AGAIN

AGAIN

Genome-wide detection of human intronic AG-gain variants in BP-ACC region

Human variants that introduce an AG in the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) can disrupt pre-mRNA splicing and result in misspliced gene products.
 
Based on our previously developed BPHunter, we delineate the BP-ACC segments of all human introns of protein-coding genes, for the first time. We find an extreme depletion of AG/YAG in the high-risk [BP+8, ACC-4] region.
 
AGAIN is a genome-wide approach to pinpoint intronic AG-gain variants (SNVs, insertions, deletions) in the BP-ACC region of human genomes. AGAIN also predicts protein-level outcomes resulting from two major missplicing consequences (new acceptor site & complete exon skipping).
 
Reference: Zhang P. et al. Genome-wide detection of human intronic AG-gain variants located between the splicing branchpoints and canonical splice acceptor sites. PNAS. 2023. [PMID:37931111] [Paper]

Human Reference Genome:

GRCh37
GRCh38

Transcripts:

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

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Provide the varaints in VCF format, with the first 5 columns (CHR, POS, ID, REF, ALT) tab-delimited.
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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 15, 2023

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