These were the only rat proteins sequenced from the final CTA 157-2 positive fraction indicating that the purification strategy was successful.
Owing to the high sequence homology between mouse and rat, the protein sequences of 540 mouse kinases were used to identify the orthologous kinases in rat, which has identified 306 kinases.
When we analysed the human CCN2/CTGF and rat CCN3/NOV protein sequences for potential N-glycosylation sites using the NetNGlyc algorithm (http://www.cbs.dtu.dk/services/NetNGlyc/), we found that both proteins carry a potential N-glycosylation site (Figure S5).
The complete set of annotated rat and NMR protein sequences were obtained from the UniProt database (http://www.uniprot.org/).org/
Previously published datasets of the human, rat and mouse GPCR protein sequences were used as queries [ 30, 44].
Query datasets were retrieved by downloading a start set of human, rat and mouse GPCR protein sequences from the Genbank database using the Entrez data-retrieval tool [ 66] in keyword searches.
A preliminary secondary structure prediction based on the human, mouse, rat, zebrafish, and fugu protein sequences suggested a topology of ten transmembrane domains (TM) with cytosolic amino and carboxy termini.
Concatenated forward and reverse sequences from the NCBI Refseq rat protein database (updated 10.18.2006; 36,496 forward sequences) [50] were used for searching.
The IPI rat protein database (version 3.40, 40381 sequences, 20547209 residues) and its reversed complement were combined and used for database searches.
This exact peptide sequence was found to exist in both mouse and rat protein homologues, and alignments of these sequences found that the specified intron is retained in both organisms, encoding an additional 37 additional amino acids (Figure 2).
