<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:s="uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:rs="urn:schemas-microsoft-com:rowset" xmlns:z="#RowsetSchema" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:odc="urn:schemas-microsoft-com:office:odc" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:q="http://schemas.xmlsoap.org/soap/envelope/" xmlns:rtc="http://microsoft.com/officenet/conferencing" xmlns:D="DAV:" xmlns:Repl="http://schemas.microsoft.com/repl/" xmlns:mt="http://schemas.microsoft.com/sharepoint/soap/meetings/" xmlns:x2="http://schemas.microsoft.com/office/excel/2003/xml" xmlns:ppda="http://www.passport.com/NameSpace.xsd" xmlns:ois="http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:dir="http://schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:dsp="http://schemas.microsoft.com/sharepoint/dsp" xmlns:udc="http://schemas.microsoft.com/data/udc" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:sub="http://schemas.microsoft.com/sharepoint/soap/2002/1/alerts/" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:sp="http://schemas.microsoft.com/sharepoint/" xmlns:sps="http://schemas.microsoft.com/sharepoint/soap/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:udcs="http://schemas.microsoft.com/data/udc/soap" xmlns:udcxf="http://schemas.microsoft.com/data/udc/xmlfile" xmlns:udcp2p="http://schemas.microsoft.com/data/udc/parttopart" xmlns:wf="http://schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:mdssi="http://schemas.openxmlformats.org/package/2006/digital-signature" xmlns:mver="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mrels="http://schemas.openxmlformats.org/package/2006/relationships" xmlns:spwp="http://microsoft.com/sharepoint/webpartpages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:pptsl="http://schemas.microsoft.com/sharepoint/soap/SlideLibrary/" xmlns:spsl="http://microsoft.com/webservices/SharePointPortalServer/PublishedLinksService" xmlns:Z="urn:schemas-microsoft-com:" xmlns:st="" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.apple-style-span
{mso-style-name:apple-style-span;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple style='word-wrap: break-word;-webkit-nbsp-mode: space;-webkit-line-break: after-white-space'><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi, Nath,<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:"Calibri","sans-serif";color:#1F497D'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for the help. However, the 28S rRNA I am looking for doesn't code any protein. It is ribosomal RNA. I guess it should be categorized as non-coding gene in the genome annotation.<o:p></o:p></span></p><p class=MsoNormal style='text-indent:.5in'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I got partial sequence of 28S for Chinese Hamster from GenBank. (GenBank: AY390526.1). 28S rRNA should be conversed between Chinese hamster and B6 mouse (the ref genome). I blat the mouse genome with the sequence from GenBank. It is very strange that I couldn’t get any significant hit (all of them were short hits everywhere in the genome). <o:p></o:p></span></p><p class=MsoNormal style='text-indent:.5in'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I would like to get about 20K flanking sequence around the 28S rRNA if I can locate the genomic sites. There could be more than one genomic location for 28S rRNA on the genome due to multiple copies of the gene. However, it seems that genome annotation did index any 28S rRNA. <o:p></o:p></span></p><p class=MsoNormal style='text-indent:.5in'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I wonder if there is a way to search all of the sequenced mouse BAC clones in Ensembl. As long as I can find a sequenced BAC that contains the 20K region with 28S rRNA, we can use the BAC sequence to design our experiment. <o:p></o:p></span></p><p class=MsoNormal style='text-indent:.5in'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks a lot for the help.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Bin<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Nathan Johnson [mailto:njohnson@ebi.ac.uk] <br><b>Sent:</b> Wednesday, May 04, 2011 7:09 AM<br><b>To:</b> Nathan Johnson<br><b>Cc:</b> Liu,Bin; dev@ensembl.org<br><b>Subject:</b> Re: [ensembl-dev] help to retrieve the genomic sequence for 28S rRNA<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Bin<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>It seems there was a temporary glitch with the Ensembl search. Searchign for '28s' on human will now bring you back many more than just the MRPS genes.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Nath<o:p></o:p></p><div><div><p class=MsoNormal>On 4 May 2011, at 13:05, Nathan Johnson wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><p class=MsoNormal>Hi Bin<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>It seems the 28S subunit is not indexed well as a protein annotation. What I think you are looking for is the MRPS genes. They are clustered in various locations across several chromosomes.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="http://www.ensembl.org/Homo_sapiens/Lucene/Details?species=Homo_sapiens;idx=Gene;end=62;q=MRPS*">http://www.ensembl.org/Homo_sapiens/Lucene/Details?species=Homo_sapiens;idx=Gene;end=62;q=MRPS*</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Look in the protein family view for evidence.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Nath<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On 29 Apr 2011, at 23:38, Liu,Bin wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> I was trying to retrieve the chromosome location of 28S rRNA from Human and Mouse genome. It was surprised that I couldn't find it.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I wonder if the 28S rRNA was annotated in both of the genomes although 28S rRNA is the well known non-coding RNA. Thanks for the help.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Bin Liu, Ph.D.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Department of Genetics<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>The University of Texas M. D. Anderson Cancer Center<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>1515 Holcombe Blvd<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Houston, TX 77030<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Phone: 713-792-0878<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Email:<span class=apple-converted-space> </span></span><span lang=EN style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><a href="mailto:bliu1@mdanderson.org">bliu1@mdanderson.org</a></span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Room No: S13.8316A</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><p class=MsoNormal>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class=apple-converted-space> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class=apple-converted-space> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Nathan Johnson<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Senior Scientific Programmer<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Ensembl Regulation<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>European Bioinformatics Institute<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Wellcome Trust Genome Campus<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Hinxton<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Cambridge CB10 1SD<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><a href="http://twitter.com/#!/ensembl">http://twitter.com/#!/ensembl</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><o:p> </o:p></span></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><br><br><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif"'><br><br></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe): <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Nathan Johnson<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Senior Scientific Programmer<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Ensembl Regulation<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>European Bioinformatics Institute<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Wellcome Trust Genome Campus<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Hinxton<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Cambridge CB10 1SD<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><a href="http://twitter.com/#!/ensembl">http://twitter.com/#!/ensembl</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><br><br><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'><br><br></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>