Answers.Body: <p>Nevermind, Answered my own question. It's a repetitive region that isn't very well understood</p>
  
  <blockquote>
    <p>The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a developmental stage- and testis-specific transcription from MSY distal heterochromatic block. We isolated two novel RNAs, which localize to Yq12 in multiple copies, show testis-specific expression, and lack active X-homologs. Experimental evidence shows that one of the above Yq12 noncoding RNAs (ncRNAs) trans-splices with CDC2L2 mRNA from chromosome 1p36.3 locus to generate a testis-specific chimeric β sv13 isoform. This 67-nt 5′UTR provided by the Yq12 transcript contains within it a Y box protein-binding CCAAT motif, indicating translational regulation of the β sv13 isoform in testis. This is also the first report of trans-splicing between a Y chromosomal and an autosomal transcript.</p>
  </blockquote>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832090/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832090/</a></p>
  
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Answers.CreationDate: 2019-04-27T23:04:16.860Z
Answers.LastActivityDate: 2019-04-29T10:08:13.387Z
Answers.LastEditDate: 2019-04-29T10:08:13.387Z
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Body: <p>Obviously there is a gap in my understanding of how sex chromosomes are annotated. I've been working on some CNV calls and noticed that most of the 2nd half of ChrY is missing annotations and no reads are being mapped there. Yq12 seems to be all NNNNNNN<a href="https://i.sstatic.net/0STLv.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/0STLv.png" alt="UCSC table browser"></a> in the hg38 reference.  </p>
  
  <p>Anyone know why? </p>
  
Tags: <sequence-annotation><read-mapping>
Title: No refseq transcripts in 2nd half of Y chromosome for HG38
ThreadText: # No refseq transcripts in 2nd half of Y chromosome for HG38
  
  (Asked by: username_0 on 2019-04-27)
  
  Obviously there is a gap in my understanding of how sex chromosomes are annotated. I've been working on some CNV calls and noticed that most of the 2nd half of ChrY is missing annotations and no reads are being mapped there. Yq12 seems to be all NNNNNNN[![UCSC table browser](https://i.sstatic.net/0STLv.png)](https://i.sstatic.net/0STLv.png) in the hg38 reference.
  
  Anyone know why?
  
  **Tags:** sequence-annotation, read-mapping
  
  
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  ## 1 answers
  
  ### Answer by username_0 on 2019-04-27. Score: 2
  
  Nevermind, Answered my own question. It's a repetitive region that isn't very well understood
  
  > The human Y chromosome, because it is enriched in repetitive DNA, has been very intractable to genetic and molecular analyses. There is no previous evidence for developmental stage- and testis-specific transcription from the male-specific region of the Y (MSY). Here, we present evidence for the first time for a developmental stage- and testis-specific transcription from MSY distal heterochromatic block. We isolated two novel RNAs, which localize to Yq12 in multiple copies, show testis-specific expression, and lack active X-homologs. Experimental evidence shows that one of the above Yq12 noncoding RNAs (ncRNAs) trans-splices with CDC2L2 mRNA from chromosome 1p36.3 locus to generate a testis-specific chimeric β sv13 isoform. This 67-nt 5′UTR provided by the Yq12 transcript contains within it a Y box protein-binding CCAAT motif, indicating translational regulation of the β sv13 isoform in testis. This is also the first report of trans-splicing between a Y chromosomal and an autosomal transcript.
  
  <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832090/>
  
  
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