5ed62dcacb3465ebcbff8e91d32a51ac528b09bf jnavarr5 Mon Mar 31 15:05:20 2025 -0700 Adding a missing <p> tag, no Remdine diff --git src/hg/htdocs/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 64ca3c1abb0..9be33d1c7bc 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -239,31 +239,33 @@ <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>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 file versions predating this update at the EBI. </p> <a name="ens"></a> <h2>The differences</h2> +<p> Some of our gene tracks look similar and contain very similar information which can be confusing. +</p> <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> <p>GENCODE uses the UCSC convention of prefixing chromosome names with "chr", e.g. "chr1" and "chrM", but Ensembl calls these "1" or "MT". At the time of writing (Ensembl 89), a few transcripts differ due to conversion issues. In addition, around 160 PAR genes are duplicated in GENCODE but only once in Ensembl. The differences affect fewer than 1% of the transcripts. Apart from gene annotation itself, the links to