Hello PY,
Thank you for your question about locating SINEs in the dog genome and for linking the related paper. We were able to take the consensus sequence from Figure 1 of the paper and BLAT (http://genome.ucsc.edu/cgi-bin/hgBlat?db=canFam3) it against the canFam3 assembly of the dog genome. We then also changed the display of the RepeatMasker track to "full", and found that the BLAT search results matched very well against a particular type of SINE elements: SINEC_Cf. You may be interested in looking at one of the matching regions to decide if these are the SINE elements you are interested in: http://genome.ucsc.edu/cgi-bin/hgTracks?db=canFam3&position=chr3%3A24259272-24259453&rmsk=full.
One of our engineers notes that any data on our website will be displayed with respect to the reference genome assembly (e.g., http://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.3/ for canFam3). In general, immortalized cell lines often have significant differences from "healthy" DNA for the same species, sometimes even different karyotypes. If you want data specific to some cell line, then you will have to figure out how that differs from the reference genome assembly.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Jonathan Casper
UCSC Genome Bioinformatics Group
Thank you very much !Let me explain my question that i ask for the conservative sequence of the dog genome,which can be insteaed by the SINE( short interspersed nuclear element),can you tell me the SINE of the dog ,i am looking forward your reply,thank you !
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