What happens to this gene?

Question

[fengzys]

I found many reads mapped to a gene in a wired way, any suggestion on what happens here?

Assuming the gene has sequence:

ABCDEFGHIJK Its complement are abcdefghijk

The reads are like:

kjihgABCDEF

What kind of chromosome rearrangement could produce this? or artifacts?

[Michael]

Is it RNA-seq? maybe a cyclic RNA?

[John]

Man, I would love to engineer an organism where there's a mobius-strip for a genome.

You'd have a co-ordinate system twice the length of the genome, but no forward or reverse strands :P hahaha.

Answer 1

[John]

Top example : http://www.biology-online.org/2/8_mutations.htm

Note that in your notation that would be "ABCfed..."

[Devon Ryan]

I think in this case it'd be a translocated inversion.

[John]

It could be, that's definitely one possibility - but if the sequencing isn't stranded it could also look like:

ABCDEFGHIJK becomes fedcbaGHIJK (first half gets inverted),

the reverse compliment of which (if you sequence the other strand) is kjihgABCDEF