I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species.

My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome. I have seen that the Human one (hg39) contains both coding and non-coding transcripts. But the Mouse (mm10) RefGene.txt only contains coding transcripts.

Why is that?

Source of the file: http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz

  • $\begingroup$ Is there a reason you're using refseq rather than the more complete annotations from Ensembl/Gencode? $\endgroup$ – Devon Ryan Apr 2 '19 at 11:31
  • $\begingroup$ Yes, it is an exercise in a course. I am to use bash shell and gawk to extract some information from several refGene.txt files. The question about the absence of non-coding transcripts in mouse is not part of the exercise, but have puzzled me. I have been looking for info about it, but I haven't a clear explanation. $\endgroup$ – jorvaor Apr 2 '19 at 12:02
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    $\begingroup$ Your title and your penultimate sentence contradict each other- the file contains only non-coding transcripts or no non-coding transcripts? $\endgroup$ – Chris_Rands Apr 2 '19 at 13:16
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    $\begingroup$ It would help if you could give us a link to the file. $\endgroup$ – terdon Apr 2 '19 at 14:27
  • $\begingroup$ Chris_Rands thank you for the observation. The file contains only coding transcripts. Edited to correct it. $\endgroup$ – jorvaor Apr 4 '19 at 21:12

It wasn't the correct file. I downloaded the file again from UCSC, compared it with the file that I was using, and they were different. This new file contained both information from coding and non-coding transcripts.

To all the kind people that took interest in my problem, I am sorry.

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