What does gene coordinates "CHR_MG117_PATCH:108783796-108806337"mean?

Question

[Kai_Qi]

Hi:

I have been analyzing RNA-seq data, in the output file the gene coordinates is listed as format like "CHR_MG117_PATCH:108783796-108806337"

What does this mean? How can I get information on this gene?

Thanks,

Answer 1

[GenoMax]

CHR_MG117_PATCH:108783796-108806337 happens to be from mouse genome. Entire patch is available here.

Genome patches are described in this FAQ section on Genome Research Consortium site.

[Kai_Qi]

Thank you for your reply! I understand now

Answer 2

[Corentin]

I am assuming you are working on the human genome.

The human reference genome is still a work in progress, so some areas need improvements, or you can have alternative sequences of the same part of the genome.

Instead of waiting for the next release of the human reference, the Genome Reference Consortium chooses to release patches / fixes for these small regions. Hence the "weird" names, for example your sequence correspond to a patch where the primary assembly was found to be incorrect.

If you want more information about this: http://www.ensembl.info/2011/05/20/accessing-non-reference-sequences-in-human/

[Kai_Qi]

Thank you for your help, your answer and the answer above help me a lot