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How to find out human mtDNA genes in d-loop control region for Indian origin only

Hi everyone,
I need help to find out the list of all mtDNA genes of Indian origin in the d-loop control region of mtDNA. I searched for databases/tools that can help me find out a list of genes, but most of the mtDNA specific databases are not working or not updated, so I don't know exactly how I should proceed for this. Can anybody help?
Thanks in advance!

gene mitochondrial genes indian origin
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updated by grant.hovhannisyan grant.hovhannisyan • written by SV • SV

Do you expect different mitochondrial genes depending on the geographical origin?

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written by WouterDeCoster WouterDeCoster

Yes, mtDNA genes based on geographical origin as Indian, but genes from the d-loop region of mtDNA.

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written by SV • SV

But there are many different haplotypes in India. What do you mean Indian origin?

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written by Gabriel R. Gabriel R.

2 answers

I think you mean variants, not genes

The defining variants for haplogroup M, which is what most people on the Indian subcontinent fall into, are 489C, 10400T, 14783C, 15043A, 15301A

I think only 489C is in the D-loop. There are a bunch of variants that define subclades of M that also fall within the d-loop control region. I'm not sure what you are looking for but this page might help:

https://www.mitomap.org/foswiki/bin/view/MITOMAP/HaplogroupMarkers

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written by Jeremy Leipzig Jeremy Leipzig

D-loop is a non-coding region, so it does not contain genes. Most probably you are looking for mtDNA haplogroups defined with D-loop. Also, take into account that the geographic origin of most of the mtDNA lineages is not known, and the most frequent haplogroup in a population might not have originated in that population (could be a founder effect, genetic drift, selection, etc). So finding the haplogroups of Indian origin can be very speculative.

For the databases, as @Jeremy mentioned, MITOMAP is the most comprehensive one, you also have hmtdb https://www.hmtdb.uniba.it/ which has more functionality compared to MITOMAP, but it was updated almost a year ago. On the other hand, its always more reliable to go through papers from large scale projects, I am pretty sure there are some for India.

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written by grant.hovhannisyan grant.hovhannisyan

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