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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 Retinal Cancer. Among its related pathways are Development NOTCH1-mediated pathway for NF-KB activity modulation and Regulation of Telomerase. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter 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

Additional gene information for RBBP4 Gene

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

Genomics for RBBP4 Gene

GeneHancer (GH) Regulatory Elements for RBBP4 Gene

Promoters and enhancers for RBBP4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I032649 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 574.9 +0.1 62 3.9 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC RBBP4 ZBTB8OS TXLNA TMEM39B TSSK3 KHDRBS1 ZBTB8A ZSCAN20 FAM229A AK2
GH01I031924 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 87.5 -715.3 -715309 22.1 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 GC01P031934 PTP4A2 TXLNA SNRNP40 KHDRBS1 RBBP4 ENSG00000229447 TSSK3 ZBTB8A TMEM39B
GH01I032262 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 87.1 -385.8 -385754 4.8 ZNF493 ZNF529 ZFP64 RARA ZNF213 SCRT2 ZNF654 ZNF680 ZBTB11 CEBPB TXLNA RBBP4 SNRNP40 KHDRBS1 TSSK3 TMEM39B ZBTB8A ZNF362 DCDC2B S100PBP
GH01I032813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 50.8 +166.1 166100 7.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 S100PBP YARS TXLNA TSSK3 RBBP4 ZBTB8A KHDRBS1 TMEM39B EIF3I FAM229A
GH01I031951 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 62.8 -695.1 -695072 9.1 DMAP1 YBX1 IRF4 YY1 E2F8 ZC3H11A MEF2D GLIS1 RCOR2 NBN SNRNP40 KHDRBS1 TXLNA RBBP4 TSSK3 TMEM39B ENSG00000229447 ZBTB8A IQCC ENSG00000228634
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RBBP4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RBBP4 gene promoter:

Genomic Locations for RBBP4 Gene

Genomic Locations for RBBP4 Gene
chr1:32,651,142-32,686,211
(GRCh38/hg38)
Size:
35,070 bases
Orientation:
Plus strand
chr1:33,116,743-33,151,812
(GRCh37/hg19)

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 (By similarity). Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1 (By similarity).

    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 isoforms=2, 3, 4143, isoforms=2, 3, 4160, isoforms=2, 3, 4178, and isoforms=2, 3, 4317
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for 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.
Family:
  • Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
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 proximal promoter sequence-specific DNA binding IDA,HDA 16217013
GO:0000980 contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding IDA,HDA 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

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)

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 IDA,TAS --
GO:0005829 cytosol IDA --
GO:0016580 Sin3 complex NAS 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

Drugs & Compounds for RBBP4 Gene

No Compound Related Data Available

Transcripts for RBBP4 Gene

Unigene Clusters for RBBP4 Gene

Retinoblastoma binding protein 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for RBBP4

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 CGAP 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

Evidence on tissue expression from TISSUES for RBBP4 Gene

  • Nervous system(4.9)
  • Eye(4.6)
  • Liver(4.4)
  • Skin(4.4)
  • Bone marrow(4.2)
  • Intestine(2.5)
  • Kidney(2.3)
  • Blood(2.1)
  • Lung(2.1)
  • Stomach(2.1)
genes like me logo Genes that share expression patterns with RBBP4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RBBP4 33
  • 99.61 (n)
dog
(Canis familiaris)
Mammalia RBBP4 33 34
  • 96.08 (n)
cow
(Bos Taurus)
Mammalia RBBP4 33 34
  • 95.37 (n)
oppossum
(Monodelphis domestica)
Mammalia RBBP4 34
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rbbp4 33
  • 93.18 (n)
mouse
(Mus musculus)
Mammalia Rbbp4 33 16 34
  • 92.24 (n)
chicken
(Gallus gallus)
Aves RBBP4 33 34
  • 86.04 (n)
lizard
(Anolis carolinensis)
Reptilia RBBP4 34
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rbbp4 33
  • 82.04 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.537 33
zebrafish
(Danio rerio)
Actinopterygii rbb4 33 34
  • 80.19 (n)
Dr.2741 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10761 33
fruit fly
(Drosophila melanogaster)
Insecta Caf1 35 33 34
  • 74.15 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003228 33
  • 72.06 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-53 33 34
  • 66.91 (n)
rba-1 35 34
  • 54 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HAT2 34 36
  • 39 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons MSI1 33
  • 63.11 (n)
soybean
(Glycine max)
eudicotyledons Gma.6467 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10708 33
rice
(Oryza sativa)
Liliopsida Os03g0640100 33
  • 62.44 (n)
Os.37345 33
barley
(Hordeum vulgare)
Liliopsida Hv.8885 33
wheat
(Triticum aestivum)
Liliopsida Ta.13849 33
corn
(Zea mays)
Liliopsida Zm.3296 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.11085 34
  • 88 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mis16 33
  • 56.62 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06679 33
  • 53.7 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4514 33
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 Variation AA Info Type
rs1000012005 -- 32,670,642(+) G/A intron_variant
rs1000033074 -- 32,681,044(+) A/G 3_prime_UTR_variant
rs1000078286 -- 32,662,113(+) T/C intron_variant
rs1000120357 -- 32,665,098(+) C/T intron_variant
rs1000276909 -- 32,659,120(+) TATATATA/TATA/TATATA 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
nsv545961 CNV loss 21841781
nsv945872 CNV duplication 23825009
nsv945873 CNV duplication 23825009

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)

Additional Variant Information for RBBP4 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RBBP4 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
retinoblastoma
  • rb1
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

Additional Disease Information for RBBP4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 JA (Molecular cell 2007) 2 3 4 58
  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 (Georgetown, Tex.) 2007) 3 4 22 58
  3. MBD3L2 interacts with MBD3 and components of the NuRD complex and can oppose MBD2-MeCP1-mediated methylation silencing. (PMID: 15701600) Jin SG … Pfeifer GP (The Journal of biological chemistry 2005) 3 4 22 58
  4. Isolation of human NURF: a regulator of Engrailed gene expression. (PMID: 14609955) Barak O … Shiekhattar R (The EMBO journal 2003) 2 3 4 58
  5. Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1). (PMID: 11784859) Kuzmichev A … Reinberg D (Molecular and cellular biology 2002) 3 4 22 58

Products for RBBP4 Gene