Found in WebWatch in Biotechniques, the Structural Exon Database, SEDB. Introductory page says:
"Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms."
To be able to use the datasets, you need to install Friend on your PC, but various searches seem to be possible without it: GenBank accession search, sequence searching, and using BLAST.
SEDB is hosted by Northeastern University in Boston, MA and is described in a paper in Bioinformatics, doi: 10.1093/bioinformatics/bth150. (DOI found in the PubMed record - see previous posting on this blog!)