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hg19.trackDb.html : Differences exist between hgwbeta and hgw2 

(RR fields taken from public MySql server, not individual machine)

29081,29246d29080
< knownGeneV45lift37 | html
< knownGeneV45lift37 | <h2>Description</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | The GENCODE Genes track (version 45, January 2024) shows high-quality manual
< knownGeneV45lift37 | annotations merged with evidence-based automated annotations across the entire
< knownGeneV45lift37 | human genome generated by the
< knownGeneV45lift37 | <a href="https://www.gencodegenes.org/" target="_blank">GENCODE project</a>.
< knownGeneV45lift37 | By default, only the basic gene set is
< knownGeneV45lift37 | displayed, which is a subset of the comprehensive gene set. The basic set represents transcripts
< knownGeneV45lift37 | that GENCODE believes will be useful to the majority of users.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes
< knownGeneV45lift37 | are not displayed by default. It contains annotations on the reference chromosomes as well as
< knownGeneV45lift37 | assembly patches and alternative loci (haplotypes).</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | Statistics for the v45 release can be found in the 
< knownGeneV45lift37 | <a target="_blank" href="https://www.gencodegenes.org/human/stats_45.html">GENCODE site</a> for this build.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | For more information on the different gene tracks, see our <a target="_blank"
< knownGeneV45lift37 | href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Display Conventions and Configuration</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes.
< knownGeneV45lift37 | It includes options to display the entire GENCODE set and pseudogenes. To customize these
< knownGeneV45lift37 | options, the respective boxes can be checked or unchecked at the top of this description page. 
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | This track also includes a variety of labels which identify the transcripts when visibility is set
< knownGeneV45lift37 | to &quot;full&quot; or &quot;pack&quot;. Gene symbols (e.g. NIPA1) are displayed by default, but
< knownGeneV45lift37 | additional options include GENCODE Transcript ID (ENST00000561183.5), UCSC Known Gene ID
< knownGeneV45lift37 | (uc001yve.4), UniProt Display ID (Q7RTP0). Additional information about gene
< knownGeneV45lift37 | and transcript names can be found in our
< knownGeneV45lift37 | <a target="_blank" href="/FAQ/FAQgenes.html#genename">FAQ</a>.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | This track, in general, follows the display conventions for <a target="_blank"
< knownGeneV45lift37 | href="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction tracks</a>. The exons for
< knownGeneV45lift37 | putative non-coding genes and untranslated regions are represented by relatively thin blocks, while
< knownGeneV45lift37 | those for coding open reading frames are thicker. 
< knownGeneV45lift37 | <p><b>Coloring</b> for the gene annotations is based on the annotation type: </p>
< knownGeneV45lift37 | <ul>
< knownGeneV45lift37 |   <li><font color="#0c0c78"><b>coding</b></font>: protein coding transcripts, including polymorphic
< knownGeneV45lift37 |        pseudogenes
< knownGeneV45lift37 |   <li><font color="#006400"><b>non-coding</b></font>: non-protein coding transcripts
< knownGeneV45lift37 |   <li><font color="#ff33ff"><b>pseudogene</b></font>: pseudogene transcript annotations
< knownGeneV45lift37 |   <li><font color="#fe0000"><b>problem</b></font>: problem transcripts (Biotypes of
< knownGeneV45lift37 |        retained_intron, TEC, or disrupted_domain)</li>
< knownGeneV45lift37 | </ul>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | This track contains an optional <a target="_blank"
< knownGeneV45lift37 | href="../goldenPath/help/hgCodonColoring.html">codon coloring feature</a> that allows users to
< knownGeneV45lift37 | quickly validate and compare gene predictions. There is also an option to display the data as
< knownGeneV45lift37 | a <a target="_blank" href="../goldenPath/help/hgWiggleTrackHelp.html">density graph</a>, which
< knownGeneV45lift37 | can be helpful for visualizing the distribution of items over a region.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <a name="squishyPack"></a>
< knownGeneV45lift37 | <h3>Squishy-pack Display</h3>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | Within a gene using the <b>pack</b> display mode, transcripts below a specified rank will be
< knownGeneV45lift37 | condensed into a view similar to <b>squish</b> mode. The <b>transcript ranking</b> approach is
< knownGeneV45lift37 | preliminary and will change in future releases. The transcripts rankings are defined by the
< knownGeneV45lift37 | following criteria for protein-coding and non-coding genes:</p>
< knownGeneV45lift37 | <b>Protein_coding genes</b>
< knownGeneV45lift37 | <ol>
< knownGeneV45lift37 |   <li>MANE or Ensembl canonical
< knownGeneV45lift37 |     <ul>
< knownGeneV45lift37 |       <li>1st: MANE Select / Ensembl canonical</li>
< knownGeneV45lift37 |       <li>2nd: MANE Plus Clinical</li>
< knownGeneV45lift37 |     </ul>
< knownGeneV45lift37 |   </li>
< knownGeneV45lift37 |   <li>Coding biotypes
< knownGeneV45lift37 |     <ul>
< knownGeneV45lift37 |       <li>1st: protein_coding and protein_coding_LoF</li>
< knownGeneV45lift37 |       <li>2nd: NMDs and NSDs</li>
< knownGeneV45lift37 |       <li>3rd: retained intron and protein_coding_CDS_not_defined</li>
< knownGeneV45lift37 |     </ul>
< knownGeneV45lift37 |   </li>
< knownGeneV45lift37 |   <li>Completeness
< knownGeneV45lift37 |     <ul>
< knownGeneV45lift37 |       <li>1st: full length</li>
< knownGeneV45lift37 |       <li>2nd: CDS start/end not found</li>
< knownGeneV45lift37 |     </ul>
< knownGeneV45lift37 |   </li>
< knownGeneV45lift37 |   <li>CARS score (only for coding transcripts)</li>
< knownGeneV45lift37 |   <li>Transcript genomic span and length (only for non-coding transcripts)</li>
< knownGeneV45lift37 | </ol>
< knownGeneV45lift37 | <b>Non-coding genes</b>
< knownGeneV45lift37 | <ol>
< knownGeneV45lift37 |   <li> Transcript biotype
< knownGeneV45lift37 |     <ul>
< knownGeneV45lift37 |       <li>1st: transcript biotype identical to gene biotype</li>
< knownGeneV45lift37 |     </ul>
< knownGeneV45lift37 |   </li>
< knownGeneV45lift37 |   <li>Ensembl canonical</li>
< knownGeneV45lift37 |   <li>GENCODE basic</li>
< knownGeneV45lift37 |   <li>Transcript genomic span</li>
< knownGeneV45lift37 |   <li>Transcript length</li>
< knownGeneV45lift37 | </ol>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Methods</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | The GENCODE v45 track was built from the <a href="https://www.gencodegenes.org/human/"
< knownGeneV45lift37 | target="_blank">GENCODE downloads</a> file 
< knownGeneV45lift37 | <code>gencode.v45.chr_patch_hapl_scaff.annotation.gff3.gz</code>. Data from other sources
< knownGeneV45lift37 | were correlated with the GENCODE data to build association tables.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Related Data</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | The GENCODE Genes transcripts are annotated in numerous tables, each of which is also available as a
< knownGeneV45lift37 | <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/" target="_blank">downloadable
< knownGeneV45lift37 | file</a>.
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | One can see a full list of the associated tables in the <a href="/cgi-bin/hgTables"
< knownGeneV45lift37 | target="_blank">Table Browser</a> by selecting GENCODE Genes from the <b>track</b> menu; this list
< knownGeneV45lift37 | is then available on the <b>table</b> menu.
< knownGeneV45lift37 | </ul>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Data access</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | GENCODE Genes and its associated tables can be explored interactively using the
< knownGeneV45lift37 | <a href="../goldenPath/help/api.html" target="_blank">REST API</a>, the
< knownGeneV45lift37 | <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the
< knownGeneV45lift37 | <a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. 
< knownGeneV45lift37 | The genePred format files for hg38 are available from our 
< knownGeneV45lift37 | <a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/">
< knownGeneV45lift37 | downloads directory</a> or in our
< knownGeneV45lift37 | <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/" target="_blank">
< knownGeneV45lift37 | GTF download directory</a>. 
< knownGeneV45lift37 | All the tables can also be queried directly from our public MySQL
< knownGeneV45lift37 | servers, with more information available on our
< knownGeneV45lift37 | <a target="_blank" href="/goldenPath/help/mysql.html">help page</a> as well as on
< knownGeneV45lift37 | <a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Credits</h2>
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | The GENCODE Genes track was produced at UCSC from the GENCODE comprehensive gene set using a
< knownGeneV45lift37 | computational pipeline developed by Jim Kent and Brian Raney.  This version of the track was
< knownGeneV45lift37 | generated by Jonathan Casper.</p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>References</h2>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>
< knownGeneV45lift37 | Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC,
< knownGeneV45lift37 | Arnan C, Barnes I <em>et al</em>.
< knownGeneV45lift37 | <a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkac1071" target="_blank">
< knownGeneV45lift37 | GENCODE: reference annotation for the human and mouse genomes in 2023</a>.
< knownGeneV45lift37 | <em>Nucleic Acids Res</em>. 2023 Jan 6;51(D1):D942-D949.
< knownGeneV45lift37 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36420896" target="_blank">36420896</a>; PMC: <a
< knownGeneV45lift37 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825462/" target="_blank">PMC9825462</a>
< knownGeneV45lift37 | </p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <p>A full list of GENCODE publications is available
< knownGeneV45lift37 | at <a href="https://www.gencodegenes.org/pages/publications.html" target="_blank">The GENCODE
< knownGeneV45lift37 | Project web site</a>.
< knownGeneV45lift37 | </p>
< knownGeneV45lift37 | 
< knownGeneV45lift37 | <h2>Data Release Policy</h2>
< knownGeneV45lift37 | <p>GENCODE data are available for use without restrictions.</p>
< knownGeneV45lift37 | 

103435,103436c103269,103272
< wgRna | are from snoRNABase, which is  maintained at the Laboratoire de Biologie
< wgRna | Mol&eacute;culaire Eucaryote.
---
> wgRna | are from 
> wgRna | <a href="https://www-snorna.biotoul.fr/" target="_blank">snoRNABase</a>, which is 
> wgRna | maintained at the <a href="https://www-lbme.biotoul.fr/uk/index.html" 
> wgRna | target="_blank">Laboratoire de Biologie Mol&eacute;culaire Eucaryote</a>.

103459,103460c103295,103297
< wgRna | The snoRNAs and scaRNAs genomic locations from snoRNABase were aligned to the
< wgRna | hg18 human genome assembly using BLAT and were then lifted to the hg19 assembly.
---
> wgRna | The snoRNAs and scaRNAs genomic locations from <a href="https://www-snorna.biotoul.fr/" 
> wgRna | target="_blank">snoRNABase</a> were aligned to the hg18 human genome assembly 
> wgRna | using BLAT and were then lifted to the hg19 assembly.