind)
- misc_differenceFeature Table Definition
- feature sequence is different from that presented in the entry and cannot be described by any other "difference" key;
The misc_difference feature should be used to describe variability that arises as a result of genetic manipulation (e.g. site directed mutagenesis).
- misc_featureFeature Table Definition
- region of biological interest which cannot be described by any other feature key; a new or rare feature.
- misc_RNAFeature Table Definition
- any transcript or RNA product that cannot be defined by other RNA keys
prim_transcript, precursor_RNA, mRNA, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, ncRNA, rRNA, tRNA, tmRNA
- misc_structureFeature Table Definition
- any secondary or tertiary nucleotide structure or conformation that cannot be described by other "Structure" keys;
- mobile_elementFeature Table Definition
- region of genome sequence containing mobile element
- modified_baseFeature Table Definition
- the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)
- mRNAFeature Table Definition
- messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR)
- ncRNAFeature Table Definition
- a non-protein-coding gene, other than ribosomal RNA (rRNA) and transfer RNA (tRNA), the functional molecule of which is the RNA transcript
- operonFeature Table Definition
- region containing polycistronic transcript including a cluster of genes that are under the control of the same regulatory sequences/promoter and in the same biological pathway
- oriTFeature Table Definition
- iorigin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization
- precursor_RNAFeature Table Definition
- any RNA species that is not yet the mature RNA product
- primer_bindFeature Table Definition
- Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. Includes site(s) for synthetic e.g., PCR primer elements
- propeptideFeature Table Definition
- propeptide coding sequence; coding sequence for the domain of a proprotein that is cleaved to form the mature protein product.
- protein_bindFeature Table Definition
- non-covalent protein binding site on nucleic acid
- regulatoryFeature Table Definition
- any region of sequence that functions in the regulation of transcription or translation
Since December 2014, the following old features have been merged into this feature.
- repeat_regionFeature Table Definition
- region of genome containing repeating units
- rep_originFeature Table Definition
- origin of replication; starting site for duplication of nucleic acid to give two identical copies
- rRNAFeature Table Definition
- mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins
- sig_peptideFeature Table Definition
- signal peptide coding sequence; coding sequence for an N-terminal domain of a secreted protein;
this domain is involved in attaching nascent polypeptide to the membrane; leader sequence
- sourceFeature Table Definition
- identifies the biological source of the specified span of the sequence.
This key is mandatory. Every entry will have, as a minimum, a single source key spanning the entire sequence.
More than one source key per sequence is permissible
- stem_loopFeature Table Definition
- hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA
- telomereFeature Table Definition
- region of biological interest identified as a telomere and which has been experimentally characterized
- tmRNAFeature Table Definition
- transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag;
the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein;
this attached tag targets the protein for destruction or proteolysis;
- transit_peptideFeature Table Definition
- transit peptide coding sequence; 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
- tRNAFeature Table Definition
- mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence
- unsureFeature Table Definition
- A small region of sequenced bases, generally 10 or fewer in its length, which could not be confidently identified.
- V_regionFeature Table Definition
- Variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains. Codes for the variable amino terminal portion. Can be made up from V_segments, D_segments, N_regions and J_segments.
- V_segmentFeature Table Definition
- Variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains. Codes for most of the variable region (V_region) and the last few amino acids of the leader peptide
- variationFeature Table Definition
- a related strain contains stable mutations from the same gene (e.g., RFLPs, polymorphisms, etc.) which differ from the presented sequence at this location (and possibly others).
- 3'UTRFeature Table Definition
- 1) region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein;
2) region at the 3' end of an RNA virus (following the last stop codon) that is not translated into a protein;
- 5'UTRFeature Table Definition
- 1) region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein;
2) region at the 5' end of an RNA virus genome (preceding the first initiation codon) that is not translated into a protein;