How To Map Ucsc Ids To Uniprot?

I have a list of ucsc ids such as:

uc003tlo.1
uc010fmh.2
uc010fmh.2
uc010fmh.2
uc010fmh.2
uc010fmh.2
uc010srq.1
uc010srq.1
uc010snr.1
uc002cpk.1
uc001vwc.3
uc001vwc.3
uc001vwc.3
uc009vwl.2
...
......
.........

How can i map them to uniprot ids. One way i thought was possible was to download the uniprot mappings from the following link: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/ and choose the zipped file :HUMAN_9606_idmapping.dat.gz This file does have the mappings but they are not complete. For example some ids such as:

uc010bhr.2
uc002xwx.2
uc003nxj.2
uc003nxk.2
uc003nxj.2
uc003nxk.2
uc003nxj.2
uc003nxk.2
uc001nyj.2
uc001ntn.1
uc003vrg.1
uc002rah.2
uc001bvd.2
uc001fec.1
uc003zzu.1
uc010zyh.1
uc001chs.2
....
........

are not present in the downloaded uniprot zipped file. Does anyone know a better method of mapping between the ids?

ucsc uniprot mapping

• 3,091 views • link

updated 12.9 years ago by Pierre Lindenbaum

• written 12.9 years ago by Hmm •

1 answer

the ucsc table knownGene contains the uniprotID

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19  -e 'select name,proteinId from knownGene as G where name in ("uc001vwc.3", "uc002cpk.1", "uc003tlo.1", "uc009vwl.2", "uc010fmh.2", "uc010snr.1", "uc010srq.1")'

+------------+-----------+
| name       | proteinId |
+------------+-----------+
| uc001vwc.3 | A6NI47    |
| uc002cpk.1 | A6NDG6    |
| uc003tlo.1 | A2VCT2    |
| uc009vwl.2 | A6NNE7    |
| uc010fmh.2 | A5A3E0    |
| uc010snr.1 | A6NCN2    |
| uc010srq.1 | A6NC17    |
+------------+-----------+

warning: but not all transcripts in knownGene have a uniprot.

• 329 views • link

written 12.9 years ago by Pierre Lindenbaum