UCSC transcript ID and Gencode Transcript ID

[Stephen Eacker]

Hello,

I’m trying to find Gencode transcript IDs for transcripts that form the knownCanonical table.  On the knownGene table, there is an “alignID” field that is described to be 

alignID

Unique identifier (GENCODE transcript ID for GENCODE Basic

This seems like it should be exactly what I need, but it returns IDs that look just like UCSC identifiers and not the Gencode/Ensembl format. 

Is there a simple way to retrieve Gencode IDs for UCSC knownGenes?

thanks,

Steve

[Brian Lee]

Dear Steve,

Thank you for using the UCSC Genome Browser and your question about connecting alignID field information from knownGene to knownCanonical.

Note that there are differences between the hg19 and hg38 databases for knownGene, that might be explaining what you are experiencing. Be sure you are querying the hg38 database in regards to your interest to find Gencode transcript IDs for transcripts that come from the knownCanonical table. For more information see the Track Description page,http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene and this blog entry: http://genome.ucsc.edu/blog/new-default-gene-set-on-grch38-gencode-basic-genes/

You can use the Table Browser to drive a selection between the two tables of knownCanonical and knownGene.

1. Go to the Table Browser and select the hg38 database: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg38 (be sure the region is set to the entire genome).

2. Set the group to "Genes..." and the track to "GENCODE v22" and change the table to "knownCanonical".

3. Change the output to "selected fields form primary and related tables" and click "get output."

4. Scroll down to the "Linked Tables" section and select "knownGene" and mark the box next to it, then scroll to the bottom and click the "allow section from checked tables".

5. Scroll to the top and from the hg38.knownCanonical section the chrom, chromStart, chromEnd, fields. From the hg38.knownGene fields section select "alignID".

6. From the very top select "get output" and you will have output such as the following:

#hg38.knownCanonical.chrom hg38.knownCanonical.chromStart hg38.knownCanonical.chromEnd hg38.knownGene.alignID
chr1 169853073 169893959 ENST00000367772.7
chr1 169795048 169854080 ENST00000359326.7
chr1 27612063 27635277 ENST00000374005.6
...

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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