Correct coordinates for the first coding exon of the Zp1 gene in the mouse genome?

Question

[kifayatvet]

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

[h.mon]

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.

[kifayatvet]

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.

[Kevin Blighe]

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

[kifayatvet]

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.

[GenoMax]

Have you checked MGI-Mouse Genome Informatics site?

Answer 1

[Kevin Blighe]

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.

[kifayatvet]

Thank you Kevin Blighe, it is more clear now.