SNAPshot is a utility program meant to export gene-structural information to sequence handling softwares, such as SnapGeneViewer and ApE.

It first maps your mRNA/cDNA sequence onto the genome (ver. JGI 3.1, including chr. Y) and returns its genomic sequence in the GenBank format with exon/intron information, along with flanking sequences, if you desire. SNAPshot uses GMAP for sequence alignment.
To import the result from SnapGeneViewer, copy and past it, or download the result and load it from SnapGeneViewer.

ex) Mapoly0001s0001.1

5' flanking sequence:
3' flanking sequence:

Full documentation for GMAP
Reference: Thomas D. Wu and Colin K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005 21: 1859-1875.