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RBM4B Gene

protein-coding   GIFtS: 50
GCID: GC11M066432

RNA Binding Motif Protein 4B

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

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RNA Binding Motif Protein 4B1 2     ZCCHC21B2
RBM301 2 3     ZCRB3B2
RNA-Binding Motif Protein 302 3     RNA-Binding Protein 4B2
RNA Binding Motif Protein 301     Zinc Finger CCHC-Type And RNA Binding Motif 3B2
RBM4L2     RNA-Binding Motif Protein 4B3
ZCCHC152     RNA-Binding Protein 303

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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RBM4B Gene:
RBM4B (RNA binding motif protein 4B) is a protein-coding gene. Diseases associated with RBM4B include down syndrome, and bipolar disorder. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NT_167190.2  NC_018922.2  
Regulatory elements:
   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 Chromatin IP Primers for RBM4B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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
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: 

  • Ubiquitination2 at Lys3, Lys27, Lys35, Lys59, Lys139
  • Modification sites at PhosphoSitePlus

  • See RBM4B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001273064.1  NP_113680.1  

    ENSEMBL proteins: 
     ENSP00000433071   ENSP00000310471   ENSP00000435239   ENSP00000433601   ENSP00000433113  
     ENSP00000475784  

    RBM4B Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding ----
    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:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RBM4B
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    miRNA
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    hsa-mir-193b-3p (MIRT041260), hsa-mir-424-5p (MIRT042450)

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    3 qRT-PCR Assays for microRNAs that regulate RBM4B:
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    SwitchGear 3'UTR luciferase reporter plasmidRBM4B 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RBM4B_HUMAN, Q9BQ04: Nucleus. Nucleus, nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    extracellular1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    RBM4B for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RBM4B
    Interactions:

        Search GeneGlobe Interaction Network for RBM4B

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    Selected Interacting proteins for RBM4B (Q9BQ041, 2, 3 ENSP000003104714) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    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): Selected biological process terms (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, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for 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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RBM4B gene (2 alternative transcripts): 
    NM_001286135.1  NM_031492.3  

    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

    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate RBM4B:
    hsa-miR-4261 hsa-miR-513a-3p hsa-miR-494
    SwitchGear 3'UTR luciferase reporter plasmidRBM4B 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat RBM4B
      QuantiFast Probe-based Assays in human, mouse, rat RBM4B

    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 

    Selected AceView cDNA sequences (see all 190):

    AI453640 AA602099 BM755525 BX117370 AA908776 BQ645418 AI129555 AW135730 
    CB242252 AW964128 BP872185 AA722657 AI363345 AL050172 AW150988 CD366526 
    BC004951 AK095158 BQ939871 BQ428264 BE328092 CR591230 AI351019 AW071932 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    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

    RBM4B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RBM4B Protein Expression

    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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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for RBM4B gene from Selected species (see all 14)    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 89.54(n)1
    94.96(a)1
      19 (4.11 cM)5
    667041  NM_025717.31  NP_079993.21 
     47565435 
    chicken
    (Gallus gallus)
    Aves LOC1008592761 RNA-binding protein 4B-like 62.02(n)
    63.57(a)
      100859276  XM_003643915.2  XP_003643963.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    76(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
    33(a)
    1 → many
    3L(7332366-7334996)
    worm
    (Caenorhabditis elegans)
    Secernentea rnp-16
    Protein RNP-1, isoform a (rnp-1) mRNA, complete cd...
    23(a)
    1 → many
    V(12192275-12194445) WBGene00004384


    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)
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    Paralogs for RBM4B gene
    RBM42  RBM14-RBM42  RBM142  
    14 SIMAP similar genes for RBM4B using alignment to 5 protein entries:     RBM4B_HUMAN (see all proteins):
    RBM4    CELF3    RBM14    SRSF5    SFRS5    CELF1
    HNRNPD    NONO    SFPQ    CELF2    ELAVL4    DAZAP1
    ELAVL2    PABPC3

    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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RBM4B (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
    ----------
    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--------
    rs3758988461,2
    C--66436791(+) ATTTAC/TTTTAA 1 -- int10--------

    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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RBM4B
    DNA2.0 Custom Variant and Variant Library Synthesis for RBM4B

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


    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)
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    PubMed articles for RBM4B gene, integrated from 10 sources (see all 24):
    (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. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 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. (EMBO J. 2003)
    4. Functional proteomic analysis of human nucleolus. (PubMed id 12429849)1, 2 Scherl A.... Diaz J.-J. (Mol. Biol. Cell 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    7. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
    8. 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. (Nat. Cell Biol. 2012)
    9. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    10. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. (PubMed id 21926972)1 (Nat. Genet. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83759 HGNC: 28842 AceView: RBM30 Ensembl:ENSG00000173914 euGenes: HUgn83759
    ECgene: RBM4B H-InvDB: RBM4B

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RBM4B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for RBM4B gene:
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    GeneCards and IP:
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