Which Genomic Coordinates Do Pter And Qter Map To?

Question

[Jimineep]

Hey

I've downloaded this file to map between cytoband locations and genomic coordinates:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz

following suggestions here (thanks!)

http://biostar.stackexchange.com/questions/4363/how-to-obtain-chromosome-locus-from-coordinates

However I have locations such as:

16pter-p13.3

Or 12q22-qter (both taken from OMIM morbid map)

So should these refer to the ranges between

0 - [max range of 16p13.3] (first case)

[min range of 12q22] - [end of chromosome 12] (second case)?

Thanks!

Answer 1

[Alex Paciorkowski]

16pter-p13.3 means the end of the short arm (p) of chromosome 16 through to band p13.3.

12q22-qter means from band 12q22 through to the end of the long arm (q) of chromosome 12.

This is standard cytogenetics nomenclature. There are a number of on-line sources to explain more, for example here or here (just the first 2 hits from a google search for "cytogenetics nomenclature").

[Jimineep]

Thanks! So in terms of the genomic coordinates then I can use 0 for pter and end of chromosom for qter?

[Alex Paciorkowski]

Yes, that should work.