DDBJ Annotated/Assembled Sequences
[Caution] DDBJ terminated accepting new submission of MGA data.
In order to accept a large scale of sequence data that provide useful information for annotation of genome assemblies/sequences, the International Nucleotide Sequence Database Collaboration (INSDC; DDBJ/EMBL-Bank/GenBank) have created a new category. The name of this new category is Mass sequence for Genome Annotation (MGA). The definition of MGA data is the following.。
- The definition of MGA data
- MGA is defined as those sequences which are produced in large quantity in view of genome annotation.
- The data which can be acceptable to the MGA category of INSDC are
- Those which include useful biological features for genome annotation ( e.g. start or end terminus of a transcript). The large of quantity here means that the number of sequences in one resource is 10,000 or more.
Sample flat file
MGA data are published a resource as a unit. The data consist of “Master record” and “Variable record” for a resource.
Common parts of information such as submitters, keywords (MGA and others), references, comments and so on. Master record is provided for every resource unit.
LOCUS ZZZZZ0000000 mRNA linear ROD 24-JAN-2005 DEFINITION Mus musculus 1 month adult cerebellum short transcripts tag. ACCESSION ZZZZZ0000000 VERSION ZZZZZ0000000.1 KEYWORDS MGA; CAGE (Cap Analysis Gene Expression). 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 1450) AUTHORS Mishima,H., Yamada,T. and Liu,G.Q. TITLE Direct Submission JOURNAL Submitted (30-NOV-2009) 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2 AUTHORS Mishima,H., Shizuoka,T. and Fuji,I TITLE The gene expression analysis of short transcripts tags JOURNAL Unpublished (2010) COMMENT The CAGE (cap analysis gene expression) is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20/21 nucleotides from 5' end mRNAs. Full-length cDNAs were at first selected with the Cap-Trapper method. Then, a specific linker (Linker1, some linker contain 5 bp sequences that have 15 variations for each rna sample) containing the ClassIIs restriction enzyme site MmeI was then ligated to the single-strand cDNA and then the second strand of cDNA synthesized. (omitted) FEATURES Location/Qualifiers source /db_xref="taxon:10090" /dev_stage="1 month adult" /mol_type="mRNA" /organism="Mus musculus" /strain="C57BL/6J" /tissue_type="cerebellum" MGA ZZZZZ0000001-ZZZZ0340780 total number of count : 856609 Header Format >[ACC#]|[submitter's identifier]|[number of sequence count]|[map]|[free text]|[db_xref1(,db_xref2,...)]| //
All nucleotide sequences of the resource unit described in the Master record, and the items specific to each sequence, such as map location, count number of the sequence, and db_xrefs.
>ZZZZZ0000001|ABC1004AA60F1902|10|9B|lipidosis-related protein Lipidosin| GI:2385656| gactgtcttcggtgaatgca >ZZZZZ0000002|ABC1003AE78G1607|5|||| gcggaagtcggaccggtcgca >ZZZZZ0000003|ABC1003AE72P1806|6|||| gggagaccgatccgggatct >ZZZZZ0000004|ABC1003AE30G1801|91|||| gagtcgggtcggtggggctgt >ZZZZZ0000005|ABC1003AA45J1501|55|||| ggggaatctgcagcctgggc >ZZZZZ0000006|ABC1003AE67B0902|152|||| gagccgtccccgacgccgcca (Followings are omitted)
|Format:||>[ACC#]|[submitter’s identifier]|[number of sequence count]|[map]|[free text]|[db_xref1(,db_xref2,…)]||
- One entry is consisted of “Header” line and nucleotide sequence.Header line starts “>” and follows six items related to each entry.Six items are delimited by “|”(pipe).
- The related information of an entry can be changed, but revise of nucleotide sequence can not be allowed. If the sequence which has already been submitted into INSDC is taken from identical resource, the item, [number of sequence count] of the entry has to be updated.
>ZZZZZ0000001|ABC1004AA60F1902|100|9B|lipidosis-related protein Lipidosin| MGI:2385656| gactgtcttcggtgaatgca
||accession number of the entry|
||identifier assigned by submitter to the entry|
||number of the count of this entry in the resouce|
||Map location (in this case, chromosome number)|
||free-text-formatted description of the entry|
||external database information of the entry|