Slc2a3 gene copy number appears to vary between rn4 and rn5
Simpfendorfer, Kim R
Hi there,
I am studying the Slc2a3 gene and noticed that in rats the copy number varies depending on which build you look at. In rn4 it is located once between Nanog and Foxj2. In rn5 it is located between Nanog and Foxj2 and again between Necap1 and Clec4a2. I was wondering if Slc2a3 is truly present twice in rats? And which rat strain was used for this reference sequence? In humans the copy number of SLc2A3 is associated with risk for RA, and in rats the Oia2 locus also confers arthritis risk.
Thanks so much,
Kim R. Simpfendorfer, PhD
Institute Scientist
Robert S. Boas Center for Genomics & Human Genetics
The Feinstein Institute for Medical Research
Room 2138, 350 Community Drive, Manhasset, NY, 11030
Tel: (516) 562-2952 Email: ksimp...@northwell.edu
Northwell Health
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Jairo Navarro Gonzalez
Thank you for using the UCSC Genome Browser and your question about the rn4/rn5 browser.
The reason why this gene "exists" twice in the browser is because of how we map RefSeq transcripts to the rn5 assembly. We take transcripts from RefSeq and BLAT them to the assembly, keeping the best matches. This particular Slc2a3 transcript aligned perfectly to two locations on chromosome 4, and thus we kept both. If use the multi-region view to look at both regions simultaneously, you can see that both regions of the genome are basically identical, indicating that perhaps this is a tandem duplication event. Furthermore, the top-level net in the region on the right of the display indicates that this is a region in rat that doesn't exist in mouse. Lastly, the rn6 assembly has roughly the same "duplicated" region. Since tandem duplications are difficult to stitch together in an assembly, this region likely wasn't included in the rn4 assembly.
Unfortunately, we do not create the assemblies. To verify whether or not this genomic sequence should exist, you should contact the Rat Genome Sequencing Consortium. You can find more information about the assembly and which strain was used here: https://www.ncbi.nlm.nih.gov/assembly/382928
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.
Jairo Navarro
UCSC Genomics Institute
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