Genomic location of MUC16

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2.2 years ago

zizigolu ★ 4.4k

Hi

I want to check the structure of Variable Number of Tandem Repeats (VNTRs) in human MUC16

How I know genomic location of MUC16 VNTRs in human reference genome (hg38)

Thanks for any idea

VNTR genome • 1.2k views

ADD COMMENT • link updated 2.2 years ago by GenoMax 154k • written 2.2 years ago by zizigolu ★ 4.4k

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A comparison of the T2T with GRCh38 shows potentially some expanded regions of repeat sequence when you compare the T2T assembly with GRCh38 : https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_009914755.1/GCF_000001405.40/23025/9606#NC_060943.1:8832360-9318975/NC_000019.10:8729546-9185048/size=10000

muc16

ADD REPLY • link 2.2 years ago by GenoMax 154k

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Thank you very much

The link shows the MUC16 gene region, not the Variable Number of Tandem Repeats (VNTRs). Do you know how to get the genomic coordinate of the VNTR in MUC16?

Thank you

ADD REPLY • link 2.2 years ago by zizigolu ★ 4.4k

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I was trying to show that depending on accuracy of assembly the information about VNTR will change. VNTR appear to be available from https://zenodo.org/record/8118376 (see the associated publication for details).

There appear to be other resources that you can explore: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10234305/

ADD REPLY • link 2.2 years ago by GenoMax 154k

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