Where can I find xenopus transcriptome? Any database suggestions?

Question

[lakhujanivijay]

Where can I find xenopus transcriptome? Any database suggestions? I want the whole transcriptome/CDS regions for X.tropicalis.

Answer 1

[natasha.sernova]

There are many sites and articles, since it's a model organism:

The main database: UCSC Xenopus tropicalis

Biostar posts:

Xenopus tropicalis:

A: Can somebody suggest names for frog genome databases? - this is your pevious question

Genes From Ucsc Genome Browser

Find Nucleotide Sequence Corresponding To Genome Regions

Transcriptome Database

Other sources:

http://www.xenbase.org/entry/

http://www.ncbi.nlm.nih.gov/pubmed/26391338

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479861/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530680/

http://jason.chuang.ca/research/xenopus/

http://www.marcottelab.org/index.php/Xenopus_Genome_Project

https://en.wikipedia.org/wiki/Xenopus

Answer 2

[GenoMax]

Take a look at this link:ftp://ftp.xenbase.org/pub/Genomics/Sequences/ (or the NCBI directory) under there.

Answer 3

[Denise CS]

You can download the cDNA sequences (in FASTA) from the Ensembl FTP site, and visualise our transcripts (annotated based on cDNA and protein evidence) in the browser.