One sequence with multiple CDS start and end annotation with BioMart Browser

Question

[david.a.mancilla]

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:

FBgn0040028|FBtr0070056|1563|1026;1;438|1563;437;1025|1711;585;1173|1174;149;586

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?

Thanks

[WouterDeCoster]

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

[david.a.mancilla]

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?

[WouterDeCoster]

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.