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 @@
-
RefSeq All – all curated and predicted annotations provided by
RefSeq.
-
RefSeq Curated – subset of RefSeq All that includes only those
annotations whose accessions begin with NM, NR, NP or YP. (NP and YP are used only for
protein-coding genes on the mitochondrion; YP is used for human only.)
-
RefSeq Predicted – subset of RefSeq All that includes those annotations whose
accessions begin with XM or XR.
-
RefSeq Other – all other annotations produced by the RefSeq group that
do not fit the requirements for inclusion in the RefSeq Curated or the
- RefSeq Predicted tracks.
+ RefSeq Predicted 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).
-
RefSeq Alignments – alignments of RefSeq RNAs to the $organism genome provided
by the RefSeq group, following the display conventions for
PSL tracks.
-
RefSeq Diffs – alignment differences between the $organism reference genome(s)
and RefSeq transcripts. (Track not currently available for every assembly.)
-
UCSC RefSeq – 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.
-
RefSeq Select+MANE (subset) – Subset of RefSeq Curated, transcripts marked as
RefSeq Select or MANE Select.