100% Identical Transcript Sequences - How Did They Manage To Put Them Into Different Loci?

Question

[PoGibas]

I stumbled upon two genes:

• ENSG00000259206 -- Chr15:82,710,856-82,726,435

• ENSG00000259310 -- Chr15:83,087,381-83,102,960

After more closer look I noticed that they are similar. So similar that I BLAST'ed loci against each other.

Surprise, surprise, they are 100% identical.
Those genes can be grouped as paralogues, but there is still some unclarity for me.

Is such similarity normal? If transcripts are 100% identical, how somebody managed to place them into different loci?

---

Edit

Three more transcipts from different loci are identical: ENST00000456123.1, ENST00000420149.1, ENST00000436568.1

[Pavel Senin]

are their flanking sequences different (utr's?)?

[PoGibas]

After extending loci 1000bp to each side I still get 100%:

blastn \
    -subject <(echo chr15 83087381 83102960 | 
                  awk '{OFS="\t"; print $1,$2-1000,$3+1000}' | 
                  bedtools getfasta -fi hg.19 -bed - -fo -) \
    -query <(echo chr15 82710856 82726435 | 
                awk '{OFS="\t"; print $1,$2-1000,$3+1000}' | 
                bedtools getfasta -fi hg.19 -bed - -fo -) |   
    grep -m1 'Identities'

Identities = 17579/17579 (100%), Gaps = 0/17579 (0%)

[Pavel Senin]

interesting indeed. they might have had some long inserts etc., but I agree, that could be a mistake

[heboping1215]

Could you tell me how to `BLAST'ed loci against each other`??

Answer 1

[Emily]

I've asked our friends at Havana to weigh in (either directly or via me) so we'll see what they say.

Follow up: heard back from Havana. Laurens says:

The duplication of this and neighbouring genes is due to a haplotype issue. There is an assembly gap between the two copies and the genomic sequence on the left side is from the RP13 haplotype, and the right side is from RP11 haplotype.

In the next genome assembly (GRCh38 I presume) this region will be replaced with an ungapped single haplotype (RP11) and it will only have one copy of this gene (and of the flanking genes).

[PoGibas]

Emily, thank you for helping!
Can you also look at this question: Gencode V15 Exons < 3Bp (e.g., ENST00000605962 - last exon is 1bp long (same Havana annotation)).

[Emily]

On it (plus some extra characters so BioStar will let me post).

[Mary]

I'm replying so that it flags me when there are new answers. I'd like to hear the details.

[Emily]

Oh dear. I edited my original post so you might not get a notification. Well this comment will do that.