why exon and intergenic region overlap

Question

[Binghong]

I want to obtain the exons and intergenic region from package (TxDb.Hsapiens.UCSC.hg38.knownGene) using the code below

hg38_exons<-as.data.frame(exonsBy(txdb_38))

genic <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene)
genic <- reduce(genic, ignore.strand=T)
hg38_intergenic <- gaps(genic)
hg38_intergenic <- hg38_intergenic[strand(hg38_intergenic) == "*"]

but I found that some exons and intergenic regions overlap, like

exon:chr1_108157462_108157620

intergenic region:chr1_107994608_108223340

is it right or something is wrong?

any guidance is appreciated!

[Pierre Lindenbaum]

exon and intron are from two alternative transcripts ?

[Binghong]

thanks for your reply! what do the two alternative transcripts mean? Do you know how to check if they are from two alternative transcripts or not?

[Pierre Lindenbaum]

what do the two alternative transcripts mean?

LIFE

[Binghong]

thanks! and do you know how to check if they are from two alternative transcripts or not?

[cpad0112]

see if you can print transcript names from the data frame, along with coordinates.

[Kevin Blighe]

What may help to explain it is that there exists an alternative haplotype in the GRCh38 reference genome at this locus, i.e.,, chr1_KV880763v1_alt - see UCSC link

[Binghong]

thanks for your reply!