Question: Correct coordinates for the first coding exon of the Zp1 gene in the mouse genome?
0
gravatar for kifayatvet
7 days ago by
kifayatvet0
kifayatvet0 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 • 126 views
ADD COMMENTlink modified 7 days ago by h.mon24k • written 7 days ago by kifayatvet0
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 7 days ago by h.mon24k

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 6 days ago by kifayatvet0

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

ADD REPLYlink modified 6 days ago • written 7 days ago by Kevin Blighe39k

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 6 days ago by kifayatvet0

Have you checked MGI-Mouse Genome Informatics site?

ADD REPLYlink written 6 days ago by genomax64k
0
gravatar for Kevin Blighe
6 days ago by
Kevin Blighe39k
Republic of Ireland
Kevin Blighe39k 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 6 days ago • written 6 days ago by Kevin Blighe39k

Thank you Kevin Blighe, it is more clear now.

ADD REPLYlink written 6 days ago by kifayatvet0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 850 users visited in the last hour