Question about how to calculate the exonFrames

[Audrey Michel]

Hi there,

I would greatly appreciate if you could clarify if exonFrames for the refGene annotation tables can be calculated from the refGene cds and exon start/end table values as I have checked previous posts and one mentions 'exonFrames cannot be derived from the refGene cds and exon start/end table values' (https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/exonFrames/genome/XRdN33qDvug/pvtwgnBxjiAJ) ?

The explanation of exonFrames is clear from the detailed explanation in (https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/exonFrame/genome/RgCwqJ9b_Q0/Mh7CJFzrLCgJ).

For example, how are the exonFrames calculated in the following example:

74 | NM_022834 | chr1 | + | 1435522 | 1442882 | 1435748 | 1439787 | 3 | 1435522,1436926,1439080, | 1435821,1437484,1442882, | 0 | VWA1 | cmpl | cmpl | 0,1,1,

Kind regards,

Audrey

[Jairo Navarro Gonzalez]

Hello Audrey,

Thank you for using the UCSC Genome Browser and your question about exon frames.

The exon frames are derived from the mRNA sequence, not the genome. In the example you shared, viewing the NM_022834 identifier on the Genome Browser shows two transcripts for the VWA1 gene. You can load the following session to view this region:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=jnavarr5&hgS_otherUserSessionName=hg19.MLQ.20159

The side-by-side alignment from the details page for NM_022834 shows the alignment of this particular transcript to the reference genome. Viewing the first exon block in the alignment shows that this exon contains 73 nucleotides. These 73 nucleotides in the first exon block encode 24 codons with an extra nucleotide remaining. This additional nucleotide will be used in the first codon for the second exon block and is given an exonFrame value of 1.

From the previously answered question you shared, the user was finding transcripts that had indels with respect to the reference. The indel shifts the exon frame for the next exon since the CDS is determined from the transcript. ExonFrames cannot be derived from the CDS and exon start/end values since these transcripts may contain indels relative to the reference genome.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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