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class="internal-link"> </nav> </div> <section id="MainContentView" class="mainview"> <header class="header"> <nav class="breadcrumb-view"> <ul> <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>TSA</a></li> </ul> </nav> <h1 class="title">TSA</h1> </header> <main class="md-content"> <p>Since 2008, INSDC has accepted the sequence data of “Transcriptome Shotgun Assembly (TSA)” categorised into TSA division for assembled cDNA sequences.</p> <p>With new sequencing technologies, INSDC has faced many requests to accept assembled EST sequences.<br /> These sequence data have become more useful than used to be, although they may not be correctly assembled or exist in nature.<br /> Therefore, INSDC decided to collect assembled EST sequences and classified them into the TSA division.<br /> See also <a href="/ddbj/transcriptome-e.html">steps of transcriptome project, categories of sequence data and their correspondences.</a></p> <p><a href="https://ddbj.nig.ac.jp/public/ddbj_database/tsa/TSA_ORGANISM_LIST.html">The list of publicized TSA data.</a></p> <p>You can submit TSA data to DDBJ through <a href="/ddbj/mss-e.html">Mass Submission System (MSS)</a>.</p> <dl> <dt>Notes on the TSA submission</dt> <dd> <ul> <li>Prior to sequence data submission, it is required to submit to <a href="/bioproject/index-e.html">BioProject Database</a> and <a href="/biosample/index-e.html">BioSample Database</a>.</li> <li>Assemblies obtained from multiple species are not acceptable, except Transcriptome Shotgun Assembly derived from environmental sample.</li> <li>The sequences of primary entries used for a TSA assembly are required to be submitted to the <a href="/ddbj/est-e.html">EST division</a> of DDBJ/ENA/GenBank, <a href="/dta/index-e.html">DDBJ Trace Archive</a> or <a href="/dra/index-e.html">DDBJ Read Archive</a>. If you have not yet submitted primary entries of your TSA data, at first, you have to submit them.</li> <li>To describe the correspondence of sequence regions between TSA and primary entries from only <a href="/ddbj/est-e.html">EST division</a> or <a href="/dta/index-e.html">DDBJ Trace Archive</a>, both locations should be prepared to describe in <a href="#PrimaryA">PRIMARY</a> line.<br /> For primary entries from <a href="/dra/index-e.html">DDBJ Read Archive</a>, cited run accession number is required to describe in <a href="#DblinkA">DBLINK</a> line.</li> <li>It is strongly recommended to include qualifiers indicating expression conditions; tissue (<a href="/ddbj/qualifiers-e.html#tissue_type">tissue_type</a>), developmental stage (<a href="/ddbj/qualifiers-e.html#dev_stage">dev_stage</a>), mating type (<a href="/ddbj/qualifiers-e.html#mating_type">mating_type</a> or <a href="/ddbj/qualifiers-e.html#sex">sex</a>) and so on. However, when the TSA sequence is constructed from two or more different origins, those conditions can not be described.</li> <li>Remove low quality reads and chimeric sequences before submission.</li> <li>The sequence must be in the 5’ to 3’ transcriptional direction.</li> </ul> </dd> <dt>Definition of primary entry for TSA</dt> <dd>Primary entries used to build a TSA sequence are RNA sequences that have been experimentally determined by their submitters and are publicly available on INSDC, <a href="https://www.ncbi.nlm.nih.gov/Traces/trace.cgi">Trace Archive</a> or <a href="https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi">Sequence Read Archive</a>.</dd> <dd> <p>It is possible that primary entries are not yet publicized at the TSA submission. However, the primary entries must be publicized by when the corresponding TSA entry is open to the public.</p> </dd> <dt>The sequence alignment rules between TSA and primary entries</dt> <dd> <ul> <li>Regions of a TSA entry can be assembled from a single EST or read so that coverage is only 1x.</li> <li>When the assembled sequence includes gap region supported by some evidence (pair end sequences, etc), you can describe gap region by sequential n’s in the sequence. The gap region must be specified by <a href="/ddbj/features-e.html#assembly_gap">assembly_gap</a> feature.</li> <li>Limits to ambiguity in the sequence out of location described with <a href="/ddbj/features-e.html#assembly_gap">assembly_gap</a> features are that; <ol> <li>the allowable percent of bases that are ‘n’ should be less than 5% and</li> <li>a TSA entry can have a stretch of no more than 5 n’ s in a row</li> </ol> </li> </ul> </dd> </dl> <h2 id="flat-file">Sample flat file</h2> <p>Aspects of TSA</p> <ul> <li>Basically, each TSA sequence submitted to DDBJ is assigned an <a href="#AccessionA">accession number</a> that consists of 4 alphabet characters and 8 digits.</li> <li><a href="#LocusA">LOCUS</a> line provides the division name, “TSA”.</li> <li>“TSA:” is shown at the beginning of <a href="#DefinitionA">DEFINITION</a> line.</li> <li>“TSA” and “Transcriptome Shotgun Assembly” are indicated in <a href="#KeywordsA">KEYWORDS</a> line.</li> <li><a href="#PrimaryA">PRIMARY</a> line provides base spans cited from sequeces of primary entries that contribute to regions of the TSA sequence.</li> </ul> <p>In case of citing <a href="/dra/index-e.html">DDBJ Read Archive</a></p> <pre><code><a id="LocusA" href="/ddbj/flat-file-e#LocusB">LOCUS</a> <a id="LocusNameA" href="/ddbj/flat-file-e#LocusNameB">IZZY01000001</a> <a id="SequenceLengthA" href="/ddbj/flat-file-e#SequenceLengthB">800 bp</a> <a id="MoleculeTypeA" href="/ddbj/flat-file-e#MoleculeTypeB">mRNA</a> <a id="MoleculeFormA" href="/ddbj/flat-file-e#MoleculeFormB">linear</a> <a id="DivisionA" href="/ddbj/flat-file-e#DivisionB">TSA</a> <a id="ModificationDateA" href="/ddbj/flat-file-e#ModificationDateB">15-OCT-2015</a> <a id="DefinitionA" href="/ddbj/flat-file-e#DefinitionB">DEFINITION</a> TSA: Mus musculus RNA, contig1_1. <a id="AccessionA" href="/ddbj/flat-file-e#AccessionB">ACCESSION</a> IZZY01000001 <a id="VersionA" href="/ddbj/flat-file-e#VersionB">VERSION</a> IZZY01000001.1 <a id="DblinkA" href="/ddbj/flat-file-e#DblinkB">DBLINK</a> BioProject:PRJDA43210 Sequence Read Archive: DRR900001 BioSample: SAMD98765431 <a id="KeywordsA" href="/ddbj/flat-file-e#KeywordsB">KEYWORDS</a> TSA; Transcriptome Shotgun Assembly. <a id="SourceA" href="/ddbj/flat-file-e#SourceB">SOURCE</a> Mus musculus (house mouse) <a id="OrganismA" href="/ddbj/flat-file-e#OrganismB">ORGANISM</a> Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus. <a id="Reference1A" href="/ddbj/flat-file-e#Reference1B">REFERENCE 1</a> (bases 1 to 800) <a id="AuthorsA" href="/ddbj/flat-file-e#AuthorsB">AUTHORS</a> Mishima,H. and Shizuoka,T. <a id="TitleA" href="/ddbj/flat-file-e#TitleB">TITLE</a> Direct Submission <a id="JournalA" href="/ddbj/flat-file-e#JournalB">JOURNAL</a> Submitted (30-SEP-2008) to the DDBJ/EMBL/GenBank databases. Contact:Hanako Mishima National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan <a id="Reference2A" href="/ddbj/flat-file-e#Reference2B">REFERENCE 2</a> AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Transcriptome shotgun assembly of mouse JOURNAL TSA Biol 12, 61-70 (2015) <a id="CommentA" href="/ddbj/flat-file-e#CommentB">COMMENT</a> ##Assembly-Data-START## Assembly Method :: Velvet v.1.1.05 Sequencing Technology :: Illumina GAIIx ##Assembly-Data-END## <a id="FeaturesA" href="/ddbj/flat-file-e#FeaturesB">FEATURES</a> Location/Qualifiers <a id="FeaturesSourceA" href="/ddbj/flat-file-e#FeaturesSourceB">source</a> <a href="/ddbj/location-e.html">1..800</a> /<a href="/ddbj/qualifiers-e.html#collection_date">collection_date</a>="2007" /<a href="/ddbj/qualifiers-e.html#db_xref">db_xref</a>="taxon:10090" /<a href="/ddbj/qualifiers-e.html#geo_loc_name">geo_loc_name</a>="Japan: Shizuoka" /<a href="/ddbj/qualifiers-e.html#mol_type">mol_type</a>="transcribed RNA" /<a href="/ddbj/qualifiers-e.html#organism">organism</a>="Mus musculus" /<a href="/ddbj/qualifiers-e.html#submitter_seqid">submitter_seqid</a>="contig1_1" <a id="BaseCountA" href="#BaseCountB">BASE COUNT</a> 199 a 203 c 198 g 200 t <a id="OriginA" href="#OriginB">ORIGIN</a> 1 attaatataa gctaaatatg tttttcaata tatattgata atagaatatc aacaatttgg : -- The rest of nucleotide sequence is omitted -- : <a id="EndA" href="/ddbj/flat-file-e#EndB">//</a></code></pre> <p>In case of citing <a href="/ddbj/est-e.html">EST</a></p> <pre class="code flat-file"><code><a href="/ddbj/flat-file-e#LocusB">LOCUS</a> <a href="/ddbj/flat-file-e#LocusNameB">IZZY01000001</a> <a href="/ddbj/flat-file-e#SequenceLengthB">800 bp</a> <a href="/ddbj/flat-file-e#MoleculeTypeB">mRNA</a> <a href="/ddbj/flat-file-e#ModificationDateB">linear</a> <a href="/ddbj/flat-file-e#DivisionB">TSA</a> <a href="/ddbj/flat-file-e#ModificationDateB">15-OCT-2015</a> <a href="/ddbj/flat-file-e#DefinitionB">DEFINITION</a> TSA: Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate dehydrogenase, complete cds. <a href="/ddbj/flat-file-e#AccessionB">ACCESSION</a> IZZY01000001 <a href="/ddbj/flat-file-e#VersionB">VERSION</a> IZZY01000001.1 <a href="/ddbj/flat-file-e#DblinkB">DBLINK</a> BioProject:PRJDA43211 BioSample: SAMD98765433 <a href="/ddbj/flat-file-e#KeywordsB">KEYWORDS</a> TSA; Transcriptome Shotgun Assembly. <a href="/ddbj/flat-file-e#SourceB">SOURCE</a> Homo sapiens (human) <a href="/ddbj/flat-file-e#OrganismB">ORGANISM</a> Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. <a href="/ddbj/flat-file-e#Reference1B">REFERENCE 1</a> (bases 1 to 800) <a href="/ddbj/flat-file-e#AuthorsB">AUTHORS</a> Mishima,H. and Shizuoka,T. <a href="/ddbj/flat-file-e#TitleB">TITLE</a> Direct Submission <a href="/ddbj/flat-file-e#JournalB">JOURNAL</a> Submitted (30-SEP-2008) to the DDBJ/EMBL/GenBank databases. Contact:Hanako Mishima National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan <a href="/ddbj/flat-file-e#Reference2B">REFERENCE 2</a> AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE EST assembly of human JOURNAL TSA Biol 12, 61-70 (2008) <a href="/ddbj/flat-file-e#CommentB">COMMENT</a> <a id="PrimaryA" href="#PrimaryB">PRIMARY</a> TSA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-599 ZZ000004.1 2-598 1-669 ZZ000005.1 11-679 2-596 ZZ000006.1 1-595 2-575 ZZ000007.1 1-574 5-676 ZZ000008.1 1-672 6-725 ZZ000009.1 1-720 59-369 ZZ000010.1 13-322 605-800 ZZ000011.1 1-196 c 1451-1550 ZZ000003.1 201-300 <a href="/ddbj/flat-file-e#FeaturesB">FEATURES</a> Location/Qualifiers <a href="/ddbj/flat-file-e#FeaturesSourceB">source</a> <a href="/ddbj/location-e.html">1..800</a> /<a href="/ddbj/qualifiers-e.html#collection_date">collection_date</a>="2007" /<a href="/ddbj/qualifiers-e.html#db_xref">db_xref</a>="taxon:9606" /<a href="/ddbj/qualifiers-e.html#geo_loc_name">geo_loc_name</a>="Japan" /<a href="/ddbj/qualifiers-e.html#mol_type">mol_type</a>="transcribed RNA" /<a href="/ddbj/qualifiers-e.html#organism">organism</a>="Homo sapiens" <a href="/ddbj/features.html#cds">CDS</a> <a href="/ddbj/location-e.html">73..669</a> /<a href="/ddbj/qualifiers-e.html#codon_start">codon_start</a>=1 /<a href="/ddbj/qualifiers-e.html#gene">gene</a>="GAPD" /<a href="/ddbj/qualifiers-e.html#product">product</a>="glyceraldehyde-3-phosphate dehydrogenase" /<a href="/ddbj/qualifiers-e.html#protein_id">protein_id</a>="LZZ00001.1" /<a href="/ddbj/qualifiers-e.html#transl_table">transl_table</a>=1 /<a href="/ddbj/qualifiers-e.html#translation">translation</a>="MWYQSLVIIEKLNLEANIGKLINTKDNINIRCRLSHTEEHSWHS -- The rest of amino acid sequence is omitted -- " <a href="#BaseCountB">BASE COUNT</a> 199 a 203 c 198 g 200 t <a href="#OriginB">ORIGIN</a> 1 attaatataa gctaaatatg tttttcaata tatattgata atagaatatc aacaatttgg : -- The rest of nucleotide sequence is omitted -- : <a href="/ddbj/flat-file-e#EndB">//</a></code></pre> </main> <aside class="related-pages"> <h2 class="caption">Related pages</h2> <div class="navigation"> <nav> <ul> <li> <a href="/ddbj/genome-e.html">Data Submission from Genome Project</a> </li> <li> <a href="/ddbj/environmental-e.html">Submission of environmental sequences</a> </li> <li> <a href="/ddbj/transcriptome-e.html">Data Submission from Transcriptome Project</a> </li> <li> <a href="/ddbj/tpa-e.html">Third Party Data (TPA)</a> </li> </ul> </nav> </div> </aside> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>