Hello, Firoz. We are not involved with the naming of the items in the RepeatMasker track. To answer portions of your question, it would probably be best to contact the authors of the track, Dr. Arian Smit and Robert Hubley, at http://www.repeatmasker.org.
To obtain the sequence for any specific item in the track, click on the item in the browser's graphical display. On that item's details page, click "View DNA for this feature" and then click the "get DNA" button. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Firoz Anwar Sent: Monday, November 21, 2011 5:21 AM To: [email protected] Subject: [Genome] Need help with Information Hi, I am a PhD student. My current project involves Repeat elements (Retrotransposons) in Human genome. I have checked ucsc genome browser for relevant file. And in the Human annotation database (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/) website i have found rmsk.txt.gz, which gives chromosomal location of the repeat elements in human chromosome. I have few questions, and i would be grateful if someone can please address them: 1. First question is: under the field repeatName most of them have HERV then some number and then "-int". My first question is does it mean intron? So it wouldnt have the gene info? Where can i get the complete sequence in that location of the chromosome? I know i can go to repbase to get the reference sequence, but i am rather after the sequences in the current genome build. 2. Some of the elements have HERV in their repeatName but some dont. Because I am new to this area, my understanding was all ERV in Human are called HERV. So why some of them start with HERV as repeatName and some start with LTR or MER in their repeatName field? I have given few examples below from the rmsk file. Chromosome start stop repeatName repeatFamilyName chrY 27387638 27395881 HERV9-int ERV1 chrY 27695203 27699373 HERVK3-int ERVK chrY 27719085 27723450 HERVL-int ERVL chrX 90706526 90709746 MER57A-int ERV1 chrX 93126842 93130433 LTR25-int ERV1 I would really appreciate if someone address the questions i have. Thank you for your cooperation. Firoz Centre for Vascular Research Lowy Cancer Research Centre University of New South Wales Sydney, Australia _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
