Question: One sequence with multiple CDS start and end annotation with BioMart Browser
gravatar for david.a.mancilla
2.8 years ago by
david.a.mancilla0 wrote:

Hi, Using the BioMart browser, I'm trying to download the CDNA Sequence from Fruitfly,
then, in Attributes I choose:

-Transcript ID
-cDNA sequences
-CDS Length
-CDS Start
-CDS End
-cDNA coding end
-cDNA coding start

But, when I get the FASTA, in some cases I get headers like the following:


There are three different CDS start and three different CDS end, and I need to determine the CDS limits of the current sequence, is it possible with this information? What can I do if not?


cds cdna biomart ensembl • 972 views
ADD COMMENTlink modified 2.8 years ago by WouterDeCoster41k • written 2.8 years ago by david.a.mancilla0

You can find information about this gene for example here, where you can read:

It is a protein_coding_gene from Drosophila melanogaster. It has 3 annotated transcripts and 3 polypeptides (2 unique).

So seems you are looking at alternative transcripts of the same gene. See also here

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

Hi, thanks for reply!
yes, I suposed that having 3 differents CDS start/end in the header, there was 3 alternative transcripts, the problem is that I'm coding a process that analizes every cDNA sequence of the fasta file downloaded from BioMart, so I have 3 different CDS for the same Transcript sequence, what'd you suggest me to do? In the header I only have one TranscriptID, should I analize this sequence three different times, one for each CDS?

ADD REPLYlink written 2.8 years ago by david.a.mancilla0

I have absolutely no idea what you are codi8ng and what you are analysing from every cDNA sequence, so I can't make a guess if it's sensible to analyse the sequence three times or just once.

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k
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