Is there a way to map the protein sequences of unknown genes that have uniprot names to ensembl genes. (command line or through api or any ways....)
Uniprot names are as follows:
YJ015_HUMAN
ZNAS2_HUMAN
CJ052_HUMAN
YJ004_HUMAN
CEAS1_HUMAN
YJ008_HUMAN
CTLFB_HUMAN
YJ018_HUMAN
ZN487_HUMAN
FRP2L_HUMAN
SRCRM_HUMAN
HUG1_HUMAN
TI23B_HUMAN
ADAS1_HUMAN
YJ001_HUMAN
DMBTL_HUMAN
YJ017_HUMAN
YJ016_HUMAN
CSC2A_HUMAN
ASA2C_HUMAN
ANTRL_HUMAN
AGA10_HUMAN
CJ085_HUMAN
CJ136_HUMAN
CJ108_HUMAN
CJ040_HUMAN
F25DE_HUMAN
YJ012_HUMAN
CJ115_HUMAN
YJ006_HUMAN
DAS1_HUMAN
CJ112_HUMAN
AKCL1_HUMAN
FA22B_HUMAN
CJ126_HUMAN
YJ013_HUMAN
CCYL2_HUMAN
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Hope this helps You. UniProt ID Mapping. Download the text file from this site and use it As you like(via a program). You can also get data by Organism wise too.
The UniProt.org Identifier Mapping service also provide a REST Web Service, see http://www.uniprot.org/faq/28#id_mapping_examples for details.
Equivalent functionality is also available via the EMBL-EBI's Protein Identifier Cross-Reference (PICR) service which provides both REST and SOAP based Web Services for automation.
Hi,
As the person who works very closely with Ensembl's xref system. Ensembl's UniProt xrefs come from two sources. The first is direct association where a UniProt annotator has made an assertion about the link between us & them. The second is an alignment using Exonerate. I haven't investigated your list in that much detail but the random selection I took had the following results
I would recommend pre-filtering this list through UniProt a trying to reduce it down to a set of proteins which you think are really missing from Ensembl. Filtering those which are retired and maybe consider if you really want to look for PE level 5 proteins. Then the best action I can suggest is to use Ensembl's Blast service to find the mappings. If you have any problems please contact our helpdesk and I'm sure we can help out a little more.
UniProtKB names are subject to change, in the case of CJ108_HUMAN the name has changed to PRR26_HUMAN, but the primary accession (Q8N8Z3) has remained the same (see http://www.uniprot.org/uniprot/Q8N8Z3?version=* for a summary of the changes to this entry). Unsurprisingly UniProt recommend the use of accession numbers over names, although names are slightly more human friendly.
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