Definition of Feature Key
The feature keys used for DDBJ submissions are as follows.
For further information of the feature key, read:
The DDBJ/EMBL/GenBank Feature Table Definition:
7.2 Appendix II: Feature keys reference.
attenuator
1) region of DNA at which regulation of termination of transcription occurs,which controls the expression of some bacterial operons
2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription
C_region
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.
CDS
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.
CAAT_signal
CAAT box; part of a conserved sequence located about 75 bp up-stream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding;
consensus=GG(C or T)CAATCT
conflict
independent determinations of the "same" sequence differ at this site or region
D-loop
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_segment
Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain.
enhancer
a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter
exon
region of genome that codes for portion of spliced mRNA, rRNA and tRNA
gap
gap in the sequence
GC_signal
GC box; a conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation;
consensus=GGGCGG
iDNA
intervening DNA; DNA which is eliminated through any of several kinds of recombination
intron
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_segment
Joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.
LTR
long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses
mat_peptide
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_binding
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_difference
feature sequence is different from that presented in the entry and cannot be described by any other "difference" key (conflict, unsure, old_sequence, mutation, or 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).
misc_feature
region of biological interest which cannot be described by any other feature key; a new or rare feature.
misc_recomb
site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys or qualifiers of source key (/proviral).
misc_RNA
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 and tRNA
misc_signal
any region containing a signal controlling or altering gene function or expression that cannot be described by other "Signal" keys (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and rep_origin)
misc_structure
any secondary or tertiary nucleotide structure or conformation that cannot be described by other "Structure" keys (stem_loop and D-loop)
modified_base
the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)
mRNA
messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR)
ncRNA
a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript
N_region
Extra nucleotides inserted between rearranged immmunoglobulin segments.
operon
region containing polycistronic transcript containing genes that encode enzymes that are in the same metabolic pathway and regulatory sequences
oriT
iorigin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization
polyA_signal
recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation;
consensus=AATAAA
polyA_site
site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation
precursor_RNA
any RNA species that is not yet the mature RNA product; may include 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron), and 3' untranslated region (3'UTR)
prim_transcript
primary (initial, unprocessed) transcript; includes 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron), and 3' untranslated region (3'UTR)
primer_bind
Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. Includes site(s) for synthetic e.g., PCR primer elements
promoter
region on a DNA molecule involved in RNA polymerase binding to initiate transcription
protein_bind
non-covalent protein binding site on nucleic acid
RBS
ribosome binding site
repeat_region
region of genome containing repeating units
rep_origin
origin of replication; starting site for duplication of nucleic acid to give two identical copies
rRNA
mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins
S_region
Switch region of immunoglobulin heavy chains. Involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin class from the same B-cell.
sig_peptide
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
source
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_loop
hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA
STS
Sequence Tagged Site. Short, single-copy DNA sequence that characterizes a mapping landmark on the genome and can be detected by PCR. A region of the genome can be mapped by determining the order of a series of STSs
TATA_signal
TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcript unit which may be involved in positioning the enzyme for correct initiation;
consensus=TATA(A or T)A(A or T)
terminator
sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription
tmRNA
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
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
tRNA
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
unsure
author is unsure of exact sequence in this region
V_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.
V_segment
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
variation
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'UTR
region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
5'UTR
region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
-10_signal
Pribnow box; a conserved region about 10 bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase;
consensus=TAtAaT
-35_signal
a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units;
consensus=[TTGACa] or [TGTTGACA]