99aa2466dea4cf74a4a226debfcbbcf388637c3a
gperez2
  Mon Feb 24 09:56:52 2025 -0800
Updating the duplicate IDs in ensemb/gencod FAQ entry, refs #35222

diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html
index fab6a0fefe0..62eee32e1f7 100755
--- src/hg/htdocs/FAQ/FAQgenes.html
+++ src/hg/htdocs/FAQ/FAQgenes.html
@@ -213,35 +213,37 @@
 <h6>Why does the UCSC RefSeq track ("refGene") include duplicates, and some transcripts map to two loci?</h6>
 
 <p>This is related to the question <a href="#ncbiRefSeq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a>
 below. Briefly, the UCSC refGene track aligns the RefSeq transcripts to the genome with BLAT, with no special filtering but a
 95% identity, the NCBI RefSeq track is NCBI's mapping and the NCBI alignments were filtered using manual annotations
 to make sure that a transcript is mapped only once, even if it is perfectly aligning twice. NCBI uses manual curation
 to decide on the best placement, for example, if a gene is annotated on chr4, any alignments, even 100% identical,
 from other chromosomes are removed. As a result, the UCSC RefSeq track contains duplicates if the transcripts align
 very well to both loci and alerts the user to this fact, where as the NCBI alignments were filtered manually
 to make sure that every transcript maps only once.
 </p>
 
 <a name="duplicatesEns"></a>
 <h6>Why does the Gencode/Ensembl tracks ("knownGene", "ensGene" or "wgEncodeGencodeVXX") include a few duplicates, and some transcripts map to two loci?</h6>
 
-<p>There are seven genes in the <a target=_blank href='https://en.wikipedia.org/wiki/Pseudoautosomal_region'>PAR regions</a>
-of the human genome. These genes have identical sequences on chrX and chrY. Because of
-the identical sequences, they used to be given identical accessions by the Ensembl team.
-Since Ensembl release 110 (identical to Gencode release 44), these genes get different
-accessions. If you see duplicates in Ensembl/Gencode files, these probably predate the changes at the EBI.</p>
+<p>The human genome has seven genes located in the <a target=_blank
+href='https://en.wikipedia.org/wiki/Pseudoautosomal_region'>pseudoautosomal regions</a> (PARs),
+which have identical sequences on both chrX and chrY. The Ensembl team assigned these genes
+identical accessions due to their identical sequences. Since Ensembl release 110 (identical to
+Gencode release 44), these genes now receive distinct accessions. If you encounter duplicates in
+Ensembl/Gencode files, they likely originate from versions predating this update at the EBI.
+</p>
 
 
 <a name="ens"></a>
 <h2>The differences</h2>
 
 Some of our gene tracks look similar and contain very similar information which can be confusing.
 
 <h6>What are Ensembl and GENCODE and is there a difference?</h6>
 
 <p> 
 Officially, the Ensembl and GENCODE gene models are the same. On the latest human and mouse genome 
 assemblies (hg38 and mm10), the identifiers, transcript sequences, and exon coordinates are almost
 identical between equivalent Ensembl and GENCODE versions (excluding <a target=_blank 
 href="FAQdownloads.html#downloadAlt">alternative sequences</a> or <a target=_blank 
 href="FAQdownloads.html#downloadFix">fix sequences</a>).</p>