RBM9

RNA binding protein, fox-1 homolog (C. elegans) 2
PDB rendering based on 2cq3.
Available structures PDB Ortholog search: PDBe, RCSB List of PDB id codes 2CQ3​
Identifiers
Symbols	RBFOX2 ; FOX2; Fox-2; HNRBP2; HRNBP2; RBM9; RTA; dJ106I20.3; fxh
External IDs	OMIM: 612149 MGI: 1933973 HomoloGene: 49375 GeneCards: RBFOX2 Gene
Gene ontology Molecular function • nucleotide binding • transcription corepressor activity • RNA binding • mRNA binding • protein binding • transcription factor binding • poly(A) RNA binding Cellular component • nucleus • nucleoplasm • cytoplasm Biological process • regulation of alternative mRNA splicing, via spliceosome • mRNA processing • RNA splicing • regulation of definitive erythrocyte differentiation • RNA metabolic process • radial glia guided migration of Purkinje cell • intracellular estrogen receptor signaling pathway • regulation of cell proliferation • negative regulation of transcription, DNA-templated • dendrite morphogenesis • neuromuscular process controlling balance Sources: Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	23543	93686
Ensembl	ENSG00000100320	ENSMUSG00000033565
UniProt	O43251	Q8BP71
RefSeq (mRNA)	NM_001031695	NM_001110827
RefSeq (protein)	NP_001026865	NP_001104297
Location (UCSC)	Chr 22: 35.74 – 36.03 Mb	Chr 15: 77.08 – 77.31 Mb
PubMed search

RNA binding motif protein 9, also known as RBM9 or FOX-2, is a protein which in humans is encoded by the RBM9 gene.^[1]

Function

RBM9 is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene.^[1]

RBM9, as determined by CLIP-seq, binds near alternatively spliced exons and regulates the inclusion or exclusion of exons during alternative splicing by binding in introns either downstream (inclusion) or upstream (exon skipping) of exons. Its presence is important for stem cell survival and knockdowns of RBM9 activate markers for apoptosis.^[2]

References

1. "Entrez Gene: RBM9 RNA binding motif protein 9".
2. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH (February 2009). "An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells". Nature Structural & Molecular Biology 16 (2): 130–137. doi:10.1038/nsmb.1545. PMC 2735254. PMID 19136955.

Further reading

• Dunham I, Shimizu N, Roe BA, et al. (1999). "The DNA sequence of human chromosome 22". Nature 402 (6761): 489–495. doi:10.1038/990031. PMID 10591208.
• Lieberman AP, Friedlich DL, Harmison G, et al. (2001). "Androgens regulate the mammalian homologues of invertebrate sex determination genes tra-2 and fox-1". Biochem. Biophys. Res. Commun. 282 (2): 499–506. doi:10.1006/bbrc.2001.4617. PMID 11401487.
• Norris JD, Fan D, Sherk A, McDonnell DP (2002). "A negative coregulator for the human ER". Mol. Endocrinol. 16 (3): 459–468. doi:10.1210/me.16.3.459. PMID 11875103.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–16903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
• Collins JE, Goward ME, Cole CG, et al. (2003). "Reevaluating human gene annotation: a second-generation analysis of chromosome 22". Genome Res. 13 (1): 27–36. doi:10.1101/gr.695703. PMC 430954. PMID 12529303.
• Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–45. doi:10.1038/ng1285. PMID 14702039.
• Collins JE, Wright CL, Edwards CA, et al. (2005). "A genome annotation-driven approach to cloning the human ORFeome". Genome Biol. 5 (10): R84. doi:10.1186/gb-2004-5-10-r84. PMC 545604. PMID 15461802.
• Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–2127. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
• Rual JF, Venkatesan K, Hao T, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature 437 (7062): 1173–1178. doi:10.1038/nature04209. PMID 16189514.
• Underwood JG, Boutz PL, Dougherty JD, et al. (2005). "Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals". Mol. Cell. Biol. 25 (22): 10005–10016. doi:10.1128/MCB.25.22.10005-10016.2005. PMC 1280273. PMID 16260614.
• Kimura K, Wakamatsu A, Suzuki Y, et al. (2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC 1356129. PMID 16344560.
• Ponthier JL, Schluepen C, Chen W, et al. (2006). "Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16". J. Biol. Chem. 281 (18): 12468–12474. doi:10.1074/jbc.M511556200. PMID 16537540.
• Lim J, Hao T, Shaw C, et al. (2006). "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration". Cell 125 (4): 801–814. doi:10.1016/j.cell.2006.03.032. PMID 16713569.