Answers.Body: <p>ENSEMBL gets their data from other sources, including a lot of RefSeq genomes which are hosted on NCBI. I've noticed that when RefSeq publishes updates to some genomes, it can take a long time to be reflected on ENSEMBL, especially for non-model genomes.</p>
  <p>You're best bet is to identify which reference genomes are available, and which is most appropriate for your use case. Things like:</p>
  <ol>
  <li>Where was the same isolated?</li>
  <li>is it annotated?</li>
  <li>is it high quality?</li>
  <li>what updates are available?</li>
  <li>which does ENSEMBL use?</li>
  </ol>
  
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Answers.CreationDate: 2024-12-13T16:47:33.470Z
Answers.Text: Thank you......
Answers.UserDisplayName: Bhavani
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Answers.UserDisplayName: dthorbur
Answers.Body: <p>Can you please explain where Ensembl is showing 4 exons for [a transcript of] the MPL gene? Are you looking at the exons for transcript <a href="https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000117400;r=1:43349263-43352736;t=ENST00000643351" rel="nofollow noreferrer">MPL-204</a> (which is tagged &quot;CDS 5' and 3' incomplete&quot;)?</p>
  <p>When I look at the transcript annotated in Ensembl as a Ensembl Canonical transcript (i.e. MPL-201), I see 12 exons defined:</p>
  <p><a href="https://asia.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000117400;mr=1:43331900-43369416;r=1:43336802-43355795;t=ENST00000372470" rel="nofollow noreferrer">https://asia.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000117400;mr=1:43331900-43369416;r=1:43336802-43355795;t=ENST00000372470</a></p>
  <p>Sequences / exons can differ between different databases, but I think the primary transcript sequences should be the same (especially if they're both coming from MANE).</p>
  
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Answers.UserDisplayName: gringer
Body: <p>I wanted to retrieve the sequence for MPL gene (exon 10 on human chromosome 1), which is implicated in chromic myeloid leukemia. The NCBI gene model <a href="https://www.ncbi.nlm.nih.gov/gene/4352#genomic-regions-transcripts-products" rel="nofollow noreferrer">displays 12 exons for the gene</a>, whereas the ENSEMBL model lists only 4 exons. The literature mentions that the pathognomonic mutations in MPL gene (MPL S505, MPL W515) are found in exon 10. I am able to retrieve the exon 10 sequence from NCBI gene, for which I need to design primers. However, the ENSEMBL DB displays only 4 exons</p>
  <ol>
  <li>Which database needs to be used for sequence retrieval if I need to design sequencing primers ?
  2.Are the sequences for genes and other parameters different in both DBs (NCBI and ENSEMBL) ?
  3.Is MANE (Minimal Annotation of Nucleotide Sequences) useful ?</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-12T18:13:28.417Z
Comments.Text: What gene? In what species? Which two _specific_ genes are you looking at on NCBI vs Ensembl?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-13T13:23:46.713Z
Comments.Text: Welcome @Bhanani glad you're here from biology SE and hope you get the answer you are seeking
Comments.UserDisplayName: M__
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Comments.Text: You wrote, "Are the sequences for genes and other parameters different in both DBs (NCBI and ENSEMBL) ?" . NO was my personal understanding @dthorbur differs. **MANE is cool BTW**. I might put together an answer if I've time. Personally I'd stick with NCBI gene (MANE is a good solution), but the ENSEMBL team will not agree with that and they did have do have a presence here so I'll wait to see if they answer.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-13T16:51:19.263Z
Comments.Text: @M__ Thank you. I agree...NCBI is user friendly
Comments.UserDisplayName: Bhavani
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Comments.CreationDate: 2024-12-13T16:52:40.327Z
Comments.Text: Please [edit] all this into the question. And make sure to also include the specific NCBI and RefSeq pages you checked so we can know what you looked at. Remember, most human genes have multiple transcripts, and "exon 10" might be included in some, skipped in others, and be the 9th or 11th or Nth exon in yet others.
Comments.UserDisplayName: terdon
Tags: <ensembl><ncbi>
Title: Gene Sequence retrieval (NCBI vs Ensembl)
ThreadText: # Gene Sequence retrieval (NCBI vs Ensembl)
  
  (Asked by: username_0 on 2024-12-12)
  
  I wanted to retrieve the sequence for MPL gene (exon 10 on human chromosome 1), which is implicated in chromic myeloid leukemia. The NCBI gene model [displays 12 exons for the gene](https://www.ncbi.nlm.nih.gov/gene/4352#genomic-regions-transcripts-products), whereas the ENSEMBL model lists only 4 exons. The literature mentions that the pathognomonic mutations in MPL gene (MPL S505, MPL W515) are found in exon 10. I am able to retrieve the exon 10 sequence from NCBI gene, for which I need to design primers. However, the ENSEMBL DB displays only 4 exons
  
  1. Which database needs to be used for sequence retrieval if I need to design sequencing primers ?
     2.Are the sequences for genes and other parameters different in both DBs (NCBI and ENSEMBL) ?
     3.Is MANE (Minimal Annotation of Nucleotide Sequences) useful ?
  
  **Tags:** ensembl, ncbi
  
  > **Comments:**
  > **username_1**: What gene? In what species? Which two _specific_ genes are you looking at on NCBI vs Ensembl?  
  > **username_2**: Welcome @Bhanani glad you're here from biology SE and hope you get the answer you are seeking  
  > **username_2**: You wrote, "Are the sequences for genes and other parameters different in both DBs (NCBI and ENSEMBL) ?" . NO was my personal understanding @username_3 differs. **MANE is cool BTW**. I might put together an answer if I've time. Personally I'd stick with NCBI gene (MANE is a good solution), but the ENSEMBL team will not agree with that and they did have do have a presence here so I'll wait to see if they answer.  
  > **username_0**: @username_2 Thank you. I agree...NCBI is user friendly  
  > **username_1**: Please [edit] all this into the question. And make sure to also include the specific NCBI and RefSeq pages you checked so we can know what you looked at. Remember, most human genes have multiple transcripts, and "exon 10" might be included in some, skipped in others, and be the 9th or 11th or Nth exon in yet others.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2024-12-13. Score: 1
  
  ENSEMBL gets their data from other sources, including a lot of RefSeq genomes which are hosted on NCBI. I've noticed that when RefSeq publishes updates to some genomes, it can take a long time to be reflected on ENSEMBL, especially for non-model genomes.
  
  You're best bet is to identify which reference genomes are available, and which is most appropriate for your use case. Things like:
  
  1. Where was the same isolated?
  2. is it annotated?
  3. is it high quality?
  4. what updates are available?
  5. which does ENSEMBL use?
  
  > **Comments:**
  > **username_0**: Thank you......  
  
  ---
  
  ### Answer by username_4 on 2024-12-14. Score: 0
  
  Can you please explain where Ensembl is showing 4 exons for [a transcript of] the MPL gene? Are you looking at the exons for transcript [MPL-204](https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000117400;r=1:43349263-43352736;t=ENST00000643351) (which is tagged "CDS 5' and 3' incomplete")?
  
  When I look at the transcript annotated in Ensembl as a Ensembl Canonical transcript (i.e. MPL-201), I see 12 exons defined:
  
  <https://asia.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000117400;mr=1:43331900-43369416;r=1:43336802-43355795;t=ENST00000372470>
  
  Sequences / exons can differ between different databases, but I think the primary transcript sequences should be the same (especially if they're both coming from MANE).
  
  
  ---
  
  