58d5e4c12295b894264e9888a1bf4dec24e200cc
cline
  Sun Jan 22 17:28:12 2012 -0800
Changing the wording around RNA accession, addressing Redmine #5983
diff --git src/hg/hgGene/info.c src/hg/hgGene/info.c
index 0116d70..3ef4cc2 100644
--- src/hg/hgGene/info.c
+++ src/hg/hgGene/info.c
@@ -74,42 +74,42 @@
 "<LI><B>retained intron</B> - The transcript contains what is an intron in \n"
 "an overlapping transcript on the same strand.  In many cases this indicates\n"
 "that the transcript was not completely processed. Unless specific steps are\n"
 "taken to isolate cytoplasmic rather than nuclear RNA, a certain fraction of the\n"
 "RNA isolated for sequencing will be incompletely processed.  Transcripts with\n"
 "retained introns should be viewed suspiciously, especially if they are long.\n"
 "However there are cases where fully mature mRNA transcripts are made with \n"
 "and without a particular intron, so transcripts with retained introns are not\n"
 "eliminated from this gene set.</LI>\n"
 "<LI><B>end bleed into intron</B> - Very often when an intron is retained, it is so\n"
 "long that the next exon is not reached and sequenced. In this case the retained\n"
 "intron can't be detected directly.  However high values of \"end bleed\" are\n"
 "strongly suggestive of a retained intron. End bleed measures how far the end of a transcript extends into an intron defined by another overlapping transcript. Note\n"
 "however that alternative promoters and alternative polyadenylation sites can\n"
 "create end bleeds in fully mature transcripts.</LI>\n"
-"<LI><B>RNA accession</B> - The RefSeq or Genbank/EMBL/DJJ accession on which\n"
-"this transcript is most closely based. Note that the splice sites when possible\n"
-"are taken from a consensus of RNA alignments rather than just from a single RNA.\n"
-"For non-RefSeq genes the bases are taken from the genome rather than the RNA.\n"
-"However the transcript does define which introns and exons are used to build\n"
-"the transcript.</LI>\n"
+"<LI><B>RNA accession</B> - The RefSeq, Genbank/EMBL/DJJ, Rfam, or tRNA accession\n"
+"accession on which this transcript is most closely based. Note that the splice\n"
+"sites when possible are taken from a consensus of RNA alignments rather than\n"
+"just from a single RNA. For non-RefSeq genes the bases are taken from the genome\n"
+"rather than the RNA.  However the transcript does define which introns and exons\n"
+"are used to build the transcript.</LI>\n"
 "<LI><B>RNA size</B> - The size of the RNA on which this transcript is most\n"
-"closely based, including the poly-A tail.</LI>\n"
+"closely based, including the poly-A tail (if any).</LI>\n"
 "<LI><B>Alignment % ID</B> - Percentage identity within of alignment of RNA\n"
 "to genome.</LI>\n"
 "<LI><B>% Coverage</B> - The percentage of the RNA covered by the alignment to\n"
-"genome. This excludes the poly-A tail.</LI>\n"
+"genome. This excludes the poly-A tail, if the RNA has one.</LI>\n"
 "<LI><B># of Alignments:</B> - The number of times this RNA aligns to the genome\n"
 "at very high stringency.  More care must be taken in interpreting genes based\n"
 "on transcripts with multiple alignments. We do substantial filtering to avoid\n"
 "pseudogenes, but extremely recent, extremely complete pseudogenes may still\n"
 "pass these filters and cause multiple alignments.</LI>\n"
 "<LI><B># of AT/AC introns</B> - The number of introns in this transcript with\n"
 "AT/AC rather than the usual GT/AG ends. There are roughly 300 genes with\n"
 "legitimate AT/AC  introns.</LI>\n"
 "<LI><B># of strange splices</B> - The number of introns that have ends which are\n"
 "neither GT/AG, GC/AG, nor AT/AC. Many of these are the result of sequencing\n"
 "errors, or polymorphisms between the DNA donors and the RNA donors.</LI>\n"
 "</UL>\n");
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