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Map Genomic Position to Protein Sequence and 3D Structure

Mapping between genome, UniProt sequence and PDB structure

Mutations in a gene can have profound effects on the function of a protein. This analysis tool highlights the gene location (i.e., the site of a SNP).

Example of SNP in Breast Cancer 1 Gene

A TGT-to-GGT transversion in codon 64 of the BRCA1 gene (see Omim) leads to substitution of glycine for cysteine. This SNP is located on chromosome 17 at genomic coordinate: 43,106,478. This mapping tool can be used to locate this position on the UniProt sequence and 3D structure

Map Genomic Position

Mapping tool displays the position of a SNP on the gene, the UniProt sequence, and 3D structure. By clicking on the green buttons, the consequences of this SNP at the gene, protein, and structure levels can be explored.

Position Mapped onto Gene View

The genomic location of this SNP is highlighted by red bar at position 43,106,478. This gene is read in reverse direction; therefore, the complement to codon ACA is TGT, which corresponds to a cysteine.

Position Mapped onto Protein Feature View

A red box highlights the Cysteine at UniProt position 64. From this diagram we can see that this position is part of a Zinc finger domain (Pfam track). The structural consequences of a mutation at this position can be analyzed by visualizing this residue in the 3D structure.

Position Mapped onto 3D Structure View

Cysteine 64 is highlighted in CPK style using PV. This cysteine forms part of a zinc finger domain and the sulfur of the cysteine (yellow) is coordinated with the zinc ion (purple). Disruption of this interaction has serious functional consequences and has been indicated in breast cancer formation.