Answers.Body: <p>Looks like a poor annotation to me. I could understand a few scattered ncRNAs being arranged in the opposite direction from the gene, but all genes being oriented identically doesn't make sense.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-26T10:41:13.493Z
Answers.LastActivityDate: 2022-10-26T10:41:13.493Z
Answers.UserDisplayName: gringer
Body: <p>I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet:</p>
  <pre><code>chr1    .       gene    2189548 2194772 .       +       .       ID=c5eaf8c1-2bb2-566f-e154-6a9be797c11f;Name=FAAP20;gene_biotype=protein_coding;gene_id=34a96673-bfab-ebbf-b2b7-f9cb73163a4a;gene_name=FAAP20
  chr1    .       transcript      2189548 2194772 .       -       .       ID=f47feeac-74ce-1543-53b6-afd9bbb8ab19;Name=rna-NM_182533.4;gene_biotype=protein_coding;gene_id=34a96673-bfab-ebbf-b2b7-f9cb73163a4a;gene_name=FAAP20;Parent=c5eaf8c1-2bb2-566f-e154-6a9be797c11f;transcript_biotype=protein_coding;transcript_name=rna-NM_182533.4;protein_id=NP_872339.3
  </code></pre>
  <p>How do I interpret this? I checked UCSC Browser and in each case it seems that the browser agrees with the transcript in each case, which seems like it should be canonical.</p>
  <p>Moreover, I observed in this file that gene orientation is always <code>+</code>. Whereas a highly curated GFF3 of the human genome represents both directions:</p>
  <pre><code># my file
  $ awk '$3 == &quot;gene&quot; {print}' filtered_potential_genes.gff | cut -f7 | sort | uniq -c
     1600 +
  # highly curated annotations
  $ awk '$3 == &quot;gene&quot; {print}' /MANE.GRCh38.v0.95.select_refseq_genomic.gff | cut -f7 | sort|  uniq -c 
     9393 +
     9191 -
  </code></pre>
  <p>According to the person who provided me the file, the existence of bidirectional transcription was indeed the motivation for this. However, it's obviously confusing to have it still be a definitive <code>+</code> rather than <code>.</code> or something to signify unstrandedness.</p>
  <p>It seems likely that this is due to an artifact in my file. Are there other interpretations? Is the standard simply that gene orientation is meaningless and transcript orientation is important?</p>
  
Tags: <sequence-annotation><gff3>
Title: What does it mean when a gene and its transcript have opposite orientations in a GFF3 file?
ThreadText: # What does it mean when a gene and its transcript have opposite orientations in a GFF3 file?
  
  (Asked by: username_0 on 2022-10-25)
  
  I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet:
  
  ```
  chr1    .       gene    2189548 2194772 .       +       .       ID=c5eaf8c1-2bb2-566f-e154-6a9be797c11f;Name=FAAP20;gene_biotype=protein_coding;gene_id=34a96673-bfab-ebbf-b2b7-f9cb73163a4a;gene_name=FAAP20
  chr1    .       transcript      2189548 2194772 .       -       .       ID=f47feeac-74ce-1543-53b6-afd9bbb8ab19;Name=rna-NM_182533.4;gene_biotype=protein_coding;gene_id=34a96673-bfab-ebbf-b2b7-f9cb73163a4a;gene_name=FAAP20;Parent=c5eaf8c1-2bb2-566f-e154-6a9be797c11f;transcript_biotype=protein_coding;transcript_name=rna-NM_182533.4;protein_id=NP_872339.3
  
  ```
  
  How do I interpret this? I checked UCSC Browser and in each case it seems that the browser agrees with the transcript in each case, which seems like it should be canonical.
  
  Moreover, I observed in this file that gene orientation is always `+`. Whereas a highly curated GFF3 of the human genome represents both directions:
  
  ```
  # my file
  $ awk '$3 == "gene" {print}' filtered_potential_genes.gff | cut -f7 | sort | uniq -c
     1600 +
  # highly curated annotations
  $ awk '$3 == "gene" {print}' /MANE.GRCh38.v0.95.select_refseq_genomic.gff | cut -f7 | sort|  uniq -c 
     9393 +
     9191 -
  
  ```
  
  According to the person who provided me the file, the existence of bidirectional transcription was indeed the motivation for this. However, it's obviously confusing to have it still be a definitive `+` rather than `.` or something to signify unstrandedness.
  
  It seems likely that this is due to an artifact in my file. Are there other interpretations? Is the standard simply that gene orientation is meaningless and transcript orientation is important?
  
  **Tags:** sequence-annotation, gff3
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-10-26. Score: 2 | Accepted answer
  
  Looks like a poor annotation to me. I could understand a few scattered ncRNAs being arranged in the opposite direction from the gene, but all genes being oriented identically doesn't make sense.
  
  
  ---
  
  