Locate Part Of Region Of Interest In Synteny Map

Question

[Bioscientist]

I don't know if anyone here does research on synteny.

For example, I have a syntenic conversion between human and fish: (human) chr1 20000 40000 (fish) chr10 50000 65000

That means 20000-40000 in human genome chr1 is corresponded to 50000-65000 in fish genome chr10 (maybe relevant functionally or conserved genes).

However, is it possible to know where any PART of 20000-40000 in human genome chr1 (say 20000-30000) can be syntenically mapped to fish genome chr10 (say 50000-60000)?

Thanks

Answer 1

[Zev.Kronenberg]

Yes you can absolutely do this.

What you are trying to do is create a lift-over chain. UCSC has this for many species and it a way to compare genomes.

Minimal steps required to generate a lift-over chain

then you can create cool plots that are hard to interpret :-).

Below is a synteny plot I made by following the steps in the link and using circos.

[Bioscientist]

looks very cool, I'll definitely look into this.thx

Answer 2

[Larry_Parnell]

Given that there are few genes in this region in human (eg, FAM138A and OR4G4P, the latter being a pseudogene), I am not sure you can effectively evaluate such a region of micro-synteny. Synteny is conserved gene order and with such a small number of genes, it will be problematic to do the analysis you'd like. On the other hand, if there are non-gene elements that are conserved between human and fish and these map near FAM138A, you can use these to evaluate the conserved order of the elements, both protein-coding and not.

[Bioscientist]

thx larry, I'm just giving an example. I'm doing whole-genome analysis. My question is, if I wanna do, or can do, how should I carry out such analysis? BY comparing sequence similarity? I can only download such database from online, but don't know how people do it