Convert UCSC isoform ID to Ensembl transcript ID

Question

[science03]

Hello everyone,

I have a few UCSC isoform IDs and I would like to convert them to the corresponding Ensembl transcript IDs. I have tried to use some online conversion tools (such as DAVID), looked up the UCSC annotation files, but couldn't yield any successful results. The IDs are part of Human hg19 genome assembly. Could anyone, please, help me with this problem?

PS: Thank you in advance!

My id list:

uc010qbi.2

uc010qbj.1

uc001iki.4

uc001ikk.2

uc001ikl.4

uc010qbk.1

uc010qbl.1

uc010qbm.1

uc001iko.4

uc001ikp.4

uc009xiw.1

uc010qbo.1

uc010qbp.1

[Maximilian Haeussler]

Sidenote: UCSC is not using these IDs anymore and has moved to Ensembl IDs. See https://genome.ucsc.edu/FAQ/FAQgenes.html#hg19 Also, the UCSC support list can be reached at [e-mail].

Answer 1

[Pierre Lindenbaum]

join with https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownToEnsembl.txt.gz

[science03]

thank you it is very useful!

Answer 2

[gperez8]

Hello,

You can convert your UCSC isoform IDs to Ensembl transcript IDs using the Table Browser. On the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), make the following selections:

1. Under Select dataset:

   clade: Mammal.

   genome: Human.

   assembly: Dec. 2013 (GRCh37/hg19)

   group: Genes and Gene Predictions

   track: UCSC Genes

   table: knownGene

2. Set the region: to “genome”

3. Next to identifiers (names/accessions):, click "paste list", and enter your list of UCSC isoform IDs
4. Set the output format to "Selected fields from primary and related tables". This will allow you to select fields of interest.
5. Click "get output"
6. On the following page, scroll down to the Linked Tables section and select "knownToEnsembl" then click "allow selection from checked tables"
7. Under hg19.knownToEnsembl fields click "check all"
8. Click "get output"

The output will then convert your UCSC isoform IDs to Ensembl transcript IDs.

If you have any follow up questions, our public help desk can always be reached at [e-mail]. You may also send questions to [e-mail] if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.