Ensembl: Genes versus Transcripts
Entering edit mode
3.5 years ago

Going under the Ensembl one can look up particular genes as well as particular transcripts. In the process of doing so you can view the sequence, such as the sequence here. Now I understand that a particular gene can have many different transcripts (the gene I link in this instance has 8 different transcripts). So what is Ensembl showing when it displays the sequence? The longest transcript? Thank you for any clarification.

gene annotation ensembl • 1.1k views
Entering edit mode

From Ensembl glossary:

For ensembl genes:

Set of Ensembl gene predictions based on experimental evidence from protein sequences and/or near-full-length cDNA available from public sequence databases. "Ensembl known genes" are predicted on the basis of species-specific database entries from manually curated UniProt/Swiss-Prot, partially manually curated RefSeq and UniProt/TrEMBL databases. Predictions of "Ensembl novel genes" are based on other experimental evidence such as protein and cDNA sequence information from related species. Golden genes are the result of a merge between a Havana transcript (manually curated) and an Ensembl gene prediction from the annotation pipeline.

For transcript:

Nucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.

and the building of a coding gene is explained here: http://asia.ensembl.org/info/genome/genebuild/automatic_coding.html

Entering edit mode
3.5 years ago

Hello nathaniel,

it is a combined view of all transcripts. You can hover your mouse over the exons and get a tooltip in which transcript this is an exon along with it's number.

fin swimmer


Login before adding your answer.

Traffic: 2090 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6