[ensembl-dev] help to retrieve the genomic sequence for 28S rRNA

Liu,Bin BLiu1 at mdanderson.org
Wed May 4 16:32:24 BST 2011


Hi, Nath,
            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.
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).
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.
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.
Thanks a lot for the help.

Bin


From: Nathan Johnson [mailto:njohnson at ebi.ac.uk]
Sent: Wednesday, May 04, 2011 7:09 AM
To: Nathan Johnson
Cc: Liu,Bin; dev at ensembl.org
Subject: Re: [ensembl-dev] help to retrieve the genomic sequence for 28S rRNA

Hi Bin

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.

Nath
On 4 May 2011, at 13:05, Nathan Johnson wrote:


Hi Bin

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.

http://www.ensembl.org/Homo_sapiens/Lucene/Details?species=Homo_sapiens;idx=Gene;end=62;q=MRPS*

Look in the protein family view for evidence.



Thanks

Nath

On 29 Apr 2011, at 23:38, Liu,Bin wrote:


Hi,
                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.
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.


Bin Liu, Ph.D.
Department of Genetics
The University of Texas M. D. Anderson Cancer Center
1515 Holcombe Blvd
Houston, TX 77030
Phone:  713-792-0878
Email: bliu1 at mdanderson.org<mailto:bliu1 at mdanderson.org>
Room No: S13.8316A

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Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
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Cambridge CB10 1SD

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_______________________________________________
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Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl







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