BPHunter

BPHunter

Genome-wide detection of human variants that disrupt intronic branchpoints

Pre-mRNA splicing, as a necessary step for protein-coding gene expression in eukaryotic cells, operates spliceosome mostly within introns to define the exon-intron boundaries and hence the coding sequences.
 
Intronic branchpoint (BP) is recognized by the spliceosome in the beginning of splicing, and constitutes a vulnerability of splicing by its potential variants. BP variants may potentially result in aberrant splicing (exon skipping, intron retention), which could be deleterious to gene produdcts.
 
BPHunter is a genome-wide approach to systematically detect intronic variants that may disrupt BP recognition, efficiently and informatively.
 
Reference: Zhang P. et al. Genome-wide detection of human variants that disrupt intronic branchpoints. PNAS. 2022. [PMID:36306325] [Paper]

Human Reference Genome:

GRCh37
GRCh38

Transcripts:

All(based on GENCODE)
Canonical(based on MANE)

Upload Variants:

Provide your variants in VCF format, with the first 5 columns (CHR, POS, ID, REF, ALT) tab-delimited.
Please limit your uploading variant file less than 10 MB (~500,000 variants, if no additional columns).
You can find a sample file here.



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Developer| Peng ZHANG   Ph.D.

Lab Head | Jean-Laurent CASANOVA   M.D., Ph.D.

Laboratory | St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University

Last Update| Sep 28, 2023

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The Rockefeller University, New York, USA

BPHunter is developed and maintained by: Peng ZHANG