SRGD: a database of splicing-related genes in 10 plants species
Our web-accessible database contains splicing-related proteins of 10 plants including nine flowering plants (three monocots (Os, Sb, Zm), six dicots (At, three legumes (Gm, Lj, Mt), Pt, Vv)) and one non-flowering plant (Pp).
A total of 3545 splicing-related proteins in 10 plant species were identified by sequence comparison and OrthoMCL(Markov Clustering algorithm) method, including 412 proteins of Arabidopsis thaliana (At), 579 proteins of Glycine max (Gm), 248 proteins of Lotus japonicus (Lj), 296 proteins of Medicago truncatula (Mt), 316 proteins of Rice Oryza sativa (Os), 330 proteins of Physcomitrella patens (Pp), 430 proteins of Populus trichocarpa (Pt), 307 proteins of Sorghum bicolour (Sb), 270 proteins of Vitis vinifera (Vv), and 365 proteins of Zea mays (Zm).
Among these splicing-related proteins, more than half of them are duplicated proteins and particularly almost all proteins of Glycine max were duplicated. All splicing-related proteins were classified into families based on corresponding families of their orthologs in Arabidopsis and orthologous clusters from OrthoMCL. More details about gene structure, chromosome location, human homolog, and domain information are available on the web, the database of Splicing-Related Genes (SRGD). The information of conserved genes in all 10 plants and species/clades specific genes are also available on the 10 separately constructed tables with each species at the first column and 9 following species on SRGD. Novel splicing-related proteins and detailed information are accessible at our web pages. Common intron positions and intron types among counterparts of all homologs within each cluster are accessible to be viewed by clicking the CIWOG-number link to our pre-generated CIWOG web. Detailed gene information is also viewable by link to PlantGDB. All gene information can be searched by either concerned species or concerned groups.