bd5ebb2dc0b10ad589ed54c3319da1fac28d2b26
max
Wed May 7 06:38:51 2025 -0700
adding html to genePred exon mouseover, refs #33749
diff --git src/hg/htdocs/goldenPath/help/codonPhase.html src/hg/htdocs/goldenPath/help/codonPhase.html
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+++ src/hg/htdocs/goldenPath/help/codonPhase.html
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+Codon phases shown on the Genome Browser
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+Gene transcript tracks, for example NCBI RefSeq and Gencode, show the codon phase of exons on mouse
+over. The text looks like this:
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+Transcript: ENST00000297261.7
+Strand: -
+Exon: Exon 2 of 3
+Codon phase: start 0, end 1: out-of-frame exon
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+The codon phase specifies where in the coding sequence the intron falls in the codon that separates two exons:
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+ - Phase 0: before the first nucleotide, cleanly between two codons.
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- Phase 1: between the first and the second nucleotide
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- Phase 2: between the second and third nucleotide
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+This means that:
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+ - The start phase of an exon is always the same as the end phase of the previous exon.
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- An exon where the end and start phases are identical can be removed without destroying the reading frame: in-frame exon.
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- An exon where start and end phases differ cannot be removed without destroying the reading frame: out-of-frame exon.
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