Question: Isoforms' unique loci
1
gravatar for marina-orlova
5.1 years ago by
Russian Federation
marina-orlova70 wrote:

Hello

Could you please advise any database which contains coordinates of unique loci for every isoform of alternatively spliced genes? Or any tool which can count them?

Cufflinks' output contains information about isoforms' FPKM but there are now coordinates for these loci. MATS detects different splice event but gives no coordinates. 

ADD COMMENTlink modified 5.1 years ago by Larry_Parnell16k • written 5.1 years ago by marina-orlova70

For which organism? For some plant genomes, there are 2, 4 or more copies of a single gene that would or could appear as different isoforms by RNA-Seq.

ADD REPLYlink written 5.1 years ago by Larry_Parnell16k

D. melanogaster

ADD REPLYlink written 5.1 years ago by marina-orlova70
1
gravatar for Larry_Parnell
5.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Try the fly genome browser @ Ensembl http://www.ensembl.org/Drosophila_melanogaster/Info/Index

 

ADD COMMENTlink written 5.1 years ago by Larry_Parnell16k

Thank  you!

ADD REPLYlink written 5.1 years ago by marina-orlova70
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