059927383e72afe59202535b4863fc016463127a
max
  Thu Sep 3 15:04:05 2026 -0700
Document that cdsStart == cdsEnd marks a non-coding transcript in genePred format, refs #38245

This convention was previously only documented indirectly, as a SQL
filtering tip on the Gene tracks FAQ page. Add it next to the
cdsStart/cdsEnd field declarations in genePred.as, genePredExt.as,
sangerGene.as, ensGene.as, knownGene.as, refFlat.as, genePred.h and
sangerGene.h, and mention it in FAQformat.html and bigGenePred.html
(via the equivalent thickStart == thickEnd check).

diff --git src/hg/lib/knownGene.as src/hg/lib/knownGene.as
index 357b26308ad..799e9859938 100644
--- src/hg/lib/knownGene.as
+++ src/hg/lib/knownGene.as
@@ -1,17 +1,17 @@
 table knownGene
 "Transcript from default gene set in UCSC browser"
 (
 string  name;               "Name of gene"
 string  chrom;              "Reference sequence chromosome or scaffold"
 char[1] strand;             "+ or - for strand"
 uint    txStart;            "Transcription start position (or end position for minus strand item)"
 uint    txEnd;              "Transcription end position (or start position for minus strand item)"
-uint    cdsStart;           "Coding region start (or end position if for minus strand item)"
-uint    cdsEnd;             "Coding region end (or start position if for minus strand item)"
+uint    cdsStart;           "Coding region start (or end position if for minus strand item); cdsStart == cdsEnd for non-coding transcripts"
+uint    cdsEnd;             "Coding region end (or start position if for minus strand item); cdsStart == cdsEnd for non-coding transcripts"
 uint    exonCount;          "Number of exons"
 uint[exonCount] exonStarts; "Exon start positions (or end positions for minus strand item)"
 uint[exonCount] exonEnds;   "Exon end positions (or start positions for minus strand item)"
 string  proteinID;          "UniProt display ID, UniProt accession, or RefSeq protein ID" 
 string  alignID;            "Unique identifier (GENCODE transcript ID for GENCODE Basic)"
 )