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    RBBP4 RB binding protein 4, chromatin remodeling factor [ Homo sapiens (human) ]

    Gene ID: 5928, updated on 27-Nov-2024

    Summary

    Official Symbol
    RBBP4provided by HGNC
    Official Full Name
    RB binding protein 4, chromatin remodeling factorprovided by HGNC
    Primary source
    HGNC:HGNC:9887
    See related
    Ensembl:ENSG00000162521 MIM:602923; AllianceGenome:HGNC:9887
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NURF55; RBAP48; lin-53
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 27.2), lymph node (RPKM 20.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RBBP4 in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32651208..32686211)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32510988..32546003)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33116809..33151812)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723870 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33077607-33078108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 694 Neighboring gene zinc finger and BTB domain containing 8 opposite strand Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33107487-33108246 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33108247-33109005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 695 Neighboring gene hESC enhancers GRCh37_chr1:33116021-33116608 and GRCh37_chr1:33116609-33117197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33154443-33154943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33160284-33161022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33167839-33168604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33168605-33169370 Neighboring gene syncoilin, intermediate filament protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 607 Neighboring gene Sharpr-MPRA regulatory region 2185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33183271-33184026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33189892-33190720 Neighboring gene Sharpr-MPRA regulatory region 8469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33200787-33201312 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33201837-33202361 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33202362-33202885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 608 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33219766-33220279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33225004-33225886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33225887-33226770 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:33227405-33227625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33231243-33232135 Neighboring gene NHS like 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33232136-33233029 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33235076-33235991 Neighboring gene Sharpr-MPRA regulatory region 15696 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6796 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:33251929-33253128 Neighboring gene tyrosyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 697 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33269619-33270293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33270294-33270967 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33275934-33276570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33276571-33277206 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33282071-33282572 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33282573-33283072 Neighboring gene S100P binding protein

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat The SIN3/HDAC complex, composed of SIN3A, SAP30, SAP18, HDAC-1 AND -2 and RbAp46/48 ,except SAP30, interacts with HIV-1 Tat in Jurkat cell PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to ATP-dependent activity, acting on DNA IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    contributes_to nucleosomal DNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA replication-dependent chromatin assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in brain development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in chromatin remodeling HDA PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of cell migration NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell fate specification NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of stem cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of ATPase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of CAF-1 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of CAF-1 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of ESC/E(Z) complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of ESC/E(Z) complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of NURF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of NURF complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of NuRD complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of NuRD complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of Sin3-type complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in chromatin HDA PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    part_of histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of protein-containing complex HDA PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone-binding protein RBBP4
    Names
    CAF-1 subunit C
    CAF-I 48 kDa subunit
    CAF-I p48
    MSI1 protein homolog
    RBBP-4
    chromatin assembly factor 1 subunit C
    chromatin assembly factor I p48 subunit
    chromatin assembly factor/CAF-1 p48 subunit
    nucleosome-remodeling factor subunit RBAP48
    retinoblastoma-binding protein 4
    retinoblastoma-binding protein p48

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001135255.2NP_001128727.1  histone-binding protein RBBP4 isoform b

      See identical proteins and their annotated locations for NP_001128727.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is one aa shorter compared to isoform a.
      Source sequence(s)
      AC114489, AK222779, DC315298
      Consensus CDS
      CCDS44105.1
      UniProtKB/Swiss-Prot
      Q09028
      Related
      ENSP00000398242.3, ENST00000414241.7
      Conserved Domains (3) summary
      sd00039
      Location:127174
      7WD40; WD40 repeat [structural motif]
      pfam12265
      Location:1887
      CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex
      cl29593
      Location:121402
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    2. NM_001135256.2NP_001128728.1  histone-binding protein RBBP4 isoform c

      See identical proteins and their annotated locations for NP_001128728.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC114489, AK222779, AK299251
      Consensus CDS
      CCDS44106.1
      UniProtKB/Swiss-Prot
      Q09028
      Related
      ENSP00000396057.2, ENST00000458695.6
      Conserved Domains (3) summary
      sd00039
      Location:93140
      7WD40; WD40 repeat [structural motif]
      pfam12265
      Location:153
      CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex
      cl29593
      Location:87368
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    3. NM_005610.3NP_005601.1  histone-binding protein RBBP4 isoform a

      See identical proteins and their annotated locations for NP_005601.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC114489, AK312571, DC315298
      Consensus CDS
      CCDS366.1
      UniProtKB/Swiss-Prot
      B2R6G9, B4DRH0, D3DPQ3, P31149, Q09028, Q53H02, Q96BV9
      Related
      ENSP00000362592.4, ENST00000373493.10
      Conserved Domains (3) summary
      sd00039
      Location:128175
      7WD40; WD40 repeat [structural motif]
      pfam12265
      Location:1988
      CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex
      cl29593
      Location:122403
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32651208..32686211
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      32510988..32546003
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)