Answers.Body: <p>If you search for those gene IDs in Ensembl, you will see that ENSCAFG00845015896 is in the primary assembly, but ENSCAFG00000017519 is deprecated, and apparently has never been in the primary assembly but originates from the genome annotation of one individual dog. I did not align the protein sequences, but on a quick look they seem identical, which is why both are connected to the same gene symbol. If your identifiers are not all from the same assembly (and sometimes even if they are), you may see several ids for the same gene symbol.</p>
  
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Answers.CreationDate: 2024-01-31T13:52:23.093Z
Answers.Text: Dear Cloudberry, thanks for your answer!
  I have another question if you please answer, you mentioned that 17519 might originated from the genome annotation of one individual dog. I thought in genome annotation for any individual, after genome sequencing and gene assembly, the gene prediction part we name regions using the refrence genome. How is that, an individual dog gene name differs from its reference genome naming? is it possible that ENSCAFG00845015896 is the updated name for ENSCAFG00000017519?
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Answers.Text: @ToTheMoon I'm not familiar with how the dog genome has been built, but I would imagine there have first been *de novo* assemblies from individual dogs, from which the primary assembly has been built. ENSCAFG00000017519 doesn't have a location in the primary assembly, so it wasn't mapped to the reference genome (because the reference didn't exist yet). When the 'offficial' assembly was built, genes were given new IDs to avoid confusion. So you're right, it's an updated ID for that gene.
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Answers.Text: thanks a lot for your answer.
Answers.UserDisplayName: ToTheMoon
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Body: <p>Hi</p>
  <p>I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but different ensemble ID. Can someone let me know how this happens? for example, for these two ensemble IDs ENSCAFG00845015896, and ENSCAFG00000017519 which are both for canines there is the same symbol of &quot;TNMD&quot;.</p>
  <p>Thanks!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-01-30T22:52:36.173Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <bioconductor><gene><ensembl><biomart>
Title: Gene ensemble vs Hugo id
ThreadText: # Gene ensemble vs Hugo id
  
  (Asked by: username_0 on 2024-01-30)
  
  Hi
  
  I have been recently struggling with the gene annotations and changing gene ID to ensemble ID. While I was doing that there were some genes for the same species that had the same gene ID but different ensemble ID. Can someone let me know how this happens? for example, for these two ensemble IDs ENSCAFG00845015896, and ENSCAFG00000017519 which are both for canines there is the same symbol of "TNMD".
  
  Thanks!
  
  **Tags:** bioconductor, gene, ensembl, biomart
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-01-31. Score: 2 | Accepted answer
  
  If you search for those gene IDs in Ensembl, you will see that ENSCAFG00845015896 is in the primary assembly, but ENSCAFG00000017519 is deprecated, and apparently has never been in the primary assembly but originates from the genome annotation of one individual dog. I did not align the protein sequences, but on a quick look they seem identical, which is why both are connected to the same gene symbol. If your identifiers are not all from the same assembly (and sometimes even if they are), you may see several ids for the same gene symbol.
  
  > **Comments:**
  > **username_0**: Dear username_2, thanks for your answer! I have another question if you please answer, you mentioned that 17519 might originated from the genome annotation of one individual dog. I thought in genome annotation for any individual, after genome sequencing and gene assembly, the gene prediction part we name regions using the refrence genome. How is that, an individual dog gene name differs from its reference genome naming? is it possible that ENSCAFG00845015896 is the updated name for ENSCAFG00000017519?  
  > **username_2**: @username_0 I'm not familiar with how the dog genome has been built, but I would imagine there have first been *de novo* assemblies from individual dogs, from which the primary assembly has been built. ENSCAFG00000017519 doesn't have a location in the primary assembly, so it wasn't mapped to the reference genome (because the reference didn't exist yet). When the 'offficial' assembly was built, genes were given new IDs to avoid confusion. So you're right, it's an updated ID for that gene.  
  > **username_0**: thanks a lot for your answer.  
  
  ---
  
  