DDBJ Annotated/Assembled Sequences
TSA
Since 2008, INSDC has accepted the sequence data of “Transcriptome Shotgun Assembly (TSA)” categorised into TSA division for assembled cDNA sequences.
With new sequencing technologies, INSDC has faced many requests to accept assembled EST sequences.
These sequence data have become more useful than used to be, although they may not be correctly assembled or exist in nature.
Therefore, INSDC decided to collect assembled EST sequences and classified them into the TSA division.
See also steps of transcriptome project, categories of sequence data and their correspondences.
The list of publicized TSA data.
You can submit TSA data to DDBJ through Mass Submission System (MSS).
- Notes on the TSA submission
-
- Prior to sequence data submission, it is required to submit to BioProject Database and BioSample Database.
- Assemblies obtained from multiple species are not acceptable, except Transcriptome Shotgun Assembly derived from environmental sample.
- The sequences of primary entries used for a TSA assembly are required to be submitted to the EST division of DDBJ/ENA/GenBank, DDBJ Trace Archive or DDBJ Read Archive. If you have not yet submitted primary entries of your TSA data, at first, you have to submit them.
- To describe the correspondence of sequence regions between TSA and primary entries from only EST division or DDBJ Trace Archive, both locations should be prepared to describe in PRIMARY line.
For primary entries from DDBJ Read Archive, cited run accession number is required to describe in DBLINK line. - It is strongly recommended to include qualifiers indicating expression conditions; tissue (tissue_type), developmental stage (dev_stage), mating type (mating_type or sex) and so on. However, when the TSA sequence is constructed from two or more different origins, those conditions can not be described.
- Remove low quality reads and chimeric sequences before submission.
- The sequence must be in the 5’ to 3’ transcriptional direction.
- Definition of primary entry for TSA
- 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, Trace Archive or Sequence Read Archive.
-
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.
- The sequence alignment rules between TSA and primary entries
-
- Regions of a TSA entry can be assembled from a single EST or read so that coverage is only 1x.
- 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 assembly_gap feature.
- Limits to ambiguity in the sequence out of location described with assembly_gap features are that;
- the allowable percent of bases that are ‘n’ should be less than 5% and
- a TSA entry can have a stretch of no more than 5 n’ s in a row
Sample flat file
Aspects of TSA
- Basically, each TSA sequence submitted to DDBJ is assigned an accession number that consists of 4 alphabet characters and 8 digits.
- LOCUS line provides the division name, “TSA”.
- “TSA:” is shown at the beginning of DEFINITION line.
- “TSA” and “Transcriptome Shotgun Assembly” are indicated in KEYWORDS line.
- PRIMARY line provides base spans cited from sequeces of primary entries that contribute to regions of the TSA sequence.
In case of citing DDBJ Read Archive
LOCUS IZZY01000001 800 bp mRNA linear TSA 15-OCT-2015
DEFINITION TSA: Mus musculus RNA, contig1_1.
ACCESSION IZZY01000001
VERSION IZZY01000001.1
DBLINK BioProject:PRJDA43210
Sequence Read Archive: DRR900001
BioSample: SAMD98765431
KEYWORDS TSA; Transcriptome Shotgun Assembly.
SOURCE Mus musculus (house mouse)
ORGANISM Mus musculus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE 1 (bases 1 to 800)
AUTHORS Mishima,H. and Shizuoka,T.
TITLE Direct Submission
JOURNAL 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
REFERENCE 2
AUTHORS Mishima,H., Shizuoka,T. and Fuji,I.
TITLE Transcriptome shotgun assembly of mouse
JOURNAL TSA Biol 12, 61-70 (2015)
COMMENT ##Assembly-Data-START##
Assembly Method :: Velvet v.1.1.05
Sequencing Technology :: Illumina GAIIx
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..800
/collection_date="2007"
/db_xref="taxon:10090"
/geo_loc_name="Japan: Shizuoka"
/mol_type="transcribed RNA"
/organism="Mus musculus"
/submitter_seqid="contig1_1"
BASE COUNT 199 a 203 c 198 g 200 t
ORIGIN
1 attaatataa gctaaatatg tttttcaata tatattgata atagaatatc aacaatttgg
:
-- The rest of nucleotide sequence is omitted --
:
//In case of citing EST
LOCUS IZZY01000001 800 bp mRNA linear TSA 15-OCT-2015
DEFINITION TSA: Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate
dehydrogenase, complete cds.
ACCESSION IZZY01000001
VERSION IZZY01000001.1
DBLINK BioProject:PRJDA43211
BioSample: SAMD98765433
KEYWORDS TSA; Transcriptome Shotgun Assembly.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 800)
AUTHORS Mishima,H. and Shizuoka,T.
TITLE Direct Submission
JOURNAL 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
REFERENCE 2
AUTHORS Mishima,H., Shizuoka,T. and Fuji,I.
TITLE EST assembly of human
JOURNAL TSA Biol 12, 61-70 (2008)
COMMENT
PRIMARY 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
FEATURES Location/Qualifiers
source 1..800
/collection_date="2007"
/db_xref="taxon:9606"
/geo_loc_name="Japan"
/mol_type="transcribed RNA"
/organism="Homo sapiens"
CDS 73..669
/codon_start=1
/gene="GAPD"
/product="glyceraldehyde-3-phosphate dehydrogenase"
/protein_id="LZZ00001.1"
/transl_table=1
/translation="MWYQSLVIIEKLNLEANIGKLINTKDNINIRCRLSHTEEHSWHS
-- The rest of amino acid sequence is omitted -- "
BASE COUNT 199 a 203 c 198 g 200 t
ORIGIN
1 attaatataa gctaaatatg tttttcaata tatattgata atagaatatc aacaatttgg
:
-- The rest of nucleotide sequence is omitted --
:
//