Human Gene RBBP4 (ENST00000373493.10_6) from GENCODE V47lift37
  Description: RB binding protein 4, chromatin remodeling factor, transcript variant 1 (from RefSeq NM_005610.3)
Gencode Transcript: ENST00000373493.10_6
Gencode Gene: ENSG00000162521.19_14
Transcript (Including UTRs)
   Position: hg19 chr1:33,116,809-33,151,812 Size: 35,004 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr1:33,116,908-33,145,306 Size: 28,399 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:33,116,809-33,151,812)mRNA (may differ from genome)Protein (425 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RBBP4_HUMAN
DESCRIPTION: RecName: Full=Histone-binding protein RBBP4; AltName: Full=Chromatin assembly factor 1 subunit C; Short=CAF-1 subunit C; AltName: Full=Chromatin assembly factor I p48 subunit; Short=CAF-I 48 kDa subunit; Short=CAF-I p48; AltName: Full=Nucleosome-remodeling factor subunit RBAP48; AltName: Full=Retinoblastoma-binding protein 4; Short=RBBP-4; AltName: Full=Retinoblastoma-binding protein p48;
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.
SUBUNIT: 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, SDS3/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.
INTERACTION: Q13547:HDAC1; NbExp=5; IntAct=EBI-620823, EBI-301834; Q8IX07:ZFPM1; NbExp=4; IntAct=EBI-620823, EBI-3942619;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the WD repeat RBAP46/RBAP48/MSI1 family.
SIMILARITY: Contains 6 WD repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RBBP4
Diseases sorted by gene-association score: retinoblastoma (30), intermediate charcot-marie-tooth neuropathy (3), retinal cancer (1), sensory system cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D013749 Tetrachlorodibenzodioxin
  • D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C009505 4,4'-diaminodiphenylmethane
  • C012606 4-vinyl-1-cyclohexene dioxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D016604 Aflatoxin B1
  • D002110 Caffeine
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 71.40 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1077.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -22.6099-0.228 Picture PostScript Text
3' UTR -2110.106506-0.324 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR020472 - G-protein_beta_WD-40_rep
IPR022052 - Histone-bd_RBBP4
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF12265 - Histone-binding protein RBBP4 or subunit C of CAF1 complex

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2XU7 - X-ray MuPIT 3GFC - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q09028
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0042393 histone binding
GO:0042826 histone deacetylase binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0008094 DNA-dependent ATPase activity
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0006260 DNA replication
GO:0006325 chromatin organization
GO:0006335 DNA replication-dependent nucleosome assembly
GO:0006336 DNA replication-independent nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007049 cell cycle
GO:0008285 negative regulation of cell proliferation
GO:0016575 histone deacetylation
GO:0031497 chromatin assembly
GO:0034080 CENP-A containing nucleosome assembly
GO:0043044 ATP-dependent chromatin remodeling
GO:0045814 negative regulation of gene expression, epigenetic
GO:0051726 regulation of cell cycle
GO:0060416 response to growth hormone
GO:0070317 negative regulation of G0 to G1 transition

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016580 Sin3 complex
GO:0016581 NuRD complex
GO:0016589 NURF complex
GO:0032991 macromolecular complex
GO:0033186 CAF-1 complex
GO:0035098 ESC/E(Z) complex


-  Descriptions from all associated GenBank mRNAs
  AK054859 - Homo sapiens cDNA FLJ30297 fis, clone BRACE2003168.
AK312571 - Homo sapiens cDNA, FLJ92946, Homo sapiens retinoblastoma binding protein 4 (RBBP4), mRNA.
AK299410 - Homo sapiens cDNA FLJ50184 complete cds, highly similar to Histone-binding protein RBBP4.
BC003092 - Homo sapiens retinoblastoma binding protein 4, mRNA (cDNA clone MGC:1393 IMAGE:3356558), complete cds.
X74262 - H.sapiens RbAp48 mRNA encoding retinoblastoma binding protein.
X71810 - H.sapiens IEF 9306 mRNA.
BC053904 - Homo sapiens retinoblastoma binding protein 4, mRNA (cDNA clone MGC:61456 IMAGE:6526200), complete cds.
JD261812 - Sequence 242836 from Patent EP1572962.
AK222779 - Homo sapiens mRNA for retinoblastoma binding protein 4 variant, clone: HEP00411.
BC075836 - Homo sapiens retinoblastoma binding protein 4, mRNA (cDNA clone MGC:88716 IMAGE:6338602), complete cds.
JD207834 - Sequence 188858 from Patent EP1572962.
AB527301 - Synthetic construct DNA, clone: pF1KB4277, Homo sapiens RBBP4 gene for retinoblastoma binding protein 4, without stop codon, in Flexi system.
DQ895712 - Synthetic construct Homo sapiens clone IMAGE:100010172; FLH186901.01L; RZPDo839B0962D retinoblastoma binding protein 4 (RBBP4) gene, encodes complete protein.
DQ892499 - Synthetic construct clone IMAGE:100005129; FLH186905.01X; RZPDo839B0972D retinoblastoma binding protein 4 (RBBP4) gene, encodes complete protein.
CU678370 - Synthetic construct Homo sapiens gateway clone IMAGE:100018259 5' read RBBP4 mRNA.
KJ897453 - Synthetic construct Homo sapiens clone ccsbBroadEn_06847 RBBP4 gene, encodes complete protein.
BT007309 - Homo sapiens retinoblastoma binding protein 4 mRNA, complete cds.
AK299251 - Homo sapiens cDNA FLJ53908 complete cds, highly similar to Histone-binding protein RBBP4.
BC015123 - Homo sapiens, Similar to retinoblastoma-binding protein 4, clone IMAGE:3686783, mRNA, partial cds.
JD174899 - Sequence 155923 from Patent EP1572962.
JD359416 - Sequence 340440 from Patent EP1572962.
JD122154 - Sequence 103178 from Patent EP1572962.
JD362902 - Sequence 343926 from Patent EP1572962.
JD045073 - Sequence 26097 from Patent EP1572962.
JD145694 - Sequence 126718 from Patent EP1572962.
JD074037 - Sequence 55061 from Patent EP1572962.
JD357717 - Sequence 338741 from Patent EP1572962.
JD501659 - Sequence 482683 from Patent EP1572962.
JD284983 - Sequence 266007 from Patent EP1572962.
JD278282 - Sequence 259306 from Patent EP1572962.
HZ483118 - JP 2015535430-A/3624: TERMINALLY MODIFIED RNA.
HZ793049 - JP 2016504050-A/4794: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC515781 - Sequence 6034 from Patent WO2014113089.
LQ073369 - Sequence 3693 from Patent EP2964234.
JD140170 - Sequence 121194 from Patent EP1572962.
JD196161 - Sequence 177185 from Patent EP1572962.
JD142618 - Sequence 123642 from Patent EP1572962.
JD142619 - Sequence 123643 from Patent EP1572962.
JD324444 - Sequence 305468 from Patent EP1572962.
JD199439 - Sequence 180463 from Patent EP1572962.
JD421430 - Sequence 402454 from Patent EP1572962.
JD179041 - Sequence 160065 from Patent EP1572962.
JD179042 - Sequence 160066 from Patent EP1572962.
JD324817 - Sequence 305841 from Patent EP1572962.
JD518092 - Sequence 499116 from Patent EP1572962.
JD117314 - Sequence 98338 from Patent EP1572962.
JD106074 - Sequence 87098 from Patent EP1572962.
JD021292 - Sequence 2316 from Patent EP1572962.
JD034501 - Sequence 15525 from Patent EP1572962.
JD182872 - Sequence 163896 from Patent EP1572962.
JD212352 - Sequence 193376 from Patent EP1572962.
JD412686 - Sequence 393710 from Patent EP1572962.
JD512634 - Sequence 493658 from Patent EP1572962.
JD179707 - Sequence 160731 from Patent EP1572962.
JD464993 - Sequence 446017 from Patent EP1572962.
JD257058 - Sequence 238082 from Patent EP1572962.
JD514963 - Sequence 495987 from Patent EP1572962.
JD472511 - Sequence 453535 from Patent EP1572962.
JD199524 - Sequence 180548 from Patent EP1572962.
JD179176 - Sequence 160200 from Patent EP1572962.
AK056550 - Homo sapiens cDNA FLJ31988 fis, clone NT2RP7008863.
AK056356 - Homo sapiens cDNA FLJ31794 fis, clone NT2RI2008808.
JD248088 - Sequence 229112 from Patent EP1572962.
JD318471 - Sequence 299495 from Patent EP1572962.
JD115949 - Sequence 96973 from Patent EP1572962.
JD157399 - Sequence 138423 from Patent EP1572962.
MA646870 - JP 2017113010-A/4794: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA734754 - JP 2017140048-A/3624: TERMINALLY MODIFIED RNA.
MA803923 - JP 2018183181-A/4794: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_prc2Pathway - The PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails

Reactome (by CSHL, EBI, and GO)

Protein Q09028 (Reactome details) participates in the following event(s):

R-HSA-3240957 Formation of PRC2-EZH2 complex
R-HSA-606326 HJURP:CENPA complex localizes to the centromere
R-HSA-1362270 Phosphorylation of LIN52 component of MuvB by DYRK1A
R-HSA-4088306 FOXM1 binds PLK1 promoter
R-HSA-4088307 FOXM1 binds CCNB1 promoter
R-HSA-4088309 FOXM1 binds CCNB2 promoter
R-HSA-1362261 p130 (RBL2) associates with MuvB to form DREAM complex
R-HSA-427404 Recruitment of ERCC6 (CSB), EHMT2 (G9a), and NuRD to the promoter of rRNA gene
R-HSA-8943780 SALL4 recruits NuRD to PTEN gene
R-HSA-8964465 DREAM complex binds the PCNA gene promoter
R-HSA-8964471 DREAM complex binds the CDC25A gene promoter
R-HSA-8964475 DREAM complex binds the TOP2A gene promoter
R-HSA-8964482 DREAM complex binds the E2F1 gene promoter
R-HSA-8964492 DREAM complex binds the RBL1 gene promoter
R-HSA-8964498 DREAM complex binds the CDC6 gene promoter
R-HSA-6805650 MTA2-NuRD complex deacetylates TP53
R-HSA-8954110 E2F6:TFDP1:EPC1 binds the PRC2 complex
R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9.
R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-212222 PRC2 recruits DNA methyltransferases
R-HSA-8943817 MECOM (EVI1) recruits polycomb repressor complexes (PRCs) to the PTEN gene promoter
R-HSA-3240295 PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter
R-HSA-5638332 PRC2 (EZH2) Core:AEBP2 methylates lysine-28 of histone H3 (H3K27)
R-HSA-212263 PRC2 trimethylates histone H3 at lysine-27
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-8953750 Transcriptional Regulation by E2F6
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-1538133 G0 and Early G1
R-HSA-156711 Polo-like kinase mediated events
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-2559583 Cellular Senescence
R-HSA-212436 Generic Transcription Pathway
R-HSA-774815 Nucleosome assembly
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-69275 G2/M Transition
R-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-6807070 PTEN Regulation
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-2262752 Cellular responses to stress
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-73886 Chromosome Maintenance
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-3214815 HDACs deacetylate histones
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-74160 Gene expression (Transcription)
R-HSA-1640170 Cell Cycle
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-1266738 Developmental Biology
R-HSA-4839726 Chromatin organization
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6G9, B4DRH0, D3DPQ3, ENST00000373493.1, ENST00000373493.2, ENST00000373493.3, ENST00000373493.4, ENST00000373493.5, ENST00000373493.6, ENST00000373493.7, ENST00000373493.8, ENST00000373493.9, NM_005610, P31149, Q09028, Q53H02, Q96BV9, RBAP48, RBBP4_HUMAN, uc318kuv.1, uc318kuv.2
UCSC ID: ENST00000373493.10_6
RefSeq Accession: NM_005610.3
Protein: Q09028 (aka RBBP4_HUMAN or RBB4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.