title: Identification and expression analysis of three novel splice variants of protein kinase A catalytic β subunit gene in the mouse using combinatorial in silico and molecular biology approaches.
abstract: The murine, bovine and human protein kinase A catalytic β (Cβ) subunit genes encode several splice variants. Ten human Cβ gene splice variants, namely Cβ1, Cβ2, Cβ3, Cβ3b, Cβ3ab, Cβ3abc, Cβ4, Cβ4b, Cβ4ab and Cβ4abc, have been reported. Four splice variants of the murine Cβ gene are homologues of human Cβ1, Cβ2, Cβ3 and Cβ4 variants. Using a combinatorial approach comprising bioinformatics tools and molecular biology techniques, we have identified three novel alternatively spliced transcript variants of the mouse Cβ gene designated Cβ5, Cβ6 and Cβ7. These transcript variants differ in their first coding exon. New exons of Cβ5 and Cβ6 variants can encode different N-terminals; however, the new exon of variant Cβ7, when spliced with exon 2, encountered a stop codon in all three reading frames and thus cannot form a functional protein. The Cβ6 variant showed an ubiquitous pattern of expression, whereas Cβ5 was not expressed in muscle tissue on postnatal days (PN)3 and 15. Also, Cβ7 was found to be expressed only in brain and muscle tissues at PN3 and was absent in all tissues examined at PN15 and PN60. The post-translational modification analysis showed characteristic signature sequence motifs in predicted proteins important for the functionality of the protein. The human homologues of variants reported in the present study have not yet been identified. The present study reports three novel splice variants that have not been identified using conventional approaches of alternative splice variant detection methods. Therefore, the approach used in the present study can be used to identify splice variants of genes in organisms. Database GenBank accession numbers: JN189786, JN189787 and JN189788.
authors.affiliation: Department of Biochemistry, AM University, Aligarh, India.
authors.forename: Abdul R
authors.initials: AR
authors.lastname: Banday
authors.forename: Shafquat
authors.initials: S
authors.lastname: Azim
authors.forename: Mohammad
authors.initials: M
authors.lastname: Tabish
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods; D054751:Cyclic AMP-Dependent Protein Kinase Catalytic Subunits / Q000235:genetics* / Q000378:metabolism; D005091:Exons / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008297:Male; D051379:Mice; D008805:Mice, Inbred A; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: D007527:Isoenzymes; D054751:Cyclic AMP-Dependent Protein Kinase Catalytic Subunits