How Is Ncbi Calculating This Intron?

Question

[hbw]

My understanding is that introns are regions of the genome spanned by adjacent exons of the same transcript/mRNA. I was looking at the mouse gene Myadm on chromosome 7 on NCBI. Most of the introns seem to follow this logic, but there are some introns displayed that are inexplicable for me. You can see this in the following screenshot or directly at this link. Where does this intron (the one selected by the two vertical red lines) come from? I can't seem to find two exons spanning the selected intron, for any gene or transcript. So how is this an intron?

Answer 1

[Chris Fields]

The track right above it has this nice descriptive legend which might help:

Name: RNA-seq intron-spanning reads, aggregate (filtered, log2 scaled), Mus musculus 104

Title: RNA-seq intron-spanning reads, aggregate (filtered, log2 scaled), NCBI Mus musculus Annotation Release 104

Comment: Coverage of introns derived from spliced RNA-seq alignments, filtered to remove low abundance alignments and some apparent retained-intron alignments near splice junctions, scaled with a log2 transform.

[hbw]

Well, I meant how is it deciding to call the region an intron, rather than calculating the coverage. I think you are talking about the legend on the coverage track. I can't seem to find two exons spanning the selected intron, for any gene or transcript. So how is this an intron?

Answer 2

[Anima Mundi]

Hello,

if I do not misunderstand what you mean, that is an intron because it is a region flanked by two 5'UTR exons, obtained by aligning a spliced cDNA sequence against the genomic sequence.