Objective: To identify the suppressor of cytokine signaling-1 (SOCS-1) of rat from the amplified gene with the help of bioinformatics to predict the deduced protein's structure and function in order to lay the foundation for further theoretical study.
Methods: The full-length rat SOCS-1 gene was amplified and identified from the GeneBank Nucleotide database, and the corresponding structure and function of its deduced protein was predicted by the bioinformatics analyzing tools online and the complicated bioinformatics software package Vector NTI suite 8.0, meanwhile the molecular cladogram was reconstructed.
Results: Two sequences were obtained by polymerase chain reaction (PCR) amplification of different SOCS-1 gene. The gene was comprised of 639 base pairs in the length, deduced 212 amino acids (aa), contained a SOCS box (aa172-aa208), a SH2 domain (aa80-aa155) and a nuclear localization sequence (aa160-aa174). The primary structure contained two linear B cell epitopes, all of them were on the surface of the protein and far away from the spatial structure.
Conclusion: SOCS-1 gene has a polymorphism, its conservative SH2 region and SOCS box are related to its inhibitory effect on the signal transduction pathway. The nucleic localization sequence may affect other nuclear transduction factors. The B cell linear epitopes may be a candidate of immunodiagnosis with promising prospects.