Retrieve exon positions from UCSC Genome Browser

Question

[QVINTVS_FABIVS_MAXIMVS]

Title says it all. I'm interested in a specific gene, say HK1. How can I retrieve the exon positions?

[Pierre Lindenbaum]

see Getting Genome Coordinates From Refseq Exon Mrna Position Data? and Exon Coordinates Of Hg19 Genome Download

Answer 1

[Michael Lawrence]

You could use rtracklayer in R:

library(rtracklayer)
ucsc <- browserSession()
query <- ucscTableQuery(ucsc, "knownGene", names="HK1")
HK1 <- track(query)
HK1.tx <- blocks(HK1)

This yields a GRangesList object, where each element contains the exon ranges for one of the 7 trancripts for HK1.