Ambystoma.org

  • Increase font size
  • Default font size
  • Decrease font size
Home Genome Resources Gene and EST Database

Gene and EST Database

Assembly V4.0: The A. mexicanum transcriptome has been deep sequenced (15,000,000 Roche 454 short sequence reads and 50K Sanger reads) and assembled. The resulting assembly V4.0 can now be BLAST searched here. Approximately 89.9% of the 14 million high quality sequences were assembled into contigs with a total length of 542 Mb.

These contigs were organized into 921,990 isogroups, representing a total of 1,057,173 isotigs. (Click here to know more about Isotigs) We have complete (~7K) or incomplete (~10K) protein-coding sequence models for ~17K human refseq proteins. We have 3K additional significant blast hits to non-human protein coding models. With respect to the tissues we have sampled (brain, limb, blood, etc) , we believe we have significant hits to >95% of the transcriptome.


New! Search for Contigs in the Latest V4.0 assembly:

Enter a contig or sequence name (e.g. contig00001, GKJVZ9C02F0B34):    

Enter a contig or sequence name (e.g. isotig00001, GKJVZ9C02F0B34):    

Search for Genes in assembly V4.0:

    (Enter a minimum of 3 characters)

Assembly V3.0:

Approximately 74% of the 3.3 million high quality sequences were assembled into contigs with a total length of 71 Mb. The final unique set of contigs and singletons from the assembly was about 915,442 sequences. We have complete (~3K) or incomplete (~12K) protein-coding sequence models for ~15K human refseq proteins.

Search for Genes in assembly V3.0:

   

If you have a sequence that you want to search against sal-site EST's, you can BLAST search it to our latest assembly here.


If you have a A. mexicanum or A. t. tigrinum sequence identifier from a prior BLAST search, you can get the sequence information using the below:

                    Enter A. mexicanum sequence id (e.g. contig00001, EPJ1Z2K01CRNZJ, C000001) :    

                    Enter A. t. tigrinum sequence id (e.g. Tig_NM_000014_Contig_1, TC00001) :