Answers.Body: <p>No, this is the same sequence. A single RefSeq accession will correspond to one sequence. However, nobody said that sequence needs to be unique in the genome. The specific sequence you are talking about, <a href="https://www.ncbi.nlm.nih.gov/nuccore/NM_001085545.1" rel="nofollow noreferrer">NM_001085545.1</a>, is a mouse transcript which can be aligned to many different regions of the mouse's chromosome X. </p>
  
  <p>This is your sequence:</p>
  
  <pre><code>&gt;NM_001085545.1
  agagaagtctaggcaggactggcagactacagcaatgcctcaaccaagaagcctctgcga
  gagcttgttctaggaattttcatcaatggggcttttagtcagcagggtcttgagatgcag
  ggattccagtctgttagagccacagccagaagccatagccggagccagctacattcctgg
  cagtcgcaagcgaaaaagaaacagtttggaggagttggcaacaagttctaatgttcatgg
  acctcaaaaccagggaatgtatccacatcaagttctcaactacatctactggaaaagggt
  taagatctcatctaatgatgcttatcaaaacttatttttggacgggcatgatagcgacat
  taaaatccgtgctctgggaaaaacatggtgtttacacaaagtatttttatgtcagtcagg
  ctactttgctaacattctcaaaggtacttggagagaatcacaccatggtgttataaatct
  gatcattaagaatgaggatattgatacccgatctctgcattttgtgtttggtgctttgta
  cacggatgcggatttgtcaataacacctctggaagttcctcaagttttggcagcagcatg
  cctgcttcgggtggatcaagtaattcagcagtgtgaaggaatcatgaaagaaactatcaa
  caggaacactgtgtgctcctattatttggcagcagaaacctatagattaaaagctgtaaa
  gacgagatgctttgaatggcttctttgcaatttgatggtacatccaagtgtggcacttta
  caaggaagtagacttgaagttgatgtatcttctagcactgtcttctgacttactagtcat
  gcaaaaggagattgatgtatataccacactaaaaatatggatgttcctttatcttaatcc
  atgctggaacggaaccatgaaacagcttttacaacacgcaaacaactggctttccaccca
  catggcatatgttgataacatcagttttcttgaaagtgaagaaggactaatatttcaacc
  agtgtttaaaaagctgagatttcagcacattatctgtgacttgacttccacaactattct
  tgaacaagatcgactaatacctatggcatggttgtcacccatttacaaacaacagtggtt
  gactttgctgcgaacacaagaatatggggtaattggaccacaagttatcaatgaacaaga
  acttgaagaatgcaccatgaggtgtggtacaatgatccccaaggatggaagatatacttg
  gaagtggtcagttggacgacttggctttcctttacgtgtgacctttaccaggcagtgtgt
  aattttaaggcaacggtgtcagaggtgtgatggttctgcttgccacaaccatatccgaaa
  tgtcatattcagaataactttggtgtgttttgattccaacaaaagagtaactttcagaaa
  gacaacaggttataaaatcctcacctttgaatataaggaggagcaaattgtaatgaaatt
  ggatagtgatgttctaaccttccctatgtgtatattctgcaatttcctttttgtaaacct
  aggaaatgcagaaaacaagtaatcttatcaattattagactgtaagtattttacaagtat
  tgaatggttcatttaatatgaaggctgtgtaatgactacagtgaagaagaccaaaaacaa
  attcaatattctttggagtctagtaccaccagaagtgactgcttccctccatcaccttat
  ttccatgtatttctgaagaaaacctttacttccaacaaagtatttgtcaaatcaaataaa
  cctaatcttctgatttaaatttaccatcgagatccaagcttggaatggaaataagagact
  atatttgcaaggtaaaacatctcaatcaatttgttaagtagatttggccctagctaaaat
  tgagacaaaataaaatcatgccattgttgaaactgttgtg
  </code></pre>
  
  <p>If you BLAT it against the mouse genome using the <a href="http://genome.ucsc.edu/cgi-bin/hgBlat" rel="nofollow noreferrer">UCSC BLAT tool</a>, you will see many hits, most of them almost perfect matches and some of them overlapping the regions given in your bed file:</p>
  
  <p><a href="https://i.sstatic.net/ywBxj.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ywBxj.png" alt="blat results"></a></p>
  
  <p>Your bed file matches the following hits in the image above:</p>
  
  <pre><code>NM_001085545.1  1954     1  1960  1960    99.9%  chrX   -     3441731   3443690   1960
  NM_001085545.1  1960     1  1960  1960   100.0%  chrX   +     3700233   3702192   1960
  NM_001085545.1  1954     1  1960  1960    99.9%  chrX   -     3750926   3752885   1960
  NM_001085545.1  1954     1  1960  1960    99.9%  chrX   +    31336369  31338328   1960
  </code></pre>
  
  <p>I don't know why your bed file has all of these various matches for NM_001085545.1, since you haven't told us what the bed file is supposed to be doing. A bed file is just a collection of regions. For all I know, that bed file is just "a few hits for sequence NM_001085545.1 in the genome". There is no reason to assume that each region in a bed file corresponds to a gene. </p>
  
  <p>So there's nothing wrong with your file, you're just dealing with a non-unique sequence from the mouse genome. And you don't have multiple sequences with the same accession, you have one sequence, one accession, but multiple hits for that sequence in the genome.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-10T19:33:27.543Z
Answers.LastActivityDate: 2019-06-10T19:33:27.543Z
Answers.UserDisplayName: terdon
Body: <p>I have a dataset composed on numerous RefSeq transcripts with names of the form NM_###### - essentially standard annotated mRNA accession numbers.  I notice that numerous transcripts which have different sequences (different start and stop sites in a gene) all have the same NM_#### accession number.  The interpretation is that they are all from the same gene, but this makes no sense to me.  Why should different transcripts with different sequences have the same name?  I understand this identifies their gene of origin, but they are still different transcripts.</p>
  
  <p>Here is an example from the .bed file I'm using.  Note they have different start and stop locations and even have different strand notations, but all have the same name.</p>
  
  <pre><code>chr     start        stop       name            score   strand
  chrX    3441730     3443690     NM_001085545    0       -   
  chrX    3700232     3702192     NM_001085545    0       +   
  chrX    3750925     3752885     NM_001085545    0       -   
  chrX    31336368    31338328    NM_001085545    0       +   
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T05:37:39.393Z
Comments.Text: Can you provide a few examples? If multiple entries have  same NM_### accession but different sequences, could that be because they are different versions? You can view the entire version history of any NM_### accession on the NCBI pages.
Comments.UserDisplayName: vkkodali
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T08:01:31.400Z
Comments.Text: What you're describing is almost certainly a mistake in your data. Different sequences don't have the same refseq IDs. Please give us an example.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T13:34:44.530Z
Comments.Text: I added an example of what I see in the .bed file.  Note that I misspoke a bit - I don't have the actual nucleotide sequences, but these all have different genomic start and stop sites, so they are effectively different sequences.
Comments.UserDisplayName: KirkD-CO
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T15:38:43.147Z
Comments.Text: Are they the exons?
Comments.UserDisplayName: Emily_Ensembl
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T16:08:00.330Z
Comments.Text: The current ensembl entry for that transcript is the only entry for that gene, it has a single exon spanning 3.70 to 3.72 Mb.  So what is that entry at 31 Mb supposed to represent?
Comments.UserDisplayName: swbarnes2
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T19:22:41.550Z
Comments.Text: Searching for the transcript name in ENSEMBLE, I see the location and strand are the same as the second line in my example (almost the same:  start = 3700233 - one different than mine, stop = 3702192, forward strand).  It is also noted as having only one exon.  I don't understand where the other 3 entries are coming from.
Comments.UserDisplayName: KirkD-CO
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-06-10T19:34:42.943Z
Comments.Text: We can't tell you that. Only the person who made the bed file can. What is the bed file supposed to be showing? As I show in my answer below, the sequence `NM_001085545` can be mapped extremely well to multiple regions of the mouse genome. So why many of those matches are included in the bed file is a question for the person who made the file.
Comments.UserDisplayName: terdon
Tags: <refseq>
Title: RefSeq transcript naming - transcript vs gene
ThreadText: # RefSeq transcript naming - transcript vs gene
  
  (Asked by: username_0 on 2019-06-10)
  
  I have a dataset composed on numerous RefSeq transcripts with names of the form NM\_###### - essentially standard annotated mRNA accession numbers. I notice that numerous transcripts which have different sequences (different start and stop sites in a gene) all have the same NM\_#### accession number. The interpretation is that they are all from the same gene, but this makes no sense to me. Why should different transcripts with different sequences have the same name? I understand this identifies their gene of origin, but they are still different transcripts.
  
  Here is an example from the .bed file I'm using. Note they have different start and stop locations and even have different strand notations, but all have the same name.
  
  ```
  chr     start        stop       name            score   strand
  chrX    3441730     3443690     NM_001085545    0       -   
  chrX    3700232     3702192     NM_001085545    0       +   
  chrX    3750925     3752885     NM_001085545    0       -   
  chrX    31336368    31338328    NM_001085545    0       +   
  
  ```
  
  **Tags:** refseq
  
  > **Comments:**
  > **username_1**: Can you provide a few examples? If multiple entries have  same NM_### accession but different sequences, could that be because they are different versions? You can view the entire version history of any NM_### accession on the NCBI pages.  
  > **username_2**: What you're describing is almost certainly a mistake in your data. Different sequences don't have the same refseq IDs. Please give us an example.  
  > **username_0**: I added an example of what I see in the .bed file.  Note that I misspoke a bit - I don't have the actual nucleotide sequences, but these all have different genomic start and stop sites, so they are effectively different sequences.  
  > **username_3**: Are they the exons?  
  > **username_4**: The current ensembl entry for that transcript is the only entry for that gene, it has a single exon spanning 3.70 to 3.72 Mb.  So what is that entry at 31 Mb supposed to represent?  
  > **username_0**: Searching for the transcript name in ENSEMBLE, I see the location and strand are the same as the second line in my example (almost the same:  start = 3700233 - one different than mine, stop = 3702192, forward strand).  It is also noted as having only one exon.  I don't understand where the other 3 entries are coming from.  
  > **username_2**: We can't tell you that. Only the person who made the bed file can. What is the bed file supposed to be showing? As I show in my answer below, the sequence `NM_001085545` can be mapped extremely well to multiple regions of the mouse genome. So why many of those matches are included in the bed file is a question for the person who made the file.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-06-10. Score: 4 | Accepted answer
  
  No, this is the same sequence. A single RefSeq accession will correspond to one sequence. However, nobody said that sequence needs to be unique in the genome. The specific sequence you are talking about, [NM\_001085545.1](https://www.ncbi.nlm.nih.gov/nuccore/NM_001085545.1), is a mouse transcript which can be aligned to many different regions of the mouse's chromosome X.
  
  This is your sequence:
  
  ```
  >NM_001085545.1
  agagaagtctaggcaggactggcagactacagcaatgcctcaaccaagaagcctctgcga
  gagcttgttctaggaattttcatcaatggggcttttagtcagcagggtcttgagatgcag
  ggattccagtctgttagagccacagccagaagccatagccggagccagctacattcctgg
  cagtcgcaagcgaaaaagaaacagtttggaggagttggcaacaagttctaatgttcatgg
  acctcaaaaccagggaatgtatccacatcaagttctcaactacatctactggaaaagggt
  taagatctcatctaatgatgcttatcaaaacttatttttggacgggcatgatagcgacat
  taaaatccgtgctctgggaaaaacatggtgtttacacaaagtatttttatgtcagtcagg
  ctactttgctaacattctcaaaggtacttggagagaatcacaccatggtgttataaatct
  gatcattaagaatgaggatattgatacccgatctctgcattttgtgtttggtgctttgta
  cacggatgcggatttgtcaataacacctctggaagttcctcaagttttggcagcagcatg
  cctgcttcgggtggatcaagtaattcagcagtgtgaaggaatcatgaaagaaactatcaa
  caggaacactgtgtgctcctattatttggcagcagaaacctatagattaaaagctgtaaa
  gacgagatgctttgaatggcttctttgcaatttgatggtacatccaagtgtggcacttta
  caaggaagtagacttgaagttgatgtatcttctagcactgtcttctgacttactagtcat
  gcaaaaggagattgatgtatataccacactaaaaatatggatgttcctttatcttaatcc
  atgctggaacggaaccatgaaacagcttttacaacacgcaaacaactggctttccaccca
  catggcatatgttgataacatcagttttcttgaaagtgaagaaggactaatatttcaacc
  agtgtttaaaaagctgagatttcagcacattatctgtgacttgacttccacaactattct
  tgaacaagatcgactaatacctatggcatggttgtcacccatttacaaacaacagtggtt
  gactttgctgcgaacacaagaatatggggtaattggaccacaagttatcaatgaacaaga
  acttgaagaatgcaccatgaggtgtggtacaatgatccccaaggatggaagatatacttg
  gaagtggtcagttggacgacttggctttcctttacgtgtgacctttaccaggcagtgtgt
  aattttaaggcaacggtgtcagaggtgtgatggttctgcttgccacaaccatatccgaaa
  tgtcatattcagaataactttggtgtgttttgattccaacaaaagagtaactttcagaaa
  gacaacaggttataaaatcctcacctttgaatataaggaggagcaaattgtaatgaaatt
  ggatagtgatgttctaaccttccctatgtgtatattctgcaatttcctttttgtaaacct
  aggaaatgcagaaaacaagtaatcttatcaattattagactgtaagtattttacaagtat
  tgaatggttcatttaatatgaaggctgtgtaatgactacagtgaagaagaccaaaaacaa
  attcaatattctttggagtctagtaccaccagaagtgactgcttccctccatcaccttat
  ttccatgtatttctgaagaaaacctttacttccaacaaagtatttgtcaaatcaaataaa
  cctaatcttctgatttaaatttaccatcgagatccaagcttggaatggaaataagagact
  atatttgcaaggtaaaacatctcaatcaatttgttaagtagatttggccctagctaaaat
  tgagacaaaataaaatcatgccattgttgaaactgttgtg
  
  ```
  
  If you BLAT it against the mouse genome using the [UCSC BLAT tool](http://genome.ucsc.edu/cgi-bin/hgBlat), you will see many hits, most of them almost perfect matches and some of them overlapping the regions given in your bed file:
  
  [![blat results](https://i.sstatic.net/ywBxj.png)](https://i.sstatic.net/ywBxj.png)
  
  Your bed file matches the following hits in the image above:
  
  ```
  NM_001085545.1  1954     1  1960  1960    99.9%  chrX   -     3441731   3443690   1960
  NM_001085545.1  1960     1  1960  1960   100.0%  chrX   +     3700233   3702192   1960
  NM_001085545.1  1954     1  1960  1960    99.9%  chrX   -     3750926   3752885   1960
  NM_001085545.1  1954     1  1960  1960    99.9%  chrX   +    31336369  31338328   1960
  
  ```
  
  I don't know why your bed file has all of these various matches for NM\_001085545.1, since you haven't told us what the bed file is supposed to be doing. A bed file is just a collection of regions. For all I know, that bed file is just "a few hits for sequence NM\_001085545.1 in the genome". There is no reason to assume that each region in a bed file corresponds to a gene.
  
  So there's nothing wrong with your file, you're just dealing with a non-unique sequence from the mouse genome. And you don't have multiple sequences with the same accession, you have one sequence, one accession, but multiple hits for that sequence in the genome.
  
  
  ---
  
  