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RBBP9 Gene

protein-coding   GIFtS: 50
GCID: GC20M018415

Retinoblastoma Binding Protein 9

(Previous name: retinoblastoma-binding protein 9)
  See RBBP9-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)
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Aliases
Retinoblastoma Binding Protein 91 2     B5T-Overexpressed Gene Protein2 3
Retinoblastoma-Binding Protein 91 2 3     B5T Overexpressed Gene Protein2
BOG2 3 5     Putative Hydrolase RBBP92
Retinoblastoma-Binding Protein 102 3     Retinoma-Binding Protein 92
RBBP-102 3     EC 3.-.-.-3
RBBP-92 3     Protein BOG3
RBBP102 3     

External Ids:    HGNC: 98921   Entrez Gene: 107412   Ensembl: ENSG000000890507   OMIM: 6029085   UniProtKB: O758843   

Export aliases for RBBP9 gene to outside databases

Previous GC identifers: GC20M018455 GC20M018462


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RBBP9 Gene:
The protein encoded by this gene is a retinoblastoma binding protein that may play a role in the regulation of
cell proliferation and differentiation. Two alternatively spliced transcript variants of this gene with identical
predicted protein products have been reported, one of which is a nonsense-mediated decay candidate. (provided by
RefSeq, Jul 2008)

GeneCards Summary for RBBP9 Gene:
RBBP9 (retinoblastoma binding protein 9) is a protein-coding gene. Diseases associated with RBBP9 include retinoblastoma. GO annotations related to this gene include hydrolase activity.

UniProtKB/Swiss-Prot: RBBP9_HUMAN, O75884
Function: May play a role in the transformation process due to its capacity to confer resistance to the
growth-inhibitory effects of TGF-beta1 through interaction with retinoblastoma and the subsequent displacement of
E2F-1

Gene Wiki entry for RBBP9 Gene


(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 at NCBI GenBank:
NC_000020.10  NT_011387.9  NC_018931.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RBBP9 gene promoter:
         STAT5B   Nkx2-5   RORalpha2   GATA-2   AREB6   CBF-B   CBF-A   CP1A   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRBBP9 promoter sequence
   Search Chromatin IP Primers for RBBP9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBBP9


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

Entrez Gene cytogenetic band: 20p11.2   Ensembl cytogenetic band:  20p11.23   HGNC cytogenetic band: 20p11.2

RBBP9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBBP9 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M018415:  view genomic region     (about GC identifiers)

Start:
18,467,184 bp from pter      End:
18,477,887 bp from pter
Size:
10,704 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RBBP9_HUMAN, O75884 (See protein sequence)
Recommended Name: Putative hydrolase RBBP9  
Size: 186 amino acids; 21000 Da
Miscellaneous: Interacts with the serine hydrolase-directed activity-based probe fluorophosphonate-rhodamine
(FP-rhodamine). This interaction is inhibited selectively and reversibly by emetine, a compound with cytotoxic
activity
1 PDB 3D structure from and Proteopedia for RBBP9:
2QS9 (3D)    
Secondary accessions: D3DW31 Q5JPH9 Q9H1D8
Alternative splicing: 2 isoforms:  O75884-1   O75884-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RBBP9: NX_O75884

Explore proteomics data for RBBP9 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys156
  • Modification sites at PhosphoSitePlus

  • See RBBP9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006597.2  
    ENSEMBL proteins: 
     ENSP00000336866  

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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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    1 InterPro protein domain:
     IPR010662 DUF1234_Hydrolase

    Graphical View of Domain Structure for InterPro Entry O75884

    ProtoNet protein and cluster: O75884

    UniProtKB/Swiss-Prot: RBBP9_HUMAN, O75884
    Similarity: Belongs to the RBBP9 family


    Find genes that share domains with RBBP9           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RBBP9_HUMAN, O75884
    Function: May play a role in the transformation process due to its capacity to confer resistance to the
    growth-inhibitory effects of TGF-beta1 through interaction with retinoblastoma and the subsequent displacement of
    E2F-1

         Genatlas biochemistry entry for RBBP9:
    Bog,retinoblastoma binding protein,murine Bog homolog,inhibiting TGFB1 activity by displacing E2F1 when
    overexpressed

         Enzyme Number (IUBMB): EC 3.-.-.-1

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0016787hydrolase activity IEA--
         
    Find genes that share ontologies with RBBP9           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for RBBP9:
     Increased gamma-H2AX phosphory  Increased number of cells in m 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for RBBP9

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    hsa-mir-124-3p (MIRT023005)

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    hsa-miR-3140-3p hsa-miR-4307 hsa-miR-607 hsa-miR-3688-3p hsa-miR-7-2* hsa-miR-196a* hsa-miR-944 hsa-miR-3622b-3p
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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
    RBBP9_HUMAN, O75884: Cytoplasm. Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3
    plasma membrane2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--
    GO:0005737cytoplasm IDA--

    Find genes that share ontologies with RBBP9           About GenesLikeMe


    (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 RBBP9
    Interactions:

        GeneGlobe Interaction Network for RBBP9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for RBBP9 (O758843 ENSP000003368664) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RBL2Q089993, ENSP000002621334I2D: score=3 STRING: ENSP00000262133
    YRDCQ86U903, ENSP000003621354I2D: score=1 STRING: ENSP00000362135
    RB1P064003, ENSP000002671634I2D: score=3 STRING: ENSP00000267163
    RBL1P287493, ENSP000003627684I2D: score=2 STRING: ENSP00000362768
    TERF2IPENSP000003000864STRING: ENSP00000300086
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042127regulation of cell proliferation IEA--

    Find genes that share ontologies with RBBP9           About GenesLikeMe



    (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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for RBBP9



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RBBP9 gene (2 alternative transcripts): 
    NM_006606.2  NM_153328.1  

    Unigene Cluster for RBBP9:

    Retinoblastoma binding protein 9
    Hs.69330  [show with all ESTs]
    Unigene Representative Sequence: BC015938
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000337227(uc002wqy.3) ENST00000493184 ENST00000491835
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    hsa-miR-3140-3p hsa-miR-4307 hsa-miR-607 hsa-miR-3688-3p hsa-miR-7-2* hsa-miR-196a* hsa-miR-944 hsa-miR-3622b-3p
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    Additional mRNA sequence: 

    AF237576.1 AK023897.1 AL832411.1 BC015938.1 BC020627.1 BC026880.1 

    8 DOTS entries:

    DT.100025211  DT.455056  DT.100700903  DT.100776420  DT.91801283  DT.97827217  DT.100645218  DT.91801284 

    Selected AceView cDNA sequences (see all 99):

    AA487794 AL844476 BF432488 BF057169 AI143270 AI913337 AI742928 AI217227 
    AI636498 AA485890 NM_006606 BQ016491 BQ643778 AA398940 AF237576 AI912987 
    NM_153328 AU143194 AI092435 AA397842 BU688774 CD513846 AW957457 BG249165 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for RBBP9    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d
    SP1:                                                            
    SP2:                    -                                       
    SP3:                    -     -                                 
    SP4:                    -           -                           


    ECgene alternative splicing isoforms for RBBP9

    (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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    RBBP9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACTGTCAAA
    RBBP9 Expression
    About this image

    RBBP9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RBBP9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.69330

    UniProtKB/Swiss-Prot: RBBP9_HUMAN, O75884
    Tissue specificity: Widely expressed. Expressed at higher levels in tumor tissues than in normal tissues

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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 chordates.

    Orthologs for RBBP9 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rbbp91 , 5 retinoblastoma binding protein 91, 5 92.07(n)1
    91.89(a)1
      2 (71.02 cM)5
    264501  NM_015754.21  NP_056569.21 
     1445422655 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004915671 putative hydrolase RBBP9-like 69.83(n)
    75.42(a)
      100491567  XM_002940097.2  XP_002940143.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufd05g112 Transcribed sequence with moderate similarity to protein more 74.36(n)    57091781 


    ENSEMBL Gene Tree for RBBP9 (if available)
    TreeFam Gene Tree for RBBP9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 RBBP9 (see all 348)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2000263051,2
    C--18466780(+) TATAT-/AA/T  
            
    AAATA
    1 -- ds50010--------
    rs605576381,2
    C--18466782(+) ATAAATATAAATAT
    ATATATA
    /-
    AATAT
    1 -- ds50011Minor allele frequency- -:0.00NA 2
    rs72713731,2
    C--18466783(+) ATAAAT/AATATA 1 -- ds50011Minor allele frequency- A:0.00NA 2
    rs72714271,2
    C,A--18466801(+) atataA/Tatata 1 -- ds50010--------
    rs72645881,2
    C,A--18466805(+) aaataA/Tatata 1 -- ds50010--------
    rs61363881,2
    C--18466814(+) tatatA/Gtaaat 1 -- ds50010--------
    rs596674471,2
    C--18466822(+) ATATA-/AA/T  
     ATATATA
    AATAT
    1 -- ds50010--------
    rs60811621,2
    A--18466823(+) atataT/Aatata 1 -- ds50011Minor allele frequency- A:0.00NA 2
    rs1914022421,2
    --18466828(+) AATATA/CTATAT 1 -- ds50010--------
    rs1846794371,2
    --18466855(+) ATATAA/TATATA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for RBBP9 (18467184 - 18477887 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for RBBP9: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RBBP9
    DNA2.0 Custom Variant and Variant Library Synthesis for RBBP9

    (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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    OMIM gene information: 602908    OMIM disorders: --

    1 disease for RBBP9:    
    About MalaCards
    retinoblastoma


    Find genes that share disorders with RBBP9           About GenesLikeMe


    Export disorders for RBBP9 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 RBBP9 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with RBBP9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A retinoblastoma-binding protein that affects cell-cycle control and confers transforming ability. (PubMed id 9697699)1, 2, 3, 9 Woitach J.T.... Thorgeirsson S.S. (Nat. Genet. 1998)
    2. Assignment of the Bog gene (RBBP9) to syntenic regions of mouse chromosome 2G1-H1 and human chromosome 20p11.2 by fluorescence in situ hybridization. (PubMed id 10449909)1, 3, 9 Woitach J.T....Thorgeirsson S.S. (Cytogenet. Cell Genet. 1999)
    3. Cloning and expression of a novel retinoblastoma binding protein cDNA, RBBP10. (PubMed id 12296629)1, 2, 9 Chen J.-Z....Mao Y.-M. (Biochem. Genet. 2002)
    4. Crystal structure of human retinoblastoma binding protein 9. (PubMed id 19004028)1, 2 Vorobiev S.M.... Tong L. (Proteins 2009)
    5. 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)
    6. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    7. RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia. (PubMed id 20080647)1, 9 Shields D.J....Cheresh D.A. (Proc. Natl. Acad. Sci. U.S.A. 2010)
    8. Human retinoblastoma binding protein 9, a serine hydrolase implicated in pancreatic cancers. (PubMed id 21933118)1 Vorobiev S.M....Tong L. (Protein Pept. Lett. 2012)
    9. Two potential biomarkers identified in mesenchymal stem cells and leukocytes of patients with sporadic amyotrophic lateral sclerosis. (PubMed id 22430187)1 Nachmany H....Weil M. (Dis. Markers 2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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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: 10741 HGNC: 9892 AceView: RBBP9 Ensembl:ENSG00000089050 euGenes: HUgn10741
    ECgene: RBBP9 H-InvDB: RBBP9

    (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 RBBP9 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RBBP9 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RBBP9 gene:
    Search GeneIP for patents involving RBBP9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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