Answers.Body: <p>CDS (<strong>C</strong>oding <strong>D</strong>omain <strong>S</strong>equence) is just the protein - the sequence that is translated to amino acids. The gene for a bacterium should include the regulatory region, including the promoter and stop codon. The bigger infrastructure that comprise gene clusters, a big feature of bacteria, is, in my opinion, an extension of &quot;the gene&quot;.</p>
  <p>The underlying issue is &quot;gene&quot; and  CDS look pretty similar for bacteria, so if it's a gene in the middle of a gene cluster, the differences are small. However, whats happened is the same nomenclature requirements for higher eukaryotes are imposed onto bacteria so in some cases its &quot;over-classification&quot;, i.e. there's a much bigger difference between a gene and CDS in a higher eukaryote.</p>
  
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Answers.Body: <p>A gene can contain more than one CDS which is the sequence that actually makes proteins.</p>
  <p>In gff file, multiple CDS features for the same gene need to be annotated by using a separate mRNA Parent feature for each, so there is always a 1:1 relationship of mRNA to CDS, like in the following schematic:</p>
  <pre><code>gene1            ================================    ID=gene1
  mRNA1            ================================    ID=mRNA1;Parent=gene1
  five_prime_UTR   ==                                  Parent=mRNA1
  CDS1               ==....=====...........==          Parent=mRNA1 (3 rows)
  three_prime_UTR                            ======    Parent=mRNA1
  mRNA2            ================================    ID=mRNA2;Parent=gene1
  exon             ====                                Parent=mRNA2
  CDS2               ==....................==          Parent=mRNA2 (2 rows)
  exon                                     ========    Parent=mRNA2
  </code></pre>
  <p>To illustrate how a gene is represented in gff file, look the figure below:
  <a href="https://i.sstatic.net/cYau7.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cYau7.png" alt="enter image description here" /></a></p>
  <p>The gene named EDEN extending from position 1000 to position 9000. It encodes three alternatively-spliced transcripts named EDEN.1, EDEN.2 and EDEN.3, the last of which has two alternative translational start sites leading to the generation of two protein coding sequences.</p>
  <p>Here is how this gene should be described using GFF3:</p>
  <pre><code>0  ##gff-version 3.1.26
   1  ##sequence-region ctg123 1 1497228
   2  ctg123 . gene            1000  9000  .  +  .  ID=gene00001;Name=EDEN
   3  ctg123 . TF_binding_site 1000  1012  .  +  .  ID=tfbs00001;Parent=gene00001
   4  ctg123 . mRNA            1050  9000  .  +  .  ID=mRNA00001;Parent=gene00001;Name=EDEN.1
   5  ctg123 . mRNA            1050  9000  .  +  .  ID=mRNA00002;Parent=gene00001;Name=EDEN.2
   6  ctg123 . mRNA            1300  9000  .  +  .  ID=mRNA00003;Parent=gene00001;Name=EDEN.3
   7  ctg123 . exon            1300  1500  .  +  .  ID=exon00001;Parent=mRNA00003
   8  ctg123 . exon            1050  1500  .  +  .  ID=exon00002;Parent=mRNA00001,mRNA00002
   9  ctg123 . exon            3000  3902  .  +  .  ID=exon00003;Parent=mRNA00001,mRNA00003
  10  ctg123 . exon            5000  5500  .  +  .  ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003
  11  ctg123 . exon            7000  9000  .  +  .  ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003
  12  ctg123 . CDS             1201  1500  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  13  ctg123 . CDS             3000  3902  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  14  ctg123 . CDS             5000  5500  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  15  ctg123 . CDS             7000  7600  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  16  ctg123 . CDS             1201  1500  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  17  ctg123 . CDS             5000  5500  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  18  ctg123 . CDS             7000  7600  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  19  ctg123 . CDS             3301  3902  .  +  0  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  20  ctg123 . CDS             5000  5500  .  +  1  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  21  ctg123 . CDS             7000  7600  .  +  1  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  22  ctg123 . CDS             3391  3902  .  +  0  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  23  ctg123 . CDS             5000  5500  .  +  1  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  24  ctg123 . CDS             7000  7600  .  +  1  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  </code></pre>
  <p>You can see more information about gff file in this <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md" rel="nofollow noreferrer">markdown</a>.</p>
  
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Answers.Text: The OP is asking about a bacterial species, so there is no splicing, no introns, none of that.
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Answers.Text: Thank you so much. I could understand.
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Body: <p>I'm investigating bacterial genome.
  In GFF file, it includes gene, CDS, tRNA or something like that in region fields.</p>
  <p>What is the difference between gene and CDS?</p>
  <p>Thant you in advance.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-14T14:02:23.180Z
Comments.Text: Please [edit] your question and show us the file. We can't really help if all we have is a description.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-16T21:04:54.913Z
Comments.Text: This question is more in the realm of pure biology than bioinformatics, and has already been asked and answered at Biology Stack Exchange: https://biology.stackexchange.com/a/11386/70838
Comments.UserDisplayName: gringer
Tags: <gene><bacteria><gff>
Title: What is difference between gene and CDS in the gff file?
ThreadText: # What is difference between gene and CDS in the gff file?
  
  (Asked by: username_0 on 2024-04-14)
  
  I'm investigating bacterial genome.
  In GFF file, it includes gene, CDS, tRNA or something like that in region fields.
  
  What is the difference between gene and CDS?
  
  Thant you in advance.
  
  **Tags:** gene, bacteria, gff
  
  > **Comments:**
  > **username_1**: Please [edit] your question and show us the file. We can't really help if all we have is a description.  
  > **username_2**: This question is more in the realm of pure biology than bioinformatics, and has already been asked and answered at Biology Stack Exchange: https://biology.stackexchange.com/a/11386/70838  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2024-04-14. Score: 3 | Accepted answer
  
  CDS (**C**oding **D**omain **S**equence) is just the protein - the sequence that is translated to amino acids. The gene for a bacterium should include the regulatory region, including the promoter and stop codon. The bigger infrastructure that comprise gene clusters, a big feature of bacteria, is, in my opinion, an extension of "the gene".
  
  The underlying issue is "gene" and CDS look pretty similar for bacteria, so if it's a gene in the middle of a gene cluster, the differences are small. However, whats happened is the same nomenclature requirements for higher eukaryotes are imposed onto bacteria so in some cases its "over-classification", i.e. there's a much bigger difference between a gene and CDS in a higher eukaryote.
  
  > **Comments:**
  > **username_0**: Thank you so much.  
  > **username_3**: @Uri thanks, upvotes are preferred to "notes of thanks".  
  
  ---
  
  ### Answer by username_4 on 2024-04-15. Score: 0
  
  A gene can contain more than one CDS which is the sequence that actually makes proteins.
  
  In gff file, multiple CDS features for the same gene need to be annotated by using a separate mRNA Parent feature for each, so there is always a 1:1 relationship of mRNA to CDS, like in the following schematic:
  
  ```
  gene1            ================================    ID=gene1
  mRNA1            ================================    ID=mRNA1;Parent=gene1
  five_prime_UTR   ==                                  Parent=mRNA1
  CDS1               ==....=====...........==          Parent=mRNA1 (3 rows)
  three_prime_UTR                            ======    Parent=mRNA1
  mRNA2            ================================    ID=mRNA2;Parent=gene1
  exon             ====                                Parent=mRNA2
  CDS2               ==....................==          Parent=mRNA2 (2 rows)
  exon                                     ========    Parent=mRNA2
  
  ```
  
  To illustrate how a gene is represented in gff file, look the figure below:
  [![enter image description here](https://i.sstatic.net/cYau7.png)](https://i.sstatic.net/cYau7.png)
  
  The gene named EDEN extending from position 1000 to position 9000. It encodes three alternatively-spliced transcripts named EDEN.1, EDEN.2 and EDEN.3, the last of which has two alternative translational start sites leading to the generation of two protein coding sequences.
  
  Here is how this gene should be described using GFF3:
  
  ```
  0  ##gff-version 3.1.26
   1  ##sequence-region ctg123 1 1497228
   2  ctg123 . gene            1000  9000  .  +  .  ID=gene00001;Name=EDEN
   3  ctg123 . TF_binding_site 1000  1012  .  +  .  ID=tfbs00001;Parent=gene00001
   4  ctg123 . mRNA            1050  9000  .  +  .  ID=mRNA00001;Parent=gene00001;Name=EDEN.1
   5  ctg123 . mRNA            1050  9000  .  +  .  ID=mRNA00002;Parent=gene00001;Name=EDEN.2
   6  ctg123 . mRNA            1300  9000  .  +  .  ID=mRNA00003;Parent=gene00001;Name=EDEN.3
   7  ctg123 . exon            1300  1500  .  +  .  ID=exon00001;Parent=mRNA00003
   8  ctg123 . exon            1050  1500  .  +  .  ID=exon00002;Parent=mRNA00001,mRNA00002
   9  ctg123 . exon            3000  3902  .  +  .  ID=exon00003;Parent=mRNA00001,mRNA00003
  10  ctg123 . exon            5000  5500  .  +  .  ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003
  11  ctg123 . exon            7000  9000  .  +  .  ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003
  12  ctg123 . CDS             1201  1500  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  13  ctg123 . CDS             3000  3902  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  14  ctg123 . CDS             5000  5500  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  15  ctg123 . CDS             7000  7600  .  +  0  ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
  16  ctg123 . CDS             1201  1500  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  17  ctg123 . CDS             5000  5500  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  18  ctg123 . CDS             7000  7600  .  +  0  ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
  19  ctg123 . CDS             3301  3902  .  +  0  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  20  ctg123 . CDS             5000  5500  .  +  1  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  21  ctg123 . CDS             7000  7600  .  +  1  ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
  22  ctg123 . CDS             3391  3902  .  +  0  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  23  ctg123 . CDS             5000  5500  .  +  1  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  24  ctg123 . CDS             7000  7600  .  +  1  ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
  
  ```
  
  You can see more information about gff file in this [markdown](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md).
  
  > **Comments:**
  > **username_1**: The OP is asking about a bacterial species, so there is no splicing, no introns, none of that.  
  > **username_0**: Thank you so much. I could understand.  
  
  ---
  
  