dd87117369624a1c9662d47db73146b78f98c2ca max Fri Nov 17 07:47:02 2023 -0800 after discussion with Francoise at NCBI, adapting refseq track docs a little diff --git src/hg/makeDb/trackDb/human/refSeqComposite.html src/hg/makeDb/trackDb/human/refSeqComposite.html index bd71253..437ba58 100644 --- src/hg/makeDb/trackDb/human/refSeqComposite.html +++ src/hg/makeDb/trackDb/human/refSeqComposite.html @@ -29,31 +29,33 @@ </strong></em></dt> <ul> <li> <em>RefSeq All</em> – all curated and predicted annotations provided by RefSeq.</li> <li> <em>RefSeq Curated</em> – subset of <em>RefSeq All</em> that includes only those annotations whose accessions begin with NM, NR, NP or YP. <small>(NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.)</small></li> <li> <em>RefSeq Predicted</em> – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.</li> <li> <em>RefSeq Other</em> – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the <em>RefSeq Curated</em> or the - <em>RefSeq Predicted</em> tracks.</li> + <em>RefSeq Predicted</em> tracks, as they do not have a product and therefore no RefSeq accession. + More than 90% are pseudogenes, T-cell receptor or immunoglobulin segments. + The few remaining entries are gene clusters (e.g. protocadherin).</li> <li> <em>RefSeq Alignments</em> – alignments of RefSeq RNAs to the $organism genome provided by the RefSeq group, following the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">PSL tracks</a>.</li> <li> <em>RefSeq Diffs</em> – alignment differences between the $organism reference genome(s) and RefSeq transcripts. <small>(Track not currently available for every assembly.)</small> </li> <li> <em>UCSC RefSeq</em> – annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the $organism genome. This track was previously known as the "RefSeq Genes" track.</li> <li> <em>RefSeq Select+MANE (subset)</em> – Subset of RefSeq Curated, transcripts marked as RefSeq Select or MANE Select.