How to obtain the Ensembl transcript ID version number?

[Min Ou]

Dear UCSC staff,

The ensGene table from hg19 does not have the Ensembl transcript ID version number. May I know where can I find it? Thank you very much!

From a no longer maintained page, there is a table called EnsemblXref3 and it has the Ensembl transcript ID version number. But I cannot find it in database hg19.

http://genome.ucsc.edu/goldenpath/gbdDescriptionsOld.html

The release log seems not mention the removal or replacement of the table EnsemblXref3:

https://genome.ucsc.edu/goldenPath/releaseLog.html

Best regards,

Min Ou

[Cath Tyner]

Hello Min Ou,

Thank you for using the UCSC Genome Browser and for submitting your question regarding best ways to map hg19 Ensembl transcript IDs to corresponding ID versions.

​In previous UCSC Genome Browser versions, ​

Ensembl version information

​ ​

​was available. However, this information has been unavailable for recent versions, including hg19. 

Ensembl's "BioMart" tool from their archived GRCh37 (hg19) browser can provide a mapping for you from a list of ENST transcript IDs:

Go to Ensembl's 'hg19' archive > BioMart
Dataset: GRCh37

Filters: Ensembl Transcript IDs
- Expand "GENE"
- Check the checkbox for "Input external references ID list"
- Paste in ENST transcript IDs or upload list

E.g.,
ENST00000456328
ENST00000489730
ENST00000505370
ENST00000538476
ENST00000608083

Attributes:
Ensembl Gene ID
Ensembl Transcript ID
Version (transcript)

Click on "Results"

Output for example:
Ensembl Gene ID Ensembl Transcript ID Version (transcript)
ENSG00000223972 ENST00000456328 2
ENSG00000069812 ENST00000489730 1
ENSG00000197530 ENST00000505370 1
ENSG00000227232 ENST00000538476 1
ENSG00000097021 ENST00000608083 1

If you have further questions about Ensembl's BioMart tool, you can contact them for help: http://www.ensembl.org/Help/Contact.

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our mailing lists below:

  * Search 

previously answered questions: 

​

UCSC Genome Browser Public Help Forum 

  * Post a question to the publicly accessible UCSC Genome Browser Public Help Forum: E

mail ​

 gen...@soe.ucsc.edu

​  

​  * Confidential/Private Data UCSC Genome Browser Help: Email

 genom...@soe.ucsc.edu

​Enjoy,​

Cath
. . .
Cath Tyner
UC Santa Cruz Genomics Institute
UCSC Genome Browser: Public Help Forum, Suggestions, Contact

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[Min Ou]

Hello Cath,

May I know which release of hg19 Ensembl version had been used in UCSC Genome Browser?

I am worried about the Ensembl transcript version might vary in Ensembl releases.

Cheers,

Min Ou

[Cath Tyner]

Hello again Min,

Thank you for posting your follow-up question in order to check for matching Ensembl data versions among

​the ​

UCSC Genome Browser for hg19 and Ensembl

​'s​

GRCh3. Both browsers are based on the Ensembl 75 data release, as described below:

From Ensembl's FAQ: 
What human genome assembly and coordinate system is Ensembl using? > Linking back to a previous Ensembl release:
"We maintain a long-term archive of the previous assembly of the human genome, GRCh37, with BLAST/BLAT, VEP and BioMart. The data in this archive is based on the Ensembl 75 data."

In the UCSC Genome Browser for hg19:

​1. ​

Go to any position in hg19. For this example, I went to the default position

​

,

​ ​

chr21:33,031,597-33,041,570.

​2. 

Under the section, "Genes and Gene Predictions," change "Ensembl Genes" to "full" track view under the drop down menu, then click the "refresh" button.

​

3. ​

At the left of the browser window, click on any Ensembl transcript ID to view the transcript description page.

For example,

​at the default position with

 the Ensembl Genes track displayed

​ in full, ​ 

you can click any transcript, such as ENST00000449339.

From the details page for ENST00000449339

​, ​the line

 "Data version

​" indicates version

75

​, ​which is also printed at the top of the detail page:

To view the version of the transcript, from the UCSC transcript detail page, click on the

 link "Ensembl Transcript: ENST00000449339" 

​which will take you to Ensembl's detail page for this transcript. ​

​U

nder the "summary" section

​, you will ​

see the transcript version and the Ensemble data release version:

"Ensembl version ENST00000449339."

"Archive EnsEMBL release 75 - February 2014"

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our mailing lists below:

  * Search 

previously answered questions: 

​

UCSC Genome Browser Public Help Forum 

  * Post a question to the publicly accessible UCSC Genome Browser Public Help Forum: E

mail ​

 gen...@soe.ucsc.edu

​  

​  * Confidential/Private Data UCSC Genome Browser Help: Email

 genom...@soe.ucsc.edu

​Enjoy,​

Cath
. . .
Cath Tyner
UC Santa Cruz Genomics Institute