Hello Hui, Interestingly, there are a few very similar mRNAs in this region. This region also has some simple repeats. Take a look at this session, with the simple repeat track turned on, to get a better idea of the context of what's going on:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kayla&hgS_otherUserSessionName=hg18_NM_001105662 You can read information on how we align the mRNAs by clicking on the blue-or-grey bar to the left of the mRNA track, to get to the details page: "GenBank human mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept." For information on the hap chromosomes, please see the gateway page for hg18, and scroll down to the botton: http://genome.ucsc.edu/cgi-bin/hgGateway For information on the _random chroms, please see this FAQ: http://genome.ucsc.edu/FAQ/FAQdownloads#download10 I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group Hui Liu wrote: > Hi all, > > I'm working on analyzing sequence base on UCSC genome database and it's > really helps a lot. And I have 2 simple question now. > > 1. In refFlat table of hg18, some mRNA have multi-records. For example, > NM_001105662 have 9 records. They have different location on the same > chromosome. I compare the sequence of those records, they are similar. > But my research need to know the conservation score for each NT and > they are different among different records. How can I decide which record > should I use for NM_001105662? > > 2. There are some strange chromosome such as chr22_h2_hap1, chr6_cox_hap1, > chr21_random and so on. So I want to know what these chromosome mean? > And if a mRNA can be found on regular chromosome as well as on these > strange > ones, can I think the one on the strange chromosome is less important? > > Thanks > > Hui > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
