Last updated:2014.11.21.

Definition of Feature Key

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.

assembly_gap C_region CDS centromere D-loop D_segment
enhancer exon gap intron J_segment LTR
mat_peptide misc_binding misc_difference misc_feature misc_RNA misc_structure
mobile_element modified_base mRNA ncRNA operon oriT
precursor_RNA primer_bind promoter protein_bind RBS regulatory
repeat_region rep_origin rRNA sig_peptide source stem_loop
telomere terminator tmRNA transit_peptide tRNA unsure
V_region V_segment variation 3'UTR 5'UTR

 

 

gap between two components of a genome or transcriptome assembly

 

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.

 

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.

 

region of biological interest identified as a centromere and which has been experimentally characterized

 

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

 

Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain.

 

region of genome that codes for portion of spliced mRNA, rRNA and tRNA

 

gap in the sequence; sequencing gap other than assembly_gap

 

a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it

 

Joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.

 

long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses

 

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)

 

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)

 

feature sequence is different from that presented in the entry and cannot be described by any other "difference" key;
unsure, variation, modified_base
Comment
The misc_difference feature should be used to describe variability that arises as a result of genetic manipulation (e.g. site directed mutagenesis).

 

region of biological interest which cannot be described by any other feature key; a new or rare feature.

 

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

 

any secondary or tertiary nucleotide structure or conformation that cannot be described by other "Structure" keys;
stem_loop, D-loop

 

region of genome sequence containing mobile element

 

the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)

 

messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR)

 

a non-protein-coding gene, other than ribosomal RNA (rRNA) and transfer RNA (tRNA), the functional molecule of which is the RNA transcript

 

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

 

iorigin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization

 

any RNA species that is not yet the mature RNA product

 

Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. Includes site(s) for synthetic e.g., PCR primer elements

 

non-covalent protein binding site on nucleic acid

 

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.

 

region of genome containing repeating units

 

origin of replication; starting site for duplication of nucleic acid to give two identical copies

 

mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins

 

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

 

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

 

hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA

 

region of biological interest identified as a telomere and which has been experimentally characterized

 

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 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

 

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

 

author is unsure of exact sequence in this region

 

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.

 

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

 

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).

 

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;

 

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;

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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