Tell Canonical Isoform/Trancsript in gencode

Hey,

is there a way to tell which of the transcripts for a given gene corresponds to the canonical isoform in the Gencode dataset? I couldn't find such information anywhere.

Best

gencode hg19 canonical isoform grch37.hg19

• 2,386 views • link

updated 8.8 years ago by Emily

• written 8.8 years ago by mollitz

1 answer

APPRIS have carried out principal isoform analysis on the GENOCDE transcripts. These are also available in Ensembl.

• 0 views • link

written 8.8 years ago by Emily

More posts like this

AlphaFold to Ensembl transcript mapping
written 4.5 years ago by Maxime •

Hello, Is there a way to find which transcripts were used to model AlphaFold structures? My goal is to start with some VCF files to …
is the lowest numbered Ensembl transcript ID always the "canonical" transcript?
written 4.7 years ago by Charles Murtaugh •

I would like to identify a "canonical" transcript for every protein-coding gene in Ensembl. For project-related reasons, I'm using the `EnsDb.Hsapiens.v75` package in R. I …
UCSC knownCanonical hg19 vs. hg38
written 5.4 years ago by Sanjar

I searched at UCSC Genome Browser's website, but couldn't find relevant information. The hg19 version of the canonical transcripts (knownCanonical) has 32K entries whereas hg38 …
TSS of canonical transcripts
written 5.9 years ago by arsala521 •

Hi everyone, I need TSS (transcription start site) of all the protein coding genes in human genome. I only want to focus on canonical transcripts …
How can I filter my RNA-seq transcript data to display ONLY novel isoforms and variants?
written 7.3 years ago by wolfgang.rumpf •

I have some RNA-seq data from (human) cancer cells and am trying to find non-canonical transcripts (e.g. splice variants, fusion products, etc.). I have already …
Do genes starting with Gm have a canonical name yet?
written 8.1 years ago by Sharon

Hi everyone Do you know if the genes starting with Gm in **mouse** have a canonical name or not? I am stuck with those when …
Number of Transcripts in GRCh38
written 8.5 years ago by boyu93 •

I downloaded several canonical GRCh38 gtf files, but I found the number of transcripts are different in each gtf. I was hoping to find one …
[hg19] Reading genes with CCDS
written 8.9 years ago by mollitz

Hey, I got a bit lost while trying to access gene sequences in the GRCH37. I downloaded CCDS coordinates (I tried datasets from Enseml an …
Mapping Splice Variant Expression Information To Tissues
written 13.5 years ago by aravind121

<p>Ensembl provides information like for a given gene, there will be several transcripts, which lead to several protein products. beacuse of alternative splicing, several proteins(isoforms) …
Human Alternative Isoforms In Uniprot
written 13.5 years ago by Pierre

<p>Hi, </p> <p>I have been working with a couple of human alternative isoforms listed in uniprot database. Now I would like to expand the study …