Answers.Body: <p>It seems so, yes. </p>
  
  <p>UCSC uses a 10Kb definition and representation for telomeres in human. In the table you shared this is consistent across all chromosomes, not only chr21. This 10kb representation is an approximation to the mean value observed in newborns and is supported by evidence like the one linked below. </p>
  
  <p>Taken from <a href="https://en.wikipedia.org/wiki/Telomere" rel="nofollow noreferrer">Wikipedia</a>: </p>
  
  <p>A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. <strong>For vertebrates</strong>, the sequence of nucleotides in telomeres is AGGGTT, with the complementary DNA strand being TCCCAA, with a single-stranded TTAGGG overhang. This sequence of <strong>TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth[ to less than 4 kilobases in old age</strong>, with the average rate of decline being greater in men than in women.</p>
  
  <p>2,500 x 6 (TCCCAA) = 15,000<br>
  (approx. 10K)</p>
  
  <p>Two interesting additional facts: </p>
  
  <p><a href="http://science.sciencemag.org/content/350/6265/1193.full" rel="nofollow noreferrer">The minimum telomere length needed to ensure human telomere protective stability in white blood cells is 3.81 kb</a><br>
  <a href="https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=715252179_oJrvVDkmdEEyM8d3cov3mFWLDTRZ&amp;clade=mammal&amp;org=Mouse&amp;db=0&amp;hgta_group=map&amp;hgta_track=gap&amp;hgta_table=gap&amp;hgta_regionType=genome&amp;position=&amp;hgta_outputType=primaryTable&amp;hgta_outFileName=" rel="nofollow noreferrer">Mouse has a 100Kb telomere representation in USCS</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-12T11:03:08.830Z
Answers.LastActivityDate: 2019-03-12T11:03:08.830Z
Answers.UserDisplayName: JRodrigoF
Body: <p>UCSC provides a database of telomere regions for each chromosome:</p>
  
  <blockquote>
    <p><a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz" rel="nofollow noreferrer">ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz</a></p>
  </blockquote>
  
  <p>It reported the telomere section in chr21 as:</p>
  
  <pre><code>grep chr21 gap.txt | grep telomere
  585 chr21   0   10000   1   N   10000   telomere    no
  952 chr21   48119895    48129895    515 N   10000   telomere    no
  </code></pre>
  
  <p>Telomere is the first 10000 bases in chr21?? But ... the region are all "N" in the reference genome!</p>
  
  <p>How does UCSC confidently give out telomere regions if they don't even know anything about the sequences?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-03-11T08:23:43.513Z
Comments.Text: Have you read any [of](https://www.ncbi.nlm.nih.gov/pubmed/29335378) [the](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292845/) [literature](https://www.ncbi.nlm.nih.gov/pubmed/25612739) on this?
Comments.UserDisplayName: Devon Ryan
Tags: <genomics>
Title: Does UCSC definition for telomere making sense?
ThreadText: # Does UCSC definition for telomere making sense?
  
  (Asked by: username_0 on 2019-03-11)
  
  UCSC provides a database of telomere regions for each chromosome:
  
  > <ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz>
  
  It reported the telomere section in chr21 as:
  
  ```
  grep chr21 gap.txt | grep telomere
  585 chr21   0   10000   1   N   10000   telomere    no
  952 chr21   48119895    48129895    515 N   10000   telomere    no
  
  ```
  
  Telomere is the first 10000 bases in chr21?? But ... the region are all "N" in the reference genome!
  
  How does UCSC confidently give out telomere regions if they don't even know anything about the sequences?
  
  **Tags:** genomics
  
  > **Comments:**
  > **username_1**: Have you read any [of](https://www.ncbi.nlm.nih.gov/pubmed/29335378) [the](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292845/) [literature](https://www.ncbi.nlm.nih.gov/pubmed/25612739) on this?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-03-12. Score: 3
  
  It seems so, yes.
  
  UCSC uses a 10Kb definition and representation for telomeres in human. In the table you shared this is consistent across all chromosomes, not only chr21. This 10kb representation is an approximation to the mean value observed in newborns and is supported by evidence like the one linked below.
  
  Taken from [Wikipedia](https://en.wikipedia.org/wiki/Telomere):
  
  A telomere is a region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. **For vertebrates**, the sequence of nucleotides in telomeres is AGGGTT, with the complementary DNA strand being TCCCAA, with a single-stranded TTAGGG overhang. This sequence of **TTAGGG is repeated approximately 2,500 times in humans. In humans, average telomere length declines from about 11 kilobases at birth[ to less than 4 kilobases in old age**, with the average rate of decline being greater in men than in women.
  
  2,500 x 6 (TCCCAA) = 15,000  
  (approx. 10K)
  
  Two interesting additional facts:
  
  [The minimum telomere length needed to ensure human telomere protective stability in white blood cells is 3.81 kb](http://science.sciencemag.org/content/350/6265/1193.full)  
  [Mouse has a 100Kb telomere representation in USCS](https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=715252179_oJrvVDkmdEEyM8d3cov3mFWLDTRZ&clade=mammal&org=Mouse&db=0&hgta_group=map&hgta_track=gap&hgta_table=gap&hgta_regionType=genome&position=&hgta_outputType=primaryTable&hgta_outFileName=)
  
  
  ---
  
  