wrong motif in STRchiv?

[strchive-bot]

Name
Manuel Hofer
Username
-
Email
manuel.hofer@meduniwien.ac.at

Description
hi,
i looked up the sca17 (TBP) in your SRTchives and says GCA as motif. But in all publications the motif is CAG interrupted sometimes with CAA. All together it is an poly glutamin (Q) problem because of CAG=Q and CAA=Q.

is this a error in your database?

greetings an thanks,
Manuel

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[hdashnow]

Thanks for the feedback. The perfect repeat in hg38 does start "GCA". It's a circular permutation of CAG, so technically accurate. But I agree that it is a little confusing. Since this is a protein-coding repeat, I agree that CAG is clearer. I'll update this in the next version.

[mhmuw]

Thanks for the feedback. The perfect repeat in hg38 does start "GCA". It's a circular permutation of CAG, so technically accurate. But I agree that it is a little confusing. Since this is a protein-coding repeat, I agree that CAG is clearer. I'll update this in the next version.

Thank you hdashnow for the quick reply,
Can you also add the CAA because it is known and published that CAG is interrupted with CAA which also codes for Glutamine which is the phato mechanism (to many Qs in a row) of this repeat.

For Example: I do have a sample Sequenced (PacBio pure target repeat expansion kit). GCA count = 31/31
But in reality there are 31CAGs with 5 CAAs between = 36/36 Glutamine in a row. The TRGT analysis based on STRchive (31/31) is not correct. Even not technically.

Greetings and thanks,

[Macayla-weiner]

Hello! This will be updated in the most recent literature update (#334). We are currently working on making another field to list interruption data, but for now that CAA interruption has been added at the end of the 'locus details' field.