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雾都

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Apr 21, 2015, 12:36:14 PM4/21/15
to genome
    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 !
131.pdf

Jonathan Casper

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Apr 22, 2015, 2:21:47 PM4/22/15
to 雾都, genome

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.

--
Jonathan Casper
UCSC Genome Bioinformatics Group


On Tue, Apr 21, 2015 at 3:34 AM, 雾都 <yanpen...@foxmail.com> wrote:
    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 !

--


雾都

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Apr 23, 2015, 10:15:22 AM4/23/15
to Jonathan Casper, genome
Hi,Jonathan
    Thank you very much ,it is very useful,but i think if you can supply some SINES of dog directly which i can not find it in the web!I want the specific sequence of the SINE.Could you help me ,i am looking forward your reply!Thank you!
PY


------------------ 原始邮件 ------------------
发件人: "Jonathan Casper"<jca...@soe.ucsc.edu>;
发送时间: 2015年4月23日(星期四) 凌晨2:21
收件人: "雾都"<yanpen...@foxmail.com>;
抄送: "genome"<gen...@soe.ucsc.edu>;
主题: Re: [genome] 131

Matthew Speir

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Apr 27, 2015, 1:07:54 PM4/27/15
to 雾都, genome
Hello PY,

You can obtain the consensus sequences for SINEs in the dog genome from the Repbase Update database, http://www.girinst.org/repbase/index.html. Accessing and downloading these repeat sequences requires the registration of an account with the Repbase site. Any questions about Repbase should be directed to Repbase themselves at http://www.girinst.org/about/contact.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group
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