Hello, Using the rat version of the Fosl2 protein produces a BLAT result versus the Rat Nov. 2004 (Baylor 3.4/rn4) Assembly. The gene is new the the RefSeq set (PROVISIONAL 12-MAR-2010) and the alignment is not of a high enough quality to be included in the rat RefSeq genes track. That is why it is not in the rat gene tracks when searching by gene symbol.
Different reference genomes will produces different BLAT results and potentially different version of proteins that are constructed using them. By the time the gene is of status = REVIEWED, there will ideally be an isoform in RefSeq based on each reference genome. Complicating all of this is a bit is the presence of Repeat masker annotation covering the same bases in the Baylor reference genome as the terminal exons for the gene. This may be the root cause of the lower alignment score (and portions of the alignment missing when using web BLAT with the protein as web BLAT uses a masked version of the genome for protein queries). If you want to align the sequence using BLAT with a close approximation of the track "RefSeq Genes" alignment parameters, obtain BLAT and the target genome, set up BLAT as described in the link below, and add in the option "-fine" to maximize sensitivity (to capture terminal exons). http://genome.ucsc.edu/FAQ/FAQblat.html Link to rat protein: http://www.ncbi.nlm.nih.gov:80/protein/6978853 top web BLAT location using protein: chr6:109,560,845-109,560,949 top web BLAT location using mRNA: chr11:24,385,131-24,385,642 details for protein BLAT: ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- browser details NP_037086.1 87 120 154 327 91.5% 6 ++ 109560845 109560949 105 details for mRNA BLAT: ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- browser details YourSeq 50 472 576 984 89.9% 11 - 24385131 24385642 512 Using the gene symbol Fosl2 in the Human Feb. 2009 (GRCh37/hg19) Assembly, identifies the gene in both the UCSC Genes and RefSeq Genes track. position of human version of the gene in human: chr2:28,615,779-28,637,514 The human version of the human protein (a RefSeq) also produces a BLAT hit in the rat assembly above, to the same general location as the rat version of the protein. Hopefully this helps to explain the data. Please let us know if you have questions, Thanks, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/2/10 3:26 PM, Klein, David (NIH/NICHD) [E] wrote: > We have a question about mapping Fosl2 to the rat genome. > > NCBI maps it unambiguously to chromosome 6 using the Celera assembly. > However, I can't seem to locate the gene using Blat or by querying the UCSC > browser with the gene symbol. > > Is there a problem in the Fosl2 region of Chr 6 in the assembly UCSC is using? > > > > David C. Klein, Ph.D., Dr. med. h.c. > Section on Neuroendocrinology > Program in Developmental Endocrinology and Genetics > The Eunice Kennedy Shriver National Institute of Child Health and Human > Development > National Institutes of Health > 49 Convent Drive > Room 6A82 > Bethesda, MD 20892-4480 > > Phone: 301-496-6915 > Fax: 301-480-3526 or -5570 > Mobile: 301-828-7254 > E-mail [email protected] > SN Web page: > http://sne.nichd.nih.gov/http://eclipse.nichd.nih.gov/nichd/sne/index.html > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
