AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse.
We have constructed a database, AS-ALPS (alternative splicing-induced alteration of protein structure), which provides information that would be useful for analyzing the effects of alternative splicing (AS) on protein structure, interactions with other bio-molecules and protein interaction networks in human and mouse. Several AS events have been revealed to contribute to the diversification of protein structure, which results in diversification of interaction partners or affinities, which in turn contributes to regulation of bio-molecular networks. Most AS variants, however, are only known at the sequence level. It is important to determine the effects of AS on protein structure and interaction, and to provide candidates for experimental targets that are relevant to network regulation by AS. For this purpose, the three-dimensional (3D) structures of proteins are valuable sources of information; however, these have not been fully exploited in any other AS-related databases. AS-ALPS is the only AS-related database that describes the spatial relationships between protein regions altered by AS ('AS regions') and both the proteins' hydrophobic cores and sites of inter-molecular interactions. This information makes it possible to infer whether protein structural stability and/or protein interaction are affected by each AS event. AS-ALPS can be freely accessed at http://as-alps.nagahama-i-bio.ac.jp and http://genomenetwork.nig.ac.jp/as-alps/.
Shionyu
Masafumi
M
Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan.
Yamaguchi
Akihiro
A
Shinoda
Kazuki
K
Takahashi
Ken-ichi
K
Go
Mitiko
M
D017398:Alternative Splicing; D000818:Animals; D018389:Codon, Nonsense; D030562:Databases, Protein; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D051379:Mice; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D020033:Protein Isoforms / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability
D018389:Codon, Nonsense; D020033:Protein Isoforms