20a6e56606f88189952c7fac787e6c0b8275fbc8
markd
  Sat May 31 12:28:24 2025 -0700
GENCODE Versions V48

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 <h2>Description</h2>
 <p>
-The GENCODE Genes track (version 48, Feb 2025 pre-release) shows high-quality manual
+The GENCODE Genes track (version 48, May 2025) shows high-quality manual
 annotations merged with evidence-based automated annotations across the entire
 human genome generated by the
 <a href="https://www.gencodegenes.org/" target="_blank">GENCODE project</a>.
 The GENCODE gene set presents a full merge
 between HAVANA manual annotation process and Ensembl automatic annotation pipeline.
 Priority is given to the manually curated HAVANA annotation using predicted
 Ensembl annotations when there are no corresponding manual annotations.
 The 48 annotation was carried out on genome assembly GRCh38 (hg38).
 </p>
 <p>
 The Ensembl human and mouse data sets are the same gene annotations as GENCODE for the
 corresponding release.
 </p>
 
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 <h2>Downloads</h2>
 <p>GENCODE GFF3 and GTF files are available from the
 <a href="https://www.gencodegenes.org/human/release_48.html" target="_blank">GENCODE release 48</a> site.</p>
 
 <h2>Verification</h2>
 
 <P>
 Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing.
 Those experiments can be found at GEO:</P>
 <ul>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30619" target="_blank"><b>GSE30619:[E-MTAB-612]</b></a> - Batch I is based on annotation from July 2008 (without pseudogenes).</li>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25711" target="_blank"><b>GSE25711:[E-MTAB-407]</b></a> - Batch II is based on annotation from April 2009. </li>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30612" target="_blank"><b>GSE30612:[E-MTAB-533]</b></a> - Batch III is verifying RGASP models for c.elegans and human.</li>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34797" target="_blank"><b>GSE34797:[E-MTAB-684]</b></a> - Batch IV is based on chromosome 3, 4 and 5 annotations from GENCODE 4 (January 2010).</li>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34820" target="_blank"><b>GSE34820:[E-MTAB-737]</b></a> - Batch V is based on annotations from GENCODE 6 (November 2010).</li>
   <li> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34821" target="_blank"><b>GSE34821:[E-MTAB-831]</b></a> - Batch VI is based on annotations from GENCODE 6 (November 2010) as well as transcript models predicted by the Ensembl Genebuild group based on the Illumina Human BodyMap 2.0 data. </li>
 </ul>
 <P> See Harrow <em>et al.</em> (2006) for information on verification
 techniques.
 </P>
 
 <h2>Release Notes</h2>
 <p>
 <span style="font-weight: bold;">GENCODE version 48 corresponds to Ensembl 114.</p>
 <p>See also: <a href="https://www.gencodegenes.org/" target="_blank">The GENCODE Project</a>
 </p>
 
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