Question: Distribution Of Isoform Length
1
gravatar for Tianyang Li
5.4 years ago by
Tianyang Li460
Beijing, China
Tianyang Li460 wrote:

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.

length isoform rna-seq • 2.0k views
ADD COMMENTlink modified 5.3 years ago by Peixe500 • written 5.4 years ago by Tianyang Li460
1

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?

ADD REPLYlink written 5.4 years ago by seidel6.1k

I mean all the transcripts in a given organism.

ADD REPLYlink written 5.3 years ago by Tianyang Li460

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

ADD REPLYlink written 5.4 years ago by Malachi Griffith15k
1
gravatar for Peixe
5.3 years ago by
Peixe500
Spain
Peixe500 wrote:

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

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Peixe500

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

ADD REPLYlink written 5.3 years ago by Tianyang Li460

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" ??

ADD REPLYlink written 5.3 years ago by Peixe500

I mean the distribution of isoforms' lengths

ADD REPLYlink written 5.3 years ago by Tianyang Li460

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

ADD REPLYlink written 5.3 years ago by Tianyang Li460
1

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.

ADD REPLYlink written 5.3 years ago by Peixe500
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1368 users visited in the last hour