What is GSS? – Genome Survey Sequences

The GSS division of DDBJ/EMBL-Bank/GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA, RNA transcript).
It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence.
The GSS division contains (but is not limited to) the following types of data:

  • random "single pass read" genome survey sequences; e.g. RAPD, RFLP, AFLP and so on.
  • cosmid/BAC/YAC end sequences
  • exon trapped genomic sequences
  • transposon-tagged sequences

You can submit GSS data to DDBJ through Mass Submission System (MSS).

 

Notes on the GSS submission

Prior to your submission, remove regions of cloning vectors from your sequences.
Clone Id is required for clone qualifer.

 

Aspects of GSS on DDBJ flat file

Though there are exceptions, no feature information is provided except source.
LOCUS line provides the division name, "GSS".
"GSS" is indicated in KEYWORDS line.

 

Sample of GSS flat file

LOCUS       GA000000                 423 bp    DNA     linear   GSS 15-OCT-2008
DEFINITION  Arabidopsis thaliana DNA, BAC clone: CIC5D1, left end, chromosome 1
            between mi303 and mi259.
ACCESSION   GA000000
VERSION     GA000000.1
KEYWORDS    GSS.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; malvids; Brassicales; Brassicaceae; Camelineae;
            Arabidopsis.
REFERENCE   1  (bases 1 to 423)
  AUTHORS   Mishima,H., Yamada,T. and Liu,G.Q.
  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., Yamada,T., Park,C.S. and Liu,G.Q.
  TITLE     Arabidopsis thaliana DNA
  JOURNAL   Unpublished (2008)
FEATURES             Location/Qualifiers
     source          1..423
                     /chromosome="1"
                     /clone="CIC5D1"
                     /clone_lib="AT01 BAC"
                     /db_xref="taxon:3702"
                     /ecotype="columbia"
                     /map="between mi303 and mi259"
                     /mol_type="genomic DNA"
                     /organism="Arabidopsis thaliana"
BASE COUNT          105 a          98 c          112 g          108 t
ORIGIN
        1 attaatataa gctaaatatg tttttcaata tatattgata atagaatatc aacaatttgg
        :
        -- The rest of nucleotide sequence is omitted --
        :
//