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

    Gene ID: 5929, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See RBBP5 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (205086142..205121978, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (204350529..204386358, complement)
    RS_2024_09 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 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. Expression and clinical role of RBQ3 in gliomas. Zhao C, et al. J Neurol Sci, 2015 Dec 15. PMID 26671109
    2. RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance. Liu H, et al. Int J Biol Macromol, 2016 Oct. PMID 27189701
    3. Retinoblastoma Binding Protein 5 Correlates with the Progression in Hepatocellular Carcinoma. Zhou H, et al. Biomed Res Int, 2018. PMID 30533424, Free PMC Article
    4. Molecular cloning of a human protein that binds to the retinoblastoma protein and chromosomal mapping. Saijo M, et al. Genomics, 1995 Jun 10. PMID 7558034
    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 (170) 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_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
      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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