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RBBP5 RB binding protein 5, histone lysine methyltransferase complex subunit [ Homo sapiens (human) ]

Gene ID: 5929, updated on 7-Apr-2024

Summary

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Official Symbol
RBBP5provided by HGNC
Official Full Name
RB binding protein 5, histone lysine methyltransferase complex subunitprovided by HGNC
Primary source
HGNC:HGNC:9888
See related
Ensembl:ENSG00000117222 MIM:600697; AllianceGenome:HGNC:9888
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
RBQ3; SWD1
Summary
This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. The encoded protein binds directly to retinoblastoma protein, which regulates cell proliferation. It interacts preferentially with the underphosphorylated retinoblastoma protein via the E1A-binding pocket B. Three alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in thyroid (RPKM 6.5), lymph node (RPKM 6.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q32.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (205086142..205121978, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (204350529..204386358, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (205055270..205091106, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 1:205012106 and 1:205012198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205016337-205016841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205023369-205024096 Neighboring gene contactin 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:205041546-205042745 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 1:205044354 and 1:205044416 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205044866 Neighboring gene Sharpr-MPRA regulatory region 1805 Neighboring gene transmembrane protein 81 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205074018 Neighboring gene glycogenin 2 pseudogene 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205075359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205089166-205089724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2375 Neighboring gene Sharpr-MPRA regulatory region 3970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205101461-205101961 Neighboring gene signal peptidase complex subunit 1-like Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205104550 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:205106956-205107504 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205110917 Neighboring gene dual serine/threonine and tyrosine protein kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205143827-205144328 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:205160687-205161231 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:205163798 Neighboring gene ribosomal protein L17 pseudogene 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Retinoblastoma Binding Protein 5 Correlates with the Progression in Hepatocellular Carcinoma. Zhou H, et al. Biomed Res Int, 2018. PMID 30533424, Free PMC Article
  2. RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance. Liu H, et al. Int J Biol Macromol, 2016 Oct. PMID 27189701
  3. Expression and clinical role of RBQ3 in gliomas. Zhao C, et al. J Neurol Sci, 2015 Dec 15. PMID 26671109
  4. Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Rahman S, et al. Proc Natl Acad Sci U S A, 2022 Sep 20. PMID 36095189, Free PMC Article
  5. Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis. Xie H, et al. Oncol Rep, 2021 Feb. PMID 33416179, Free PMC Article

See all (161) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Long noncoding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA1455p/RBBP5 axis.
    Title: Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis.
  2. We used a hybrid methods approach to study the assembly and biochemical function of the minimally active MLL1 complex (MLL1, WDR5 and RbBP5)..We identified a new interaction site between the MLL1 SET domain and the WD40 beta-propeller domain of RbBP5, and demonstrate the susceptibility of the catalytic function of the complex to disruption of individual interaction sites.
    Title: The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions.
  3. We identified an internal interaction between the WD40 propeller and the C-terminal distal region in RBBP5, which assisted the maintenance of the compact conformation of the MLL1 complex. We also discovered a vertebrate-specific motif in the C-terminal distal region of RBBP5 that contributed to nucleosome recognition and methylation of nucleosomes by the MLL1 complex.
    Title: The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.
  4. Our nuclear magnetic resonance binding data supports the hypothesis that in addition to the role of RbBP5 in catalytic activation, its beta-propeller domain is a platform for the recruitment of the MLL complexes to chromatin targets through its direct interaction with nucleic acids.
    Title: The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites.
  5. RBBP5 plays an important role in the progression of hepatocellular carcinoma.
    Title: Retinoblastoma Binding Protein 5 Correlates with the Progression in Hepatocellular Carcinoma.
  6. Results from a study on gene expression variability markers in early-stage human embryos shows that RBBP5 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
    Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
  7. this study shows that during epithelial-mesenchymal transition in the prostate cancer cell line RbBP5 binding is increased in the vicinity of Snail transcription start site
    Title: Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell.
  8. different cancer mutations in MLL1 lead to a loss or increase in activity, illustrating the complex and tumor-specific role of MLL1 in carcinogenesis.
    Title: Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex.
  9. role of RBQ3 in the development of multiple myeloma
    Title: RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance.
  10. This study demonstrated that RBQ3 might play an important role in glioma, and RBQ3 inhibitors might be novel anti-tumor agents.
    Title: Expression and clinical role of RBQ3 in gliomas.
Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to estrogen IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription initiation-coupled chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of MLL1 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of MLL1 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of MLL1/2 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of MLL3/4 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of MLL3/4 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of Set1C/COMPASS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
retinoblastoma-binding protein 5
Names
RBBP-5
SWD1, Set1c WD40 repeat protein, homolog
retinoblastoma-binding protein RBQ-3

NCBI Reference Sequences (RefSeq)

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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_001193272.2 → NP_001180201.1  retinoblastoma-binding protein 5 isoform 2

    See identical proteins and their annotated locations for NP_001180201.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AK290137, AL583832, BC037284, BQ020418, DA797022
    Consensus CDS
    CCDS53463.1
    UniProtKB/TrEMBL
    B4DMM7
    Related
    ENSP00000356132.1, ENST00000367164.1
    Conserved Domains (2) summary
    sd00039
    Location:29 → 64
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30 → 322
    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_001193273.2 → NP_001180202.1  retinoblastoma-binding protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001180202.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two different splice sites in the coding region which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 3) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AK296978, AL583832, BC075059, BQ020418, DA797022
    UniProtKB/TrEMBL
    B4DLF8
    Conserved Domains (2) summary
    COG2319
    Location:10 → 194
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:75 → 120
    7WD40; WD40 repeat [structural motif]

  3. NM_005057.4 → NP_005048.2  retinoblastoma-binding protein 5 isoform 1

    See identical proteins and their annotated locations for NP_005048.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
    Source sequence(s)
    AL583832, BC075059, BQ020418, DA797022
    Consensus CDS
    CCDS30983.1
    UniProtKB/Swiss-Prot
    A8K272, Q15291, Q7Z6D8, Q8NDZ7
    UniProtKB/TrEMBL
    B4DMM7
    Related
    ENSP00000264515.6, ENST00000264515.11
    Conserved Domains (2) summary
    sd00039
    Location:29 → 64
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30 → 322
    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_2023_10

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
    205086142..205121978 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426902.1 → XP_047282858.1  retinoblastoma-binding protein 5 isoform X3

  2. XM_047426907.1 → XP_047282863.1  retinoblastoma-binding protein 5 isoform X5

  3. XM_047426905.1 → XP_047282861.1  retinoblastoma-binding protein 5 isoform X4

  4. XM_011509833.4 → XP_011508135.1  retinoblastoma-binding protein 5 isoform X2

    See identical proteins and their annotated locations for XP_011508135.1

    UniProtKB/TrEMBL
    B4DMM7
    Conserved Domains (2) summary
    sd00039
    Location:29 → 64
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30 → 322
    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 ...

  5. XM_047426894.1 → XP_047282850.1  retinoblastoma-binding protein 5 isoform X1

  6. XM_047426912.1 → XP_047282868.1  retinoblastoma-binding protein 5 isoform X7

  7. XM_047426908.1 → XP_047282864.1  retinoblastoma-binding protein 5 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    204350529..204386358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338012.1 → XP_054193987.1  retinoblastoma-binding protein 5 isoform X3

  2. XM_054338014.1 → XP_054193989.1  retinoblastoma-binding protein 5 isoform X5

  3. XM_054338013.1 → XP_054193988.1  retinoblastoma-binding protein 5 isoform X4

  4. XM_054338011.1 → XP_054193986.1  retinoblastoma-binding protein 5 isoform X2

  5. XM_054338010.1 → XP_054193985.1  retinoblastoma-binding protein 5 isoform X1

  6. XM_054338016.1 → XP_054193991.1  retinoblastoma-binding protein 5 isoform X7

  7. XM_054338015.1 → XP_054193990.1  retinoblastoma-binding protein 5 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15291.2 GenPept UniProtKB/Swiss-Prot:Q15291

Gene LinkOut

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