9b5f3d76a56c8f5e1957869c0faeea4be5182256 markd Sat May 31 12:56:22 2025 -0700 GENCODE Versions V48lift38 diff --git src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html index 6fc527510cb..aca7734bb9d 100644 --- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html +++ src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html @@ -1,158 +1,162 @@ </P> <H2>Description</H2> <P> The aim of the <a href="https://www.gencodegenes.org/" target="_blank">GENCODE Genes project</a> (Harrow <em>et al.</em>, 2006) is to produce a set of highly accurate annotations of evidence-based gene features on the human reference genome. This includes the identification of all protein-coding loci with associated alternative splice variants, non-coding with transcript evidence in the public databases (NCBI/EMBL/DDBJ) and pseudogenes. A high quality set of gene structures is necessary for many research studies such as comparative or evolutionary analyses, or for experimental design and interpretation of the results.</p> <p> The GENCODE Genes tracks display the high-quality manual annotations merged with evidence-based automated annotations across the entire human genome. The GENCODE gene set presents a full merge between HAVANA manual annotation and Ensembl automatic annotation. Priority is given to the manually curated HAVANA annotation using predicted Ensembl annotations when there are no corresponding manual annotations. With each release, there is an increase in the number of annotations that have undergone manual curation. This annotation was carried out on the GRCh37 (hg19) genome assembly. </p> <p>Experimental verification details are given in each descriptions for each track. Transcript Support Levels were determined for version 10 onwards based on evidence provided by GenBank mRNA and EST sequences. Versions 7 and 10 are being used in data analysis by the ENCODE consortium.</p> NOTE</B>: Due to the UCSC Genome Browser using the NC_001807 mitochondrial genome sequence (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the GENCODE mitochondrial sequences are not available in the UCSC Genome Browser. These annotations are available for download in the <a HREF="https://www.gencodegenes.org/releases/"TARGET="_BLANK"> GENCODE GTF files</a>. </p> <p> For more information on the different gene tracks, see our <a target=_blank href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p> <h2>Display Conventions</h2> <P> These are multi-view composite tracks that contain differing data sets (<EM>views</EM>). Instructions for configuring multi-view tracks are <A HREF="/goldenPath/help/multiView.html" TARGET=_BLANK>here</A>. Only some subtracks are shown by default. The user can select which subtracks are displayed via the display controls on the track details pages. Further details on display conventions and data interpretation are available in the track descriptions.</p> <h2>Data access</h2> <p> GENCODE Genes and its associated tables can be explored interactively using the <a href="../goldenPath/help/api.html" target="_blank">REST API</a>, the <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the <a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. The GENCODE data files for hg19 are available in our <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/"> downloads directory</a> as wgEncodeGencode* in genePred format. All the tables can also be queried directly from our public MySQL servers, with instructions on this method available on our <a target="_blank" href="/goldenPath/help/mysql.html">MySQL help page</a> and on <a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p> <h2>Release Notes</h2> <p> +<span style="font-weight: bold;">GENCODE version 48lift37 (mapped from GRCh38 to GRCh37)</span> +corresponds to Ensembl 114. +</p> +<p> <span style="font-weight: bold;">GENCODE version 47lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 113. </p> <p> <span style="font-weight: bold;">GENCODE version 46lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 112. </p> <p> <span style="font-weight: bold;">GENCODE version 45lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 111. </p> <p> <span style="font-weight: bold;">GENCODE version 43lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 109. </p> <p> <span style="font-weight: bold;">GENCODE version 42lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 108. </p> <p> <span style="font-weight: bold;">GENCODE version 41lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 107. </p> <p> <span style="font-weight: bold;">GENCODE version 40lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 106. </p> <p> <span style="font-weight: bold;">GENCODE version 39lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 105. </p> <p> <span style="font-weight: bold;">GENCODE version 38lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 104. </p> <p> <span style="font-weight: bold;">GENCODE version 37lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 103. </p> <p> <span style="font-weight: bold;">GENCODE version 36lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 102. </p> <p> <span style="font-weight: bold;">GENCODE version 35lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 101. </p> <p> <span style="font-weight: bold;">GENCODE version 34lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 100. </p> <p> <span style="font-weight: bold;">GENCODE version 33lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 99. </p> <p> <span style="font-weight: bold;">GENCODE version 30lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 96. </p> <p> <span style="font-weight: bold;">GENCODE version 29lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 94. </p> <p> <span style="font-weight: bold;">GENCODE version 28lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 92. </p> <p> <span style="font-weight: bold;">GENCODE version 27lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 90. </p> <p> <span style="font-weight: bold;">GENCODE version 24lift37 (mapped from GRCh38 to GRCh37)</span> corresponds to Ensembl 83. </p> <span style="font-weight: bold;">GENCODE version 19</span> corresponds to Ensembl 74 and Vega 54. </p> <span style="font-weight: bold;">GENCODE version 17</span> corresponds to Ensembl 72 and Vega 52. </p> <span style="font-weight: bold;">GENCODE version 14</span> corresponds to Ensembl 69 and Vega 49 </p> <span style="font-weight: bold;">GENCODE version 7</span> corresponds to Ensembl 62 and Vega 42 and is used in ENCODE analysis. </p> <p> See also: <a href="https://www.gencodegenes.org/human/releases.html" target="_blank">The GENCODE Project Release History</a>. </p> <!--#insert file="../../wgEncodeGencodeCredits1.shared.html"-->