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<li> <a href="https://www.ddbj.nig.ac.jp/index-e.html">Home</a> </li> <li> <a href="https://www.ddbj.nig.ac.jp/ddbj/index-e.html">ddbj</a> </li> <li><a>Feature key</a></li> </ul> </nav> <h1 class="title">Feature key</h1> </header> <main class="md-content"> <p>The feature keys used and recommended for DDBJ submissions are as follows.</p> <h2 id="usage">Feature/Qualifier Usage Matrix</h2> <p>The chart, <a href="https://docs.google.com/spreadsheets/d/1qosakEKo-y9JjwUO_OFcmGCUfssxhbFAm5NXUAnT3eM/">Feature/Qualifier usage matrix</a>, explains recommended combinations of feature and qualifier keys for DDBJ submissions.</p> <p>For more detail of available combinations of feature and qualifier keys in INSDC entries, read: <a href="/ddbj/feature-table-e.html">Feature Table Definition</a>: <a href="/ddbj/feature-table-e.html#7.2">7.2 Appendix II: Feature keys reference</a>.</p> <h2 id="definition-of-feature-key">Definition of Feature key</h2> <h3 id="assembly_gapfeature-table-definition">assembly_gap<a name="assembly_gap"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#assembly_gap">Feature Table Definition</a></span></h3> <p>gap between two components of a <a href="/ddbj/genome-e.html">genome</a> or <a href="/ddbj/transcriptome-e.html">transcriptome</a> assembly</p> <h3 id="c_regionfeature-table-definition">C_region<a name="C_region"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#C_region">Feature Table Definition</a></span></h3> <p>Constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains. <br /> Includes one or more exons depending on the particular chain.</p> <h3 id="cdsfeature-table-definition">CDS<a name="cds"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#CDS">Feature Table Definition</a></span></h3> <p>coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stopcodon). <br /> See also <a href="/ddbj/cds-e.html">the page about CDS feature</a>.</p> <h3 id="centromerefeature-table-definition">centromere<a name="centromere"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#centromere">Feature Table Definition</a></span></h3> <p>region of biological interest identified as a centromere and which has been experimentally characterized</p> <h3 id="d-loopfeature-table-definition">D-loop<a name="D-loop"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#D-loop">Feature Table Definition</a></span></h3> <p>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;<br /> 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</p> <h3 id="d_segmentfeature-table-definition">D_segment<a name="D_segment"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#D_segment">Feature Table Definition</a></span></h3> <p>Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain.</p> <h3 id="exonfeature-table-definition">exon<a name="exon"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#exon">Feature Table Definition</a></span></h3> <p>region of genome that codes for portion of spliced <a href="/ddbj/feature-table-e.html#mRNA">mRNA</a>, <a href="/ddbj/feature-table-e.html#rRNA">rRNA</a> and <a href="/ddbj/feature-table-e.html#tRNA">tRNA</a></p> <h3 id="gapfeature-table-definition">gap<a name="gap"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#gap">Feature Table Definition</a></span></h3> <p>gap in the sequence; sequencing gap other than <a href="#assembly_gap">assembly_gap</a></p> <h3 id="intronfeature-table-definition">intron<a name="intron"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#intron">Feature Table Definition</a></span></h3> <p>a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (<a href="/ddbj/feature-table-e.html#exon">exon</a>s) on either side of it</p> <h3 id="j_segmentfeature-table-definition">J_segment<a name="J_segment"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#J_segment">Feature Table Definition</a></span></h3> <p>Joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.</p> <h3 id="mat_peptidefeature-table-definition">mat_peptide<a name="mat_peptide"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#mat_peptide">Feature Table Definition</a></span></h3> <p>mature peptide or protein coding sequence; coding sequence for the mature or final peptide or protein product following post-translational modification. <br /> The location does not include the stop codon (unlike the corresponding <a href="/ddbj/feature-table-e.html#CDS">CDS</a>)</p> <h3 id="misc_bindingfeature-table-definition">misc_binding<a name="misc_binding"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#misc_binding">Feature Table Definition</a></span></h3> <p>site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other binding key;<br /> <a href="/ddbj/feature-table-e.html#primer_bind">primer_bind</a> or <a href="/ddbj/feature-table-e.html#protein_bind">protein_bind</a></p> <h3 id="misc_differencefeature-table-definition">misc_difference<a name="misc_difference"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#misc_difference">Feature Table Definition</a></span></h3> <p>feature sequence is different from that presented in the entry and cannot be described by any other “difference” key;<br /> <a href="/ddbj/feature-table-e.html#variation">variation</a>, <a href="/ddbj/feature-table-e.html#modified_base">modified_base</a> <br /> Comment <br /> The misc_difference feature should be used to describe variability that arises as a result of genetic manipulation (e.g. site directed mutagenesis).</p> <h3 id="misc_featurefeature-table-definition">misc_feature<a name="misc_feature"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#misc_feature">Feature Table Definition</a></span></h3> <p>region of biological interest which cannot be described by any other feature key; a new or rare feature.</p> <h3 id="misc_rnafeature-table-definition">misc_RNA<a name="misc_RNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#misc_RNA">Feature Table Definition</a></span></h3> <p>any transcript or RNA product that cannot be defined by other RNA keys <br /> <a href="/ddbj/feature-table-e.html#prim_transcript">prim_transcript</a>, <a href="/ddbj/feature-table-e.html#precursor_RNA">precursor_RNA</a>, <a href="/ddbj/feature-table-e.html#mRNA">mRNA</a>, <a href="/ddbj/feature-table-e.html#5UTR">5’UTR</a>, <a href="/ddbj/feature-table-e.html#3UTR">3’UTR</a>, <a href="/ddbj/feature-table-e.html#exon">exon</a>, <a href="/ddbj/feature-table-e.html#CDS">CDS</a>, <a href="/ddbj/feature-table-e.html#sig_peptide">sig_peptide</a>, <a href="/ddbj/feature-table-e.html#transit_peptide">transit_peptide</a>, <a href="/ddbj/feature-table-e.html#mat_peptide">mat_peptide</a>, <a href="/ddbj/feature-table-e.html#intron">intron</a>, <a href="/ddbj/feature-table-e.html#polyA_site">polyA_site</a>, <a href="/ddbj/feature-table-e.html#ncRNA">ncRNA</a>, <a href="/ddbj/feature-table-e.html#rRNA">rRNA</a>, <a href="/ddbj/feature-table-e.html#tRNA">tRNA</a>, <a href="/ddbj/feature-table-e.html#tmRNA">tmRNA</a></p> <h3 id="misc_structurefeature-table-definition">misc_structure<a name="misc_structure"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#misc_structure">Feature Table Definition</a></span></h3> <p>any secondary or tertiary nucleotide structure or conformation that cannot be described by other “Structure” keys; <br /> <a href="/ddbj/feature-table-e.html#stem_loop">stem_loop</a>, <a href="/ddbj/feature-table-e.html#D-loop">D-loop</a></p> <h3 id="mobile_elementfeature-table-definition">mobile_element<a name="mobile_element"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#mobile_element">Feature Table Definition</a></span></h3> <p>region of genome sequence containing mobile element</p> <h3 id="modified_basefeature-table-definition">modified_base<a name="modified_base"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#modified_base">Feature Table Definition</a></span></h3> <p>the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the <a href="/ddbj/qualifiers-e.html#mod_base">mod_base</a> qualifier value)</p> <h3 id="mrnafeature-table-definition">mRNA<a name="mRNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#mRNA">Feature Table Definition</a></span></h3> <p>messenger RNA; includes 5’untranslated region (<a href="/ddbj/feature-table-e.html#5UTR">5’UTR</a>), coding sequences (<a href="/ddbj/feature-table-e.html#CDS">CDS</a>, <a href="/ddbj/feature-table-e.html#exon">exon</a>) and 3’untranslated region (<a href="/ddbj/feature-table-e.html#3UTR">3’UTR</a>)</p> <h3 id="ncrnafeature-table-definition">ncRNA<a name="ncRNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#ncRNA">Feature Table Definition</a></span></h3> <p>a non-protein-coding gene, other than ribosomal RNA (<a href="/ddbj/feature-table-e.html#rRNA">rRNA</a>) and transfer RNA (<a href="/ddbj/feature-table-e.html#tRNA">tRNA</a>), the functional molecule of which is the RNA transcript</p> <h3 id="operonfeature-table-definition">operon<a name="operon"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#operon">Feature Table Definition</a></span></h3> <p>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</p> <h3 id="oritfeature-table-definition">oriT<a name="oriT"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#oriT">Feature Table Definition</a></span></h3> <p>iorigin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization</p> <h3 id="precursor_rnafeature-table-definition">precursor_RNA<a name="precursor_RNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#precursor_RNA">Feature Table Definition</a></span></h3> <p>any RNA species that is not yet the mature RNA product</p> <h3 id="primer_bindfeature-table-definition">primer_bind<a name="primer_bind"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#primer_bind">Feature Table Definition</a></span></h3> <p>Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. <br /> Includes site(s) for synthetic e.g., PCR primer elements</p> <h3 id="propeptidefeature-table-definition">propeptide<a name="propeptide"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#propeptide">Feature Table Definition</a></span></h3> <p>propeptide coding sequence; coding sequence for the domain of a proprotein that is cleaved to form the mature protein product.</p> <h3 id="protein_bindfeature-table-definition">protein_bind<a name="protein_bind"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#protein_bind">Feature Table Definition</a></span></h3> <p>non-covalent protein binding site on nucleic acid</p> <h3 id="regulatoryfeature-table-definition">regulatory<a name="regulatory"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#regulatory">Feature Table Definition</a></span></h3> <p>any region of sequence that functions in the regulation of transcription or translation <br /> Since December 2014, the following old features have been merged into this feature.</p> <ul> <li>attenuator –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”attenuator”</li> <li>CAAT_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”CAAT_signal”</li> <li>enhancer –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”enhancer”</li> <li>GC_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”GC_signal”</li> <li>-35_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”minus_35_signal”</li> <li>-10_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”minus_10_signal”</li> <li>polyA_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”polyA_signal_sequence”</li> <li>promoter –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”promoter”</li> <li>RBS –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”ribosome_binding_site”</li> <li>TATA_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”TATA_box”</li> <li>terminator –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”terminator”</li> <li>misc_signal –> regulatory feature with /<a href="/ddbj/qualifiers-e.html#regulatory_class">regulatory_class</a>=”other”</li> </ul> <h3 id="repeat_regionfeature-table-definition">repeat_region<a name="repeat_region"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#repeat_region">Feature Table Definition</a></span></h3> <p>region of genome containing repeating units</p> <h3 id="rep_originfeature-table-definition">rep_origin<a name="rep_origin"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#rep_origin">Feature Table Definition</a></span></h3> <p>origin of replication; starting site for duplication of nucleic acid to give two identical copies</p> <h3 id="rrnafeature-table-definition">rRNA<a name="rRNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#rRNA">Feature Table Definition</a></span></h3> <p>mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins</p> <h3 id="sig_peptidefeature-table-definition">sig_peptide<a name="sig_peptide"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#sig_peptide">Feature Table Definition</a></span></h3> <p>signal peptide coding sequence; coding sequence for an N-terminal domain of a secreted protein; <br /> this domain is involved in attaching nascent polypeptide to the membrane; leader sequence</p> <h3 id="sourcefeature-table-definition">source<a name="source"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#source">Feature Table Definition</a></span></h3> <p>identifies the biological source of the specified span of the sequence. <br /> This key is mandatory. Every entry will have, as a minimum, a single source key spanning the entire sequence. <br /> More than one source key per sequence is permissible</p> <h3 id="stem_loopfeature-table-definition">stem_loop<a name="stem_loop"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#stem_loop">Feature Table Definition</a></span></h3> <p>hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA</p> <h3 id="telomerefeature-table-definition">telomere<a name="telomere"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#telomere">Feature Table Definition</a></span></h3> <p>region of biological interest identified as a telomere and which has been experimentally characterized</p> <h3 id="tmrnafeature-table-definition">tmRNA<a name="tmRNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#tmRNA">Feature Table Definition</a></span></h3> <p>transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag; <br /> the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; <br /> this attached tag targets the protein for destruction or proteolysis;</p> <h3 id="transit_peptidefeature-table-definition">transit_peptide<a name="transit_peptide"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#transit_peptide">Feature Table Definition</a></span></h3> <p>transit peptide coding sequence; coding sequence for an N-terminal domain of a nuclear-encoded organellar protein; <br /> this domain is involved in post-translational import of the protein into the organelle</p> <h3 id="trnafeature-table-definition">tRNA<a name="tRNA"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#tRNA">Feature Table Definition</a></span></h3> <p>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</p> <h3 id="unsurefeature-table-definition">unsure<a name="unsure"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#unsure">Feature Table Definition</a></span></h3> <p>A small region of sequenced bases, generally 10 or fewer in its length, which could not be confidently identified.</p> <h3 id="v_regionfeature-table-definition">V_region<a name="V_region"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#V_region">Feature Table Definition</a></span></h3> <p>Variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains. <br /> Codes for the variable amino terminal portion. Can be made up from V_segments, D_segments, N_regions and J_segments.</p> <h3 id="v_segmentfeature-table-definition">V_segment<a name="V_segment"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#V_segment">Feature Table Definition</a></span></h3> <p>Variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains. <br /> Codes for most of the variable region (V_region) and the last few amino acids of the leader peptide</p> <h3 id="variationfeature-table-definition">variation<a name="variation"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#variation">Feature Table Definition</a></span></h3> <p>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).</p> <h3 id="3utrfeature-table-definition">3’UTR<a name="3UTR"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#3UTR">Feature Table Definition</a></span></h3> <p>1) region at the 3’ end of a mature transcript (following the stop codon) that is not translated into a protein; <br /> 2) region at the 3’ end of an RNA virus (following the last stop codon) that is not translated into a protein;</p> <h3 id="5utrfeature-table-definition">5’UTR<a name="5UTR"></a><span class="right-alignment"><a href="/ddbj/feature-table-e.html#5UTR">Feature Table Definition</a></span></h3> <p>1) region at the 5’ end of a mature transcript (preceding the initiation codon) that is not translated into a protein; <br /> 2) region at the 5’ end of an RNA virus genome (preceding the first initiation codon) that is not translated into a protein;</p> </main> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>