Distribution Of Isoform Length

Question

[Tianyang Li]

Is there any paper that contains the distribution of isoform length in different organisms? Here I'm interested in all the transcripts of an organism.

I've seen papers on the length distribution of transcript length in bacteria, but I haven't found anything for isoform length in different organisms.

[seidel]

Do you mean the distribution of all transcripts produced by all loci in a given organism? If so, would you expect a different shaped distribution if you considered only one transcript per locus versus all known isoforms from that locus? Or are you looking for something more relative, such as the range of isoform sizes produced per locus, per organism?

[Tianyang Li]

I mean all the transcripts in a given organism.

[Malachi Griffith]

Good follow up. I agree that this question could use a bit more clarification...

Answer 1

[Peixe]

Hi @Tmy1018;

Have you given a look to the Ensembl Genome browser? Just write the name/ID of the gene, and it will take you to a result page like this. In this example, i've done it for gorilla BRCA2, and in there you get all the isoforms and its length, for this gene (isoforms are given with this kind of identifier ENSZZZTXXXXXXXXXX, with "T" standing for "transcript", "Z" describing the species, and "Xs" is the ID).

If you are familiar with the Ensemble Compara API, you can do it programatically through it... :)

Hope this could help!

Cheers,

peixe

[Tianyang Li]

Can I get statistics for all of the isoforms of an organism?

[Peixe]

Don'know what happens to the link above... This should be the correct one. http://www.ensembl.org/Gorilla_gorilla/Transcript/Summary?db=core;g=ENSGGOG00000015808;r=13:14169243-14261094;t=ENSGGOT00000011464

@Tmy1018, What do you mean with "statistics" ??

[Tianyang Li]

I mean the distribution of isoforms' lengths

[Tianyang Li]

I think it's best if I can get the statistics for all the isoforms from all different loci.

[Peixe]

Hmmm... I don't know for sure if you can do it with the API... But it makes sense to me it could be possible, even if i'm not familiar with that API. Otherwise, you will have to retrieve the info you want manually on the link above for each isoform for each gene.