question about annotation of rn45s gene in mouse

[Carolina Gemma]

Hello,

 

I have a question regarding the annotation of the mouse Rn45s gene in the mouse: In one of my next generation sequencing experiments this region chr17:39,842,153-39,849,643 came out as one of the most significant regions affected by the treatment in the particular set up of my experiment. When I look at this region in the UCSC genome browser it says it corresponds to the Rn45s gene (I’m looking at the mm10 assembly) and when I click with the mouse on that gene it says it corresponds to the Mus musculus non-coding RNA, oocyte_piRNA3616, complete sequence. In the Ensembl genome browser this particular region appears as a novel processed transcript RP23-81C12.1. I’m therefore confused as to whether this region corresponds to the Rn45s gene in the mouse. It seems to me that it’s probably a not well annotated region that contains some lincRNAs but I’m not completely sure. I would appreciate if someone can help me to clarify this.

Kind regards

Carolina

 

 

 

 

[Brian Lee]

Dear Carolina,

Thank you for using the UCSC Genome Browser and your question about the gene annotation in the mm10 browser in the region of chr17:39,842,153-39,849,643.

When the mouse mm10 gene table was built, it was based on data that appears to have changed. When you click the link for what we annotate as the referenced Rn45s gene, you can find under the Gene Model Information, http://genome.ucsc.edu/cgi-bin/hgGene?db=mm10&hgg_gene=Rn45s#info, a reference to a "RNA accession: NR_046233.1."

A visit to NCBI to the record for this RNA, http://www.ncbi.nlm.nih.gov/nuccore/NR_046233.1, has the note, "This record was temporarily removed by RefSeq staff for additional review." There is a link to the previous version, http://www.ncbi.nlm.nih.gov/nuccore/NR_046233.1?report=genbank, where you will see the original Rn45s annotation.

The Ensembl gene annotation for this site, http://uswest.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000097971;r=17:39843013-39846341, has the line, "Prediction Method Manual annotation (determined on a case-by-case basis) from the Havana project." In comparison, you can read about the multi-step pipeline used to build our UCSC genes annotation, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&g=knownGene, by reading our "Methods" section.

A future build of our mouse UCSC genes annotation for this region will likely change, corresponding with updates in the status of the underlying RefSeq and GenBank RNAs used to build our gene annotation (as described in our "Methods" section).

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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