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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RBM4B Gene

protein-coding   GIFtS: 48
GCID: GC11M066432

RNA Binding Motif Protein 4B

(Previous name: RNA binding motif protein 30)
(Previous symbol: RBM30)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
RNA Binding Motif Protein 4B1 2     RBM4L2
RBM301 2 3     ZCCHC152
RNA Binding Motif Protein 301 2     ZCCHC21B2
RNA-Binding Motif Protein 302 3     ZCRB3B2
RNA-Binding Motif Protein 4B2 3     RNA-Binding Protein 4B2
RNA-Binding Protein 302 3     Zinc Finger CCHC-Type And RNA Binding Motif 3B2

External Ids:    HGNC: 288421   Entrez Gene: 837592   Ensembl: ENSG000001739147   UniProtKB: Q9BQ043   

Export aliases for RBM4B gene to outside databases

Previous GC identifers: GC11M066190 GC11M062761


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RBM4B Gene: 
RBM4B (RNA binding motif protein 4B) is a protein-coding gene. Diseases associated with RBM4B include down syndrome. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is RBM4.

UniProtKB/Swiss-Prot: RBM4B_HUMAN, Q9BQ04
Function: Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to
the 3'-UTR of the PER1 mRNA (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NT_167190.1  NC_018922.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RBM4B gene promoter:
         c-Fos   NF-1   AP-1   c-Ets-1   CREB   HOXA5   deltaCREB   c-Myb   c-Jun   ATF   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RBM4B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RBM4B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q13   Ensembl cytogenetic band:  11q13.2   HGNC cytogenetic band: 11q13

RBM4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBM4B gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M066432:  view genomic region     (about GC identifiers)

Start:
66,432,469 bp from pter      End:
66,445,392 bp from pter
Size:
12,924 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RBM4B_HUMAN, Q9BQ04 (See protein sequence)
Recommended Name: RNA-binding protein 4B  
Size: 359 amino acids; 40150 Da
Subunit: Interacts with TNPO3, which may mediate nuclear import of the protein
Subcellular location: Nucleus. Nucleus, nucleolus
1 PDB 3D structure from and Proteopedia for RBM4B:
2DGT (3D)    
Secondary accessions: B3KT83

Explore the universe of human proteins at neXtProt for RBM4B: NX_Q9BQ04

Explore proteomics data for RBM4B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BQ04

  • RBM4B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RBM4B Protein Expression
    REFSEQ proteins: NP_113680.1  
    ENSEMBL proteins: 
     ENSP00000433071   ENSP00000310471   ENSP00000435239   ENSP00000433601   ENSP00000433113  
     ENSP00000475784  

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    Cloud-Clone Corp. Proteins for RBM4B 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005730nucleolus IEA--

    RBM4B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    ZCCHC: Zinc fingers, CCHC domain containing
    RBM: RNA binding motif (RRM) containing

    3 InterPro protein domains:
     IPR012677 Nucleotide-bd_a/b_plait
     IPR000504 RRM_dom
     IPR001878 Znf_CCHC

    Graphical View of Domain Structure for InterPro Entry Q9BQ04

    ProtoNet protein and cluster: Q9BQ04

    2 Blocks protein domains:
    IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
    IPB001878 C2HC-type zinc-finger signature


    UniProtKB/Swiss-Prot: RBM4B_HUMAN, Q9BQ04
    Similarity: Contains 1 CCHC-type zinc finger
    Similarity: Contains 2 RRM (RNA recognition motif) domains


    RBM4B for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RBM4B_HUMAN, Q9BQ04
    Function: Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to
    the 3'-UTR of the PER1 mRNA (By similarity)

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--
         
    RBM4B for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for RBM4B:
     Big cells  Increased gamma-H2AX phosphory 

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rbm4b):
     endocrine/exocrine gland  homeostasis/metabolism 

    RBM4B for phenotypes           About GeneDecksing

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidRBM4B 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RBM4B

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    5/10 Interacting proteins for RBM4B (Q9BQ042, 3 ENSP000003104714) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MRPS9P829332, 3MINT-64676 I2D: score=4 
    MYZAPP0CAP12, 3MINT-65213 I2D: score=4 
    HNRNPMP522722, 3, ENSP000003253764MINT-67839 I2D: score=5 STRING: ENSP00000325376
    APCP250543, ENSP000002574304I2D: score=3 STRING: ENSP00000257430
    POLR2MP0CAP23I2D: score=3 
    About this table

    Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0006417regulation of translation ISS--
    GO:0007623circadian rhythm ISS--
    GO:0008380RNA splicing IEA--
    GO:0010628positive regulation of gene expression IEA--

    RBM4B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RBM4B

    Search CenterWatch for drugs/clinical trials and news about RBM4B

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for RBM4B gene: 
    NM_031492.2  

    Unigene Cluster for RBM4B:

    RNA binding motif protein 4B
    Hs.618713  [show with all ESTs]
    Unigene Representative Sequence: AK095158
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000525754(uc001oja.3) ENST00000310046(uc001ojb.3) ENST00000531969
    ENST00000534198 ENST00000528106 ENST00000529195 ENST00000524637 ENST00000531036

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    hsa-miR-4261 hsa-miR-513a-3p hsa-miR-494
    SwitchGear 3'UTR luciferase reporter plasmidRBM4B 3' UTR sequence
    Inhib. RNA
    Products:
         
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    Additional mRNA sequence: 

    AK095158.1 AL050172.1 BC003503.1 BC004951.1 

    16 DOTS entries:

    DT.100653463  DT.452822  DT.100645691  DT.65287805  DT.95365132  DT.91911756  DT.307590  DT.99980711 
    DT.120685127  DT.91764529  DT.95225754  DT.95364673  DT.119624  DT.452733  DT.75169450  DT.91678764 

    24/190 AceView cDNA sequences (see all 190):

    NM_031492 BM755525 BI908139 CB242252 AA602099 AI651442 AW135730 BC003503 
    BM750086 BM750084 AI927433 BM926817 AW071932 AI129555 AI929021 AI869327 
    CR614869 BQ025645 CD366526 BM981663 AL050172 AI363345 BU543030 CR591230 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RBM4B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGTGGCAAG
    RBM4B Expression
    About this image


    See RBM4B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RBM4B

    SOURCE GeneReport for Unigene cluster: Hs.618713

    UniProtKB/Swiss-Prot: RBM4B_HUMAN, Q9BQ04
    Tissue specificity: Expressed in liver and kidney (at protein level). Ubiquitously expressed

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RBM4B gene from 7/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rbm4b1 , 5 RNA binding motif protein 4B1, 5 90.85(n)1
    96.92(a)1
      19 (4.11 cM)5
    667041  NM_025717.31  NP_079993.21 
     47565435 
    chicken
    (Gallus gallus)
    Aves LOC4255621 RNA-binding protein 4B-like 82.08(n)
    93.75(a)
      425562  XM_003643529.1  XP_003643577.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    73(a)
    1 → many
    GL343961.1(42871-54220)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia MGC758932 hypothetical protein MGC75893 72.67(n)    BC063354.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc25a012 wufc25a01 76.45(n)   324299  BC044503.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta lark6
    lark
    32(a)
    1 → many
    3L(7332366-7334996)
    worm
    (Caenorhabditis elegans)
    Secernentea rnp-16
    RNA-binding protein rnp-1
    21(a)
    1 → many
    V(12192275-12194445)


    ENSEMBL Gene Tree for RBM4B (if available)
    TreeFam Gene Tree for RBM4B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RBM4B gene
    RBM42  RBM14-RBM42  RBM142  
    14 SIMAP similar genes for RBM4B using alignment to 4 protein entries:     RBM4B_HUMAN (see all proteins):
    RBM4    CELF3    RBM14    SRSF5    SFRS5    CELF1
    RBM14-RBM4    HNRNPD    NONO    SFPQ    CELF2    ELAVL4
    DAZAP1    ELAVL2

    RBM4B for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for RBM4B
    PGOHUM00000249447


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/234 SNPs in RBM4B are shown (see all 234)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0647664
    ----see VAR_0647662 E V mis40--------
    rs1411528671,2
    --62775430(+) GGCTCA/GAGATG 1 -- us2k10--------
    rs1389509561,2
    F--66436455(+) TTGTAT/CGCAGA 2 /A syn11Minor allele frequency- C:0.00NA 4550
    rs2003347251,2
    C--66436464(+) GAAGCC/TCTGCC 2 A syn11Minor allele frequency- T:0.00EU 1323
    rs617417471,2
    C,F--66436470(+) GCTGCC/TGCCGC 2 A syn12Minor allele frequency- T:0.01NS NA 4628
    rs1428963091,2
    C,F--66436490(+) CTCATA/GAGAGC 2 H Y mis11Minor allele frequency- G:0.00NA 4550
    rs1487319621,2
    C,F--66436501(+) GGACCC/TGGTAT 2 Q R mis11Minor allele frequency- T:0.00NA 4550
    rs2012026841,2
    --66436507(+) GGTATC/TGCTTA 2 Q R mis10--------
    rs2001923631,2
    --66436632(+) ACACGA/CCCCGT 2 G syn10--------
    rs771736561,2
    C--66436689(+) CGATAC/GCAGCC 2 C W mis10--------

    HapMap Linkage Disequilibrium report for RBM4B (66432469 - 66445392 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for RBM4B:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv897791CNV Loss21882294
    nsv522277CNV Loss19592680
    nsv518919CNV Loss19592680
    nsv897790CNV Loss21882294
    nsv897789CNV Gain21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for RBM4B:    About MalaCards
    down syndrome    


    RBM4B for disorders           About GeneDecksing


    Export disorders for RBM4B gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RBM4B gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with RBM4B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. A novel splicing regulator shares a nuclear import pathway with SR proteins. (PubMed id 12628928)1, 2 Lai M.-C.... Tarn W.-Y. (2003)
    4. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (2002)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    6. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (2013)
    7. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    8. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    9. Large-scale genome-wide association analysis of bipol ar disorder identifies a new susceptibility locus near ODZ4. (PubMed id 21926972)1 Sklar P....Purcell S.M. (2011)
    10. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. (PubMed id 21248752)2 Varela I....Futreal P.A. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 83759 HGNC: 28842 AceView: RBM30 Ensembl:ENSG00000173914 euGenes: HUgn83759
    ECgene: RBM4B H-InvDB: RBM4B

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RBM4B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RBM4B gene:
    Search GeneIP for patents involving RBM4B

    GeneCards and IP:
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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