I am wondering about the exact physical position and the Ensembl name for TLR1 gene in Bovine genome. The NCBI (https://www.ncbi.nlm.nih.gov/gene/574090 ) shows TLR1 in chromosome 6 without any clue about its physical position. The Ensembl does not give any results for TLR1 (https://useast.ensembl.org/Cow/Search/Results?q=TLR1;site=ensembl;facet_species=Cow;page=1;perpage=10;facet_feature_type=Gene). Some researchers showed TLR1, 6 and 10 to locate in regions of 59 MB in chromosome 6, but zooming into the region I only saw TLR6 and 10 located in the region (https://useast.ensembl.org/Bos_taurus/Location/View?db=core;r=6:59689368-59689468;source=dbSNP;v=rs55617254;vdb=variation;vf=2044109;time=1524594764 ) I also followed other study which genotypes several SNPs (rs55617254, rs55617441, rs43702940, rs55617193) in bovine TLR1 and I tried to search TLR1 position based on these SNPs. However, I found SNPs were either mapped in TLR6 or could not map in Ensembl database. Perhaps, I lost some improtant information during searching, so it could be nice if anyone who work with TLR1 could share physical position and the Ensembl name for TLR1 gene? Thank you for your help.
You can check NCBI map viewer it shows the location of the gene. See the attached file.
The alternate way to locate the gene is to download the genome and create a local database in Bioedit. Download the TLR1 protein sequence from Uniprot and do a Blast (TBLASTN) search against the local database. It will locate the gene on to the chromosome perfectly. (You can also do this online in Bovine genome.org, but unfortunately it is not working now)
Thank you, the mapview did not tell me exact position. By the way, I got an answer from Vertebrate Gene Nomenclature Committee,
We at the VGNC (Vertebrate Gene Nomenclature Committee, https://vertebrate.genenames.org) have not yet assigned a bovine gene with the name TLR1, and it is our gene names that are displayed in both NCBI Gene and Ensembl. When I look at our HCOP tool (https://www.genenames.org/cgi-bin/hcop) which aggregates orthology predictions, for human TLR1 no cow ortholog is predicted by any of the resources, which is unusual, instead it only brings back bovine TLR6 (see attached screenshot).
However, I see there is an (unreviewed) bovine TLR1 sequence in UniProt (B5TYW4), so I used BLAT to place that sequence in UMD_3.1.1, where it gave a best hit on chromosome 6 at 59687279-59689654, and also showed it was flanked by two related hits which are most similar to human TLR10 and TLR6 (see attached screenshot). This also fits perfectly with PMID 16950576, which describes "TLR6-TLR1-TLR10 in a approximately 50 kb region of bovine chromosome 6". It appears that these three loci have not been correctly automatically annotated by either RefSeq or Ensembl, probably due their similarity, and instead TLR1 and TLR6 have been merged into a single locus which is currently called TLR6, while in reality bovine TLR1 lies between TLR6 and TLR10 in the cow genome. Perhaps RefSeq can manually correct this annotation.
Hi Do
try the UCSC database where you have a genome browser and a table browser. with the Bos_taurus_UMD_3.1.1/bosTau8) Assembly, TLR1 has this position chr6:59,687,173-59,689,488.
fred
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