resource for number of exons and their rank in transcript · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

resource for number of exons and their rank in transcript

Any resource where I can get information about a gene with all its transcript , protein and contributing exons. Also information about number of exons contributing a particular transcript and their exon rank. In Ensembl information is available, but for many transcripts many exon ranks are missing .

transcript exon-rank exon

• 2,969 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by RT!37 •

1 answer

biomaRt should get you pretty close. If you access the biomaRt Ensembl MySQL server directly, you may be able to get even closer.

• 0 views • link

updated 6.7 years ago by Ram

• written 10.7 years ago by Sean Davis

Thanks a lot !!!

• 0 views • link

written 10.7 years ago by RT!37 •

Log in to answer this question.

More posts like this

Get Exon Sequence from biomaRt given ENST transcript ID and exon number.
written 3.4 years ago by acererak •

Hello, I have been trying to use biomart to extract the sequence given the Ensembl ENST transcript ID and a particular exon number. I also …
number of exons
written 4.5 years ago by anba •

Hi, I need to obtain list with four columns gene_name genomic_length max_number_of_exons max_number_of_introns and I can't find this information in aggegation format. I need to …
The exon numbers of each transcript,
written 5.1 years ago by haasroni •

I am looking for information about the exons that compose each transcript of a specific gene. For example: transcript 1, exons: 1,2,5 transcript2, exons: 1,2,3,4,5,6,7 …
gene feature extraction from ensembl ID/gene name
written 9.3 years ago by rajesh

Hii I have a list of gene including their ensembl ID and transcript ID. I have to retrieve information related to gene like number of …
exon pfam domain overlap
written 11.3 years ago by Duff

Hi Biostars I have a number of exon from various genes that are high confidence for differential splicing. I have used biomaRt (Ensembl) to capture …
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
written 12.5 years ago by pristanna

<p>Hi everyone, </p> <p>I need a bed file containing starts and ends of the exons, gene name and number of the exon - but just …
Get Exons & Introns Using Ensembl Rest Api
written 12.7 years ago by Gungor Budak

Hello all I have some gene IDs from Ensembl and I want to get their transcripts' exons and introns (sequences) so that later I can …
What Is A "Gene"? Redundancies In Refseq Versus Ensembl
written 13.2 years ago by Johanna Schott

<p>Whenever I annotate microarray probes or RNASeq reads and want to have information at the gene level, I deal with the following problem: In order …
Datasource For Human Generic Exons?
written 15.6 years ago by Alastair Kerr

<p>I wish to compare how sets of values differ on average along human genes. My fear is that I may get artefacts based on splice …
Getting All Exons From Ensembl...
written 16.0 years ago by Steve Moss

Hi, I'm interested in whether anyone has worked up a solution for retrieving all unique exons from Ensembl in relation to the gene IDs and …