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why exon and intergenic region overlap

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!

intergenic exons region
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written by Binghong • Binghong

exon and intron are from two alternative transcripts ?

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written by Pierre Lindenbaum Pierre Lindenbaum

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?

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written by Binghong • Binghong

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

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written by Binghong • Binghong

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

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written by cpad0112 cpad0112

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

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written by Kevin Blighe Kevin Blighe

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