Hi James, You are correct that the mm9/NCBI37 assembly is from the reference strain, C57BL/6J. However, after some quick research, I was unable to determine which hemoglobin beta allele the strain has. What I can do, is explain why you're seeing Hbb-b1 twice in UCSC Genes and provide you with some additional resources for looking data regarding the hemoglobin beta subunits in the browser.
First of all, the UCSC Genes track on mm9 is fairly old (last updated in September of 2007), and since that version was created, it seems that the RefSeq records for the hemoglobin beta subunits have been significantly updated. Actually, we are actively working on an updated version of the UCSC Genes track which can be previewed here: http://genome-preview.ucsc.edu/ On the preview browser, you can open UCSC Genes (which will be the new version of the track) and go to chr7:110,959,007-110,976,897. You'll see that the second instance of Hbb-b1 that you referred to is now more accurately called Beta-s. Another great resource is the RefSeq Genes track. Turn on the RefSeq Genes track (on either the preview website or the public website), and you'll see that in addition to Hbb-b1 and Beta-s, it also displays a transcript called Hbb-b2. If you click on any of these items in the RefSeq Genes track, you'll see the alignment identity each has against the reference genome. With Hbb-b2, you can see that it only has 96.8% alignment with the reference genome, which is why it was not included in the UCSC Genes track (you can see from the description page of the UCSC Genes track that alignments of less than 98% identity are discarded). Another thing that I wanted to point out is that the Hbb-b1 and the Beta-s sequences are quite similar. When I obtained the sequence for each of these from their Genbank pages (linked to from from RefSeq Genes track details) and then, one at a time, blatted them against the genome, I found that the second best alignment (in both cases around 98% identity) is actually the location of the other. There was actually only a single base pair difference in the exon regions (there were other differences in the untranslated regions). I hope this information is helpful! Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group James Jacobs wrote, On 3/25/2011 11:20 AM: > Hi, > > my name is James Jacobs and I'm a Heme/Onc Fellow at Children's Hospital& > Research Center at Oakland. I'm currently doing research that involves > C57Bl/6J mice. I'm relatively new to the UCSC Genome Browser and I have a > question about the July 2007 assembly > > The assembly notes state that it is from the C57BL/6J strain. In my reading > of the liturature, I have noted that the C57Bl/6J mice have the "single" > genotype at their hemoglobin beta chain (there are different genotypes such > as "single" and diffuse" depending on the strain of mouse). > > In the Genome Browser at position Chr7:110,961,038-110,962,437 there is a > hemoglobin beta chain that is marked as Hbb-b1 and in the descriptive notes > it is called the hemoglobin D major chain. > > At position Chr7:110,975,048-110,976,441 there is another hemoglobin beta > chain that is also marked as Hbb-b1. In the descriptive notes, this is also > labeled as hemoglobin D major chain. > > I'm confused because the C57Bl/6J mice are not suppose to have hemoglobin D. > They are suppose to have hemoglobin S (single). > > Do you have any insight into this? I'm trying to clarify these results > before I go on to the next phase of my experiment. Any help you might be > able to offer would be greatly appreciated. Thanks so much for your time, > > James E. Jacobs MD, MPH > > > > CONFIDENTIALITY NOTICE: This electronic message (and any attachments) is > intended to be for the use only of the named recipient, and may contain > information that is confidential or privileged. If you are not the intended > recipient, you are hereby notified that any disclosure, copying, distribution > or use of the contents of this message is strictly prohibited. If you have > received this message in error or are not the named recipient, please notify > us immediately by contacting the sender at the electronic mail address noted > above, and delete and destroy all copies of this message (and any > attachments). Thank you. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
