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Aliases for RBBP4 Gene

Aliases for RBBP4 Gene

  • RB Binding Protein 4, Chromatin Remodeling Factor 2 3 5
  • Retinoblastoma-Binding Protein 4 2 3 4
  • Nucleosome-Remodeling Factor Subunit RBAP48 3 4
  • Chromatin Assembly Factor I P48 Subunit 3 4
  • Chromatin Assembly Factor 1 Subunit C 3 4
  • Retinoblastoma-Binding Protein P48 3 4
  • CAF-I 48 KDa Subunit 3 4
  • CAF-1 Subunit C 3 4
  • CAF-I P48 3 4
  • RBAP48 3 4
  • RBBP-4 3 4
  • Chromatin Assembly Factor/CAF-1 P48 Subunit 3
  • Retinoblastoma Binding Protein 4 2
  • Histone-Binding Protein RBBP4 3
  • MSI1 Protein Homolog 3
  • NURF55 3
  • Lin-53 3

External Ids for RBBP4 Gene

Previous GeneCards Identifiers for RBBP4 Gene

  • GC01P032927
  • GC01P032058
  • GC01P032543
  • GC01P032619
  • GC01P032785
  • GC01P032889
  • GC01P033116
  • GC01P031231

Summaries for RBBP4 Gene

Entrez Gene Summary for RBBP4 Gene

  • This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. It is present in protein complexes involved in histone acetylation and chromatin assembly. It is part of the Mi-2 complex which has been implicated in chromatin remodeling and transcriptional repression associated with histone deacetylation. This encoded protein is also part of co-repressor complexes, which is an integral component of transcriptional silencing. It is found among several cellular proteins that bind directly to retinoblastoma protein to regulate cell proliferation. This protein also seems to be involved in transcriptional repression of E2F-responsive genes. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

GeneCards Summary for RBBP4 Gene

RBBP4 (RB Binding Protein 4, Chromatin Remodeling Factor) is a Protein Coding gene. Diseases associated with RBBP4 include Retinoblastoma and Intermediate Charcot-Marie-Tooth Neuropathy. Among its related pathways are Regulation of retinoblastoma protein and Regulation of nuclear SMAD2/3 signaling. GO annotations related to this gene include RNA polymerase II core promoter proximal region sequence-specific DNA binding and histone deacetylase binding. An important paralog of this gene is RBBP7.

UniProtKB/Swiss-Prot for RBBP4 Gene

  • Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.

Gene Wiki entry for RBBP4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RBBP4 Gene

Genomics for RBBP4 Gene

Regulatory Elements for RBBP4 Gene

Enhancers for RBBP4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F032626 0.7 ENCODE 16.8 -23.2 -23249 2.2 CTCF BCOR PKNOX1 MTA2 BHLHE40 ZMYM3 TBX21 IKZF1 NBN ZBTB33 SYNC RBBP4 ZBTB8OS ZBTB8A EIF3I TMEM234 ENSG00000224066 DCDC2B GC01M032619 LOC102723870
GH01F032771 1 ENCODE 10.7 +123.0 122976 5.1 HDGF SIN3A ARID4B ZNF48 ZNF2 ZNF766 GLIS2 ZNF143 ZNF548 PAF1 KPNA6 FNDC5 EIF3I KIAA1522 ENSG00000224409 SYNC YARS S100PBP RBBP4 ZBTB8OS
GH01F032496 1 Ensembl ENCODE 10.6 -154.8 -154842 0.6 HDGF ETV1 CEBPG YY1 IRF9 PRDM10 ZNF362 RNF2 HLF CEBPB ENSG00000254553 ZBTB8B ZBTB8A ENSG00000224409 RBBP4 ZBTB8OS LOC105378629 FNDC5 GC01P032498
GH01F032494 0.8 ENCODE 10.6 -156.8 -156766 1.7 SOX13 PKNOX1 ATF1 TAL1 CEBPG ZFHX2 NCOR1 TRIM24 PRDM10 ZNF600 ENSG00000254553 ZBTB8B ZBTB8A RBBP4 ZBTB8OS LOC105378629 FNDC5 TSSK3 GC01P032498
GH01F032796 0.8 ENCODE 10.4 +148.0 147997 5.5 HDGF PKNOX1 ZMYM3 KLF17 ZNF664 GLIS2 SCRT2 FOS MAFK ZNF652 FNDC5 KIAA1522 SYNC RBBP4 ZBTB8OS S100PBP
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RBBP4 on UCSC Golden Path with GeneCards custom track

Promoters for RBBP4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001518967 -242 3401 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1

Genomic Location for RBBP4 Gene

Chromosome:
1
Start:
32,651,142 bp from pter
End:
32,686,211 bp from pter
Size:
35,070 bases
Orientation:
Plus strand

Genomic View for RBBP4 Gene

Genes around RBBP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBBP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBBP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBBP4 Gene

Proteins for RBBP4 Gene

  • Protein details for RBBP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q09028-RBBP4_HUMAN
    Recommended name:
    Histone-binding protein RBBP4
    Protein Accession:
    Q09028
    Secondary Accessions:
    • B2R6G9
    • B4DRH0
    • D3DPQ3
    • P31149
    • Q53H02
    • Q96BV9

    Protein attributes for RBBP4 Gene

    Size:
    425 amino acids
    Molecular mass:
    47656 Da
    Quaternary structure:
    • Interacts with SUV39H1 and HDAC7 (By similarity). Binds directly to helix 1 of the histone fold of histone H4, a region that is not accessible when H4 is in chromatin. Subunit of the chromatin assembly factor 1 (CAF-1) complex, which is composed of RBBP4, CHAF1B and CHAF1A. Subunit of the core histone deacetylase (HDAC) complex, which is composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core HDAC complex associates with SIN3A, ARID4B/SAP180, SAP18, SAP30, SAP130, SUDS3/SAP45 and possibly ARID4A/RBP1 and ING1 to form the SIN3 HDAC complex. The core HDAC complex may also associate with MTA2, MBD3, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylase complex (the NuRD complex). The NuRD complex may also interact with MBD3L1 and MBD3L2. Interacts with MTA1. Subunit of the PRC2/EED-EZH2 complex, which is composed of at least EED, EZH2, RBBP4, RBBP7 and SUZ12. The PRC2/EED-EZH2 complex may also associate with HDAC1. Component of the PRC2/EED-EZH1 complex, which includes EED, EZH1, SUZ12, RBBP4 and AEBP2. Part of the nucleosome remodeling factor (NURF) complex which consists of SMARCA1; BPTF; RBBP4 and RBBP7. Interacts with the viral protein-binding domain of the retinoblastoma protein (RB1). Interacts with SPEN/MINT. Interacts with BRCA1. Interacts with CREBBP, and this interaction may be enhanced by the binding of phosphorylated CREB1 to CREBBP. Component of the DREAM complex (also named LINC complex) at least composed of E2F4, E2F5, LIN9, LIN37, LIN52, LIN54, MYBL1, MYBL2, RBL1, RBL2, RBBP4, TFDP1 and TFDP2. The complex exists in quiescent cells where it represses cell cycle-dependent genes. It dissociates in S phase when LIN9, LIN37, LIN52 and LIN54 form a subcomplex that binds to MYBL2. Interacts with PHF6.

    Three dimensional structures from OCA and Proteopedia for RBBP4 Gene

    Alternative splice isoforms for RBBP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBBP4 Gene

Post-translational modifications for RBBP4 Gene

  • Ubiquitination at Lys 143, Lys 160, Lys 178, and Lys 317
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for RBBP4 (RBBP4)

No data available for DME Specific Peptides for RBBP4 Gene

Domains & Families for RBBP4 Gene

Suggested Antigen Peptide Sequences for RBBP4 Gene

Graphical View of Domain Structure for InterPro Entry

Q09028

UniProtKB/Swiss-Prot:

RBBP4_HUMAN :
  • Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
  • Contains 6 WD repeats.
Family:
  • Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
Similarity:
  • Contains 6 WD repeats.
genes like me logo Genes that share domains with RBBP4: view

Function for RBBP4 Gene

Molecular function for RBBP4 Gene

UniProtKB/Swiss-Prot Function:
Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.

Gene Ontology (GO) - Molecular Function for RBBP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 contributes_to RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 16217013
GO:0000980 contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding IDA 16217013
GO:0004407 histone deacetylase activity TAS --
GO:0005515 protein binding IPI 7503932
GO:0008094 contributes_to DNA-dependent ATPase activity IDA 14609955
genes like me logo Genes that share ontologies with RBBP4: view
genes like me logo Genes that share phenotypes with RBBP4: view

Animal Model Products

miRNA for RBBP4 Gene

miRTarBase miRNAs that target RBBP4

Clone Products

  • Addgene plasmids for RBBP4

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBBP4 Gene

Localization for RBBP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBBP4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RBBP4 gene
Compartment Confidence
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for RBBP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 14718166
GO:0005634 nucleus IDA 14609955
GO:0005654 nucleoplasm TAS --
GO:0016580 Sin3 complex NAS 17827154
GO:0016581 NuRD complex NAS,IDA 17827154
genes like me logo Genes that share ontologies with RBBP4: view

Pathways & Interactions for RBBP4 Gene

genes like me logo Genes that share pathways with RBBP4: view

Gene Ontology (GO) - Biological Process for RBBP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication IEA --
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0006338 chromatin remodeling IDA 14609955
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with RBBP4: view

No data available for SIGNOR curated interactions for RBBP4 Gene

Transcripts for RBBP4 Gene

Unigene Clusters for RBBP4 Gene

Retinoblastoma binding protein 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for RBBP4

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RBBP4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b
SP1: -
SP2:
SP3:
SP4:

Relevant External Links for RBBP4 Gene

GeneLoc Exon Structure for
RBBP4
ECgene alternative splicing isoforms for
RBBP4

Expression for RBBP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RBBP4 Gene

Protein differential expression in normal tissues from HIPED for RBBP4 Gene

This gene is overexpressed in NK cells (11.2) and Fetal ovary (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RBBP4 Gene



Protein tissue co-expression partners for RBBP4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RBBP4 Gene:

RBBP4

SOURCE GeneReport for Unigene cluster for RBBP4 Gene:

Hs.16003
genes like me logo Genes that share expression patterns with RBBP4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RBBP4 Gene

Orthologs for RBBP4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RBBP4 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia RBBP4 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RBBP4 34
  • 99.61 (n)
dog
(Canis familiaris)
Mammalia RBBP4 34 35
  • 96.08 (n)
cow
(Bos Taurus)
Mammalia RBBP4 34 35
  • 95.37 (n)
oppossum
(Monodelphis domestica)
Mammalia RBBP4 35
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rbbp4 34
  • 93.18 (n)
mouse
(Mus musculus)
Mammalia Rbbp4 34 16 35
  • 92.24 (n)
chicken
(Gallus gallus)
Aves RBBP4 34 35
  • 86.04 (n)
lizard
(Anolis carolinensis)
Reptilia RBBP4 35
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rbbp4 34
  • 82.04 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.537 34
zebrafish
(Danio rerio)
Actinopterygii rbb4 34 35
  • 80.19 (n)
Dr.2741 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10761 34
fruit fly
(Drosophila melanogaster)
Insecta Caf1 36 34 35
  • 74.15 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003228 34
  • 72.06 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-53 34 35
  • 66.91 (n)
rba-1 36 35
  • 54 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HAT2 35 37
  • 39 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons MSI1 34
  • 63.11 (n)
soybean
(Glycine max)
eudicotyledons Gma.6467 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10708 34
rice
(Oryza sativa)
Liliopsida Os03g0640100 34
  • 62.44 (n)
Os.37345 34
barley
(Hordeum vulgare)
Liliopsida Hv.8885 34
wheat
(Triticum aestivum)
Liliopsida Ta.13849 34
corn
(Zea mays)
Liliopsida Zm.3296 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11085 35
  • 88 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mis16 34
  • 56.62 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06679 34
  • 53.7 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4514 34
Species where no ortholog for RBBP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for RBBP4 Gene

ENSEMBL:
Gene Tree for RBBP4 (if available)
TreeFam:
Gene Tree for RBBP4 (if available)

Paralogs for RBBP4 Gene

Variants for RBBP4 Gene

Sequence variations from dbSNP and Humsavar for RBBP4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs10127811 -- 32,685,741(+) AGGTA(C/T)AAAAG intron-variant, utr-variant-3-prime
rs1045114 -- 32,681,307(+) ATTTT(A/C)AGAGT utr-variant-3-prime
rs1048216 -- 32,650,519(-) GCAGG(A/T)AGAGG upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs10543592 -- 32,659,575(+) CAAAA(-/CAAAA)GAAAA intron-variant
rs10552041 -- 32,658,947(+) TAAAC(-/AA/AT)ACGTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RBBP4 Gene

Variant ID Type Subtype PubMed ID
esv3429895 CNV insertion 20981092
nsv1113099 CNV deletion 24896259
nsv160489 CNV deletion 16902084
nsv461039 CNV loss 19166990
nsv519188 CNV loss 19592680
nsv945873 CNV duplication 23825009
nsv945872 CNV duplication 23825009
nsv545961 CNV loss 21841781

Variation tolerance for RBBP4 Gene

Residual Variation Intolerance Score: 28.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.96; 19.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RBBP4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBBP4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBBP4 Gene

Disorders for RBBP4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RBBP4 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinoblastoma
  • retinoblastoma, trilateral
intermediate charcot-marie-tooth neuropathy
retinal cancer
  • malignant neoplasm of retina
sensory system cancer
- elite association - COSMIC cancer census association via MalaCards
Search RBBP4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RBBP4

Genetic Association Database (GAD)
RBBP4
Human Genome Epidemiology (HuGE) Navigator
RBBP4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RBBP4
genes like me logo Genes that share disorders with RBBP4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBBP4 Gene

Publications for RBBP4 Gene

  1. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. (PMID: 17531812) Litovchick L. … DeCaprio J.A. (Mol. Cell 2007) 2 3 4 64
  2. LINC, a human complex that is related to pRB-containing complexes in invertebrates regulates the expression of G2/M genes. (PMID: 17671431) Schmit F. … Gaubatz S. (Cell Cycle 2007) 3 4 22 64
  3. MBD3L2 interacts with MBD3 and components of the NuRD complex and can oppose MBD2-MeCP1-mediated methylation silencing. (PMID: 15701600) Jin S.-G. … Pfeifer G.P. (J. Biol. Chem. 2005) 3 4 22 64
  4. Isolation of human NURF: a regulator of Engrailed gene expression. (PMID: 14609955) Barak O. … Shiekhattar R. (EMBO J. 2003) 2 3 4 64
  5. Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1). (PMID: 11784859) Kuzmichev A. … Reinberg D. (Mol. Cell. Biol. 2002) 3 4 22 64

Products for RBBP4 Gene

Sources for RBBP4 Gene

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