Question: Correct coordinates for the first coding exon of the Zp1 gene in the mouse genome?
0
gravatar for kifayatvet
8 months ago by
kifayatvet10
kifayatvet10 wrote:

Which of the following four genome coordinates is correct for the first coding exon of the Zp1 gene in the mouse genome?

chr19:10,914,296-10,914,453
chr19:10,920,404-10,920,601
chr19:10,988,787-10,988,943
chr19:10,994,894-10,994,905
gene genome • 312 views
ADD COMMENTlink modified 8 months ago by h.mon28k • written 8 months ago by kifayatvet10
1

This seems like homework, if it is, please search the information yourself, it is probably against the code of conduct to ask someone else to do your homework.

There are several mouse genome versions (e.g. mm9 mm10), several annotations (e.g., Ensembl, NCBI, ENCODE), and several isoforms of the gene (Ensembl for example lists two isoforms: ENSMUST00000168708, ENSMUST00000025641). You have to be specific about what you are asking.

ADD REPLYlink written 8 months ago by h.mon28k

actually, this question was asked by a friend to me and I did try to answer by using UCSC Genome Browser but the answer is not matching with any of the given options for genome coordinates. thats why asked.

ADD REPLYlink written 8 months ago by kifayatvet10

Playing a quiz? Can you please provide some background. Also, which genome build?

ADD REPLYlink modified 8 months ago • written 8 months ago by Kevin Blighe51k

actually, this question was asked by a friend to me and I did try to answer by using UCSC Genome Browser but the answer is not matching with any of the given options for genome coordinates. that's why asked. if you have any idea please share.

ADD REPLYlink written 8 months ago by kifayatvet10

Have you checked MGI-Mouse Genome Informatics site?

ADD REPLYlink written 8 months ago by genomax74k
0
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe51k
Kevin Blighe51k wrote:

I see where the difficulty may lie.

Based on mm10 genome build.

The first co-ordinates map to the final exon. The second co-ordinates map to the first exon. This gene is transcribed from the negative strand; so, on the browser, exon numbers increment going 'backwards'. Other genes are transcribed from the positive strand, in which case the exon numbers increment going 'forward' (look at Erbb2 in mouse).

Does this clarify it?

Unfortunately, the simplistic model of transcription that we learn in school has to be thrown out entirely. Transcription is not such a rigid processes that follows rules as we portrayed many years ago. Although most genes are transcribed from either the positive or negative strand, there are many cases where a gene has an anti-sense transcript product (e.g. Xist and Tsix), in which case polymerase collision can occur. Many of these anti-sense transcripts may be functionless, but some are very much functional.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Kevin Blighe51k

Thank you Kevin Blighe, it is more clear now.

ADD REPLYlink written 8 months ago by kifayatvet10
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