RBM9

Protein-coding gene in the species Homo sapiens
RBFOX2
Available structures
PDBOrtholog search: PDBe RCSB
List of PDB id codes

2CQ3

Identifiers
AliasesRBFOX2, FOX2, Fox-2, HNRBP2, HRNBP2, RBM9, RTA, dJ106I20.3, fxh, RNA binding protein, fox-1 homolog 2, RNA binding fox-1 homolog 2
External IDsOMIM: 612149; MGI: 1933973; HomoloGene: 49375; GeneCards: RBFOX2; OMA:RBFOX2 - orthologs
Gene location (Human)
Chromosome 22 (human)
Chr.Chromosome 22 (human)[1]
Chromosome 22 (human)
Genomic location for RBFOX2
Genomic location for RBFOX2
Band22q12.3Start35,738,736 bp[1]
End36,028,824 bp[1]
Gene location (Mouse)
Chromosome 15 (mouse)
Chr.Chromosome 15 (mouse)[2]
Chromosome 15 (mouse)
Genomic location for RBFOX2
Genomic location for RBFOX2
Band15|15 D3Start77,078,990 bp[2]
End77,307,004 bp[2]
RNA expression pattern
Bgee
HumanMouse (ortholog)
Top expressed in
  • ganglionic eminence

  • cerebellar cortex

  • cerebellar hemisphere

  • right hemisphere of cerebellum

  • smooth muscle tissue

  • stromal cell of endometrium

  • superior frontal gyrus

  • Achilles tendon

  • body of uterus

  • muscle of thigh
Top expressed in
  • genital tubercle

  • lateral septal nucleus

  • ventromedial nucleus

  • ganglionic eminence

  • tail of embryo

  • superior frontal gyrus

  • mammillary body

  • dentate gyrus of hippocampal formation granule cell

  • lateral geniculate nucleus

  • cerebellar cortex
More reference expression data
BioGPS


More reference expression data
Gene ontology
Molecular function
  • transcription corepressor activity
  • transcription factor binding
  • protein binding
  • RNA binding
  • nucleic acid binding
  • mRNA binding
Cellular component
  • nucleus
  • nucleoplasm
  • cytoplasm
  • cytosol
Biological process
  • neuromuscular process controlling balance
  • dendrite morphogenesis
  • mRNA processing
  • regulation of alternative mRNA splicing, via spliceosome
  • nervous system development
  • regulation of RNA splicing
  • regulation of cell population proliferation
  • RNA splicing
  • radial glia guided migration of Purkinje cell
  • regulation of definitive erythrocyte differentiation
  • RNA metabolic process
  • negative regulation of transcription, DNA-templated
  • intracellular estrogen receptor signaling pathway
  • fibroblast growth factor receptor signaling pathway
Sources:Amigo / QuickGO
Orthologs
SpeciesHumanMouse
Entrez

23543

93686

Ensembl

ENSG00000277564
ENSG00000100320

ENSMUSG00000033565

UniProt

O43251

Q8BP71

RefSeq (mRNA)
NM_001031695
NM_001082576
NM_001082577
NM_001082578
NM_001082579

NM_014309
NM_001349982
NM_001349983
NM_001349989
NM_001349990
NM_001349991
NM_001349992
NM_001349994
NM_001349995
NM_001349996
NM_001349997
NM_001349998
NM_001349999
NM_001394108
NM_001394109
NM_001394110
NM_001394111
NM_001394112
NM_001394113
NM_001394114
NM_001394115

NM_001110827
NM_001110828
NM_001110829
NM_001110830
NM_001286417

NM_001286418
NM_001286419
NM_053104
NM_175387
NM_001358770
NM_001358771
NM_001358772

RefSeq (protein)
NP_001026865
NP_001076045
NP_001076046
NP_001076047
NP_001076048

NP_055124
NP_001336911
NP_001336912
NP_001336918
NP_001336919
NP_001336920
NP_001336921
NP_001336923
NP_001336924
NP_001336925
NP_001336926
NP_001336927
NP_001336928

NP_001104297
NP_001104298
NP_001104299
NP_001104300
NP_001273346

NP_001273347
NP_001273348
NP_444334
NP_780596
NP_001345699
NP_001345700
NP_001345701

Location (UCSC)Chr 22: 35.74 – 36.03 MbChr 15: 77.08 – 77.31 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

RNA binding motif protein 9 (RBM9), also known as Rbfox2, is a protein which in humans is encoded by the RBM9 gene.[5]

Function

Rbfox2 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 splicing in the nervous system and other cell types. Rbfox2 and the related protein Rbfox1 bind to conserved (U)GCAUG RNA motifs in the introns adjacent to many alternatively spliced exons and promotes inclusion or exclusion of the alternative exon in mature transcripts.[6][7] 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.[5]

Rbfox2, 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 Rbfox2 activate markers for apoptosis.[8]

See also

References

  1. ^ a b c ENSG00000100320 GRCh38: Ensembl release 89: ENSG00000277564, ENSG00000100320 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000033565 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b "Entrez Gene: RBM9 RNA binding motif protein 9".
  6. ^ Jin, Y. (2003-02-17). "A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG". The EMBO Journal. 22 (4): 905–912. doi:10.1093/emboj/cdg089. ISSN 1460-2075. PMC 145449. PMID 12574126.
  7. ^ Ponthier, Julie L.; Schluepen, Christina; Chen, Weiguo; Lersch, Robert A.; Gee, Sherry L.; Hou, Victor C.; Lo, Annie J.; Short, Sarah A.; Chasis, Joel A.; Winkelmann, John C.; Conboy, John G. (2006-03-14). "Fox-2 Splicing Factor Binds to a Conserved Intron Motif to Promote Inclusion of Protein 4.1R Alternative Exon 16". Journal of Biological Chemistry. 281 (18): 12468–12474. doi:10.1074/jbc.m511556200. ISSN 0021-9258. PMID 16537540.
  8. ^ 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. Bibcode:1999Natur.402..489D. 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. S2CID 16858834.
  • 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. Bibcode:2002PNAS...9916899M. 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. Bibcode:2005Natur.437.1173R. doi:10.1038/nature04209. PMID 16189514. S2CID 4427026.
  • 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.

External links

  • Overview of all the structural information available in the PDB for UniProt: O43251 (RNA binding protein fox-1 homolog 2) at the PDBe-KB.
  • v
  • t
  • e
  • 2cq3: solution structure of RNA binding domain in RNA binding motif protein 9
    2cq3: solution structure of RNA binding domain in RNA binding motif protein 9
  • 2err: NMR Structure of the RNA Binding Domain of Human Fox-1 in Complex with UGCAUGU
    2err: NMR Structure of the RNA Binding Domain of Human Fox-1 in Complex with UGCAUGU


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