text: user4351: 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
  
  user4351: 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.
  Edited 30/12/2020:
  To add a bit of clarity; the link in the question is the correct link from which to download the correct file. The file with which I was working from the beginning was the wrong one, but I don't really know where I got it from the first time.
  
original_text: 4351: <p>I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species.</p>
  
  <p>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.</p>
  
  <p>Why is that?</p>
  
  <p>Source of the file: <a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz</a></p>
   4351: <p>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.</p>
  <p>To all the kind people that took interest in my problem, I am sorry.</p>
  <p>Edited 30/12/2020:
  To add a bit of clarity; the link in the question is the correct link from which to download the correct file. The file with which I was working from the beginning was the wrong one, but I don't really know where I got it from the first time.</p>
  