Thank you for using the UCSC Genome Browser and your question about exonFrames in the refGene table, and for including information around NM_001282171 to provide a useful example of your inquiry.
track name="NM_001282171" description="refGene NM_001282171 chr19_KI270922v1_alt:92407-143045; Exon5 deletion 123,732-123,733"
chr19_KI270922v1_alt 92406 143045 NM_001282171 0 + 92443 123738 0 9 71,300,294,51,105,38,13,550,23, 0,3252,5104,8567,30720,31287,31327,31438,50616,
The exon frames come from the mRNA, not the genome, and this example you provided represents a transcript where there are deletions in respect to the reference. In the attached session you will see that there is a codon with a gap at chr19_KI270922v1_alt:123,732-123,733.
Since the coding region is determined from the mRNA transcript, not from the aligned genomic chunk, exonFrames cannot be derived from the refGene cds and exon start/end table values, as it sounds you are trying to implement in your code.
One place to see these alignment details is also when clicking a RefSeq gene in the browser where you will find a section titled "mRNA/Genomic Alignments" where you can further click a link titled "View details of parts of alignment within browser window." There you can scroll down to a section titled "Side by Side Alignment" and see dots indicating a deletion in the alignment:
000896 a..ag 000898
>>>>>> | || >>>>>>
123731 aacag 123735
I hope this information was helpful. Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu
All the best,
UCSC Genome Bioinformatics Group