Answers.Body: <p>Gencode is correct (when in doubt, always assume Gencode/Ensembl is correct when it differs from UCSC). What presumably happened is that the UCSC annotation pipeline noticed that Hba-a1 and Hba-a2 are nearly identical (they produce the same protein and have minimal nucleotide difference) and just misannotated.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-05T17:27:06.743Z
Answers.Text: As a general rule, it is usually safe to believe Gencode over RefSeq and RefSeq over UCSC (not because UCSC is bad, but because it isn't manually curated).
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-05T09:37:28.423Z
Answers.LastActivityDate: 2018-01-05T09:37:28.423Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I was browsering the UCSC viewer of the genome at <a href="https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&amp;lastVirtModeType=default&amp;lastVirtModeExtraState=&amp;virtModeType=default&amp;virtMode=0&amp;nonVirtPosition=&amp;position=chr11%3A32271127%2D32368934&amp;hgsid=650939229_Ph2CmqBGLyApOC2IRsw66VU7fSYT" rel="nofollow noreferrer" title="Genome position">this region</a>.</p>
  
  <p>UCSC genes label two genes as Hba-a2 while GENCODE thinks the left one is Hba-a1</p>
  
  <p>Which annotation is correct?</p>
  
Tags: <ucsc><genome-browser>
Title: Hba-a2 has two copies on UCSC genome browser
ThreadText: # Hba-a2 has two copies on UCSC genome browser
  
  (Asked by: username_0 on 2018-01-04)
  
  I was browsering the UCSC viewer of the genome at [this region](https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A32271127%2D32368934&hgsid=650939229_Ph2CmqBGLyApOC2IRsw66VU7fSYT "Genome position").
  
  UCSC genes label two genes as Hba-a2 while GENCODE thinks the left one is Hba-a1
  
  Which annotation is correct?
  
  **Tags:** ucsc, genome-browser
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-01-05. Score: 2 | Accepted answer
  
  Gencode is correct (when in doubt, always assume Gencode/Ensembl is correct when it differs from UCSC). What presumably happened is that the UCSC annotation pipeline noticed that Hba-a1 and Hba-a2 are nearly identical (they produce the same protein and have minimal nucleotide difference) and just misannotated.
  
  > **Comments:**
  > **username_2**: As a general rule, it is usually safe to believe Gencode over RefSeq and RefSeq over UCSC (not because UCSC is bad, but because it isn't manually curated).  
  
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