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    RBBP6 RB binding protein 6, ubiquitin ligase [ Homo sapiens (human) ]

    Gene ID: 5930, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RBBP6provided by HGNC
    Official Full Name
    RB binding protein 6, ubiquitin ligaseprovided by HGNC
    Primary source
    HGNC:HGNC:9889
    See related
    Ensembl:ENSG00000122257 MIM:600938; AllianceGenome:HGNC:9889
    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
    PACT; MY038; P2P-R; RBQ-1; SNAMA
    Summary
    The retinoblastoma tumor suppressor (pRB) protein binds with many other proteins. In various human cancers, pRB suppresses cellular proliferation and is inactivated. Cell cycle-dependent phosphorylation regulates the activity of pRB. This gene encodes a protein which binds to underphosphorylated but not phosphorylated pRB. Multiple alternatively spliced transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 15.6), testis (RPKM 14.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBBP6 in Genome Data Viewer
    Location:
    16p12.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (24539566..24572863)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (24816493..24849790)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (24550887..24584184)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, U7 small nuclear 24 pseudogene Neighboring gene uncharacterized LOC105371143 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:24493839-24494713 Neighboring gene Sharpr-MPRA regulatory region 9346 Neighboring gene Sharpr-MPRA regulatory region 12060 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:24550550-24551544 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:24551545-24552537 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:24586737-24587396 Neighboring gene acyl-CoA-binding domain-containing protein 7-like Neighboring gene trinucleotide repeat containing adaptor 6A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10600 Neighboring gene long intergenic non-protein coding RNA 1567

    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. cDNA sequence and chromosomal localization of a novel human protein, RBQ-1 (RBBP6), that binds to the retinoblastoma gene product. Sakai Y, et al. Genomics, 1995 Nov 1. PMID 8595913
    2. Expression and function of retinoblastoma binding protein 6 (RBBP6) in human lung cancer. Motadi LR, et al. Immunobiology, 2011 Oct. PMID 21676486
    3. DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways. Pugh DJ, et al. BMC Struct Biol, 2006 Jan 5. PMID 16396680, Free PMC Article
    4. De-regulation of the RBBP6 isoform 3/DWNN in human cancers. Mbita Z, et al. Mol Cell Biochem, 2012 Mar. PMID 22139301
    5. Analysis of the expression and association of retinoblastoma binding protein 6 with the JNK signaling pathway in prostate cancers. Guan WY, et al. Cell Biol Int, 2020 Oct. PMID 32662898

    See all (142) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Abnormal expression of long non-coding RNA FGD5-AS1 affects the development of ovarian cancer through regulating miR-107/RBBP6 axis.
      Title: Abnormal expression of long non-coding RNA FGD5-AS1 affects the development of ovarian cancer through regulating miR-107/RBBP6 axis.
    2. RBBP6 activates the pre-mRNA 3' end processing machinery in humans.
      Title: RBBP6 activates the pre-mRNA 3' end processing machinery in humans.
    3. The lncRNA SLCO4A1-AS1/miR-876-3p/RBBP6 axis regulates cell proliferation and apoptosis in acute lymphocytic leukemia via the JNK signaling pathway.
      Title: The lncRNA SLCO4A1-AS1/miR-876-3p/RBBP6 axis regulates cell proliferation and apoptosis in acute lymphocytic leukemia via the JNK signaling pathway.
    4. Analysis of the expression and association of retinoblastoma binding protein 6 with the JNK signaling pathway in prostate cancers.
      Title: Analysis of the expression and association of retinoblastoma binding protein 6 with the JNK signaling pathway in prostate cancers.
    5. RBBP6 aggravates the progression of ovarian cancer by targeting PIK3R6.
      Title: RBBP6 aggravates the progression of ovarian cancer by targeting PIK3R6.
    6. RBBP6, a RING finger-domain E3 ubiquitin ligase, induces epithelial-mesenchymal transition and promotes metastasis of colorectal cancer.
      Title: RBBP6, a RING finger-domain E3 ubiquitin ligase, induces epithelial-mesenchymal transition and promotes metastasis of colorectal cancer.
    7. In the present study, elevated expression of PACT was detected in cisplatin-resistant A2780/CP cells relative to cisplatin-sensitive A2780cells.
      Title: PACT cessation overcomes ovarian cancer cell chemoresistance to cisplatin by enhancing p53-mediated apoptotic pathway.
    8. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30.
      Title: Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
    9. RBBP6 might potentiate cervical carcinoma cell viability.
      Title: RBBP6 promotes human cervical carcinoma malignancy via JNK signaling pathway.
    10. Results from a study on gene expression variability markers in early-stage human embryos shows that RBBP6 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.
    Submit: New GeneRIF Correction See all GeneRIFs (25)

    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
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Voxelwise genome-wide association study (vGWAS).
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    capsid gag The interaction of HIV-1 CA with human cellular retinoblastoma binding protein 6 (RBBP6) is identified by yeast two-hybrid screen PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686P0638, DKFZp761B2423

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in somite development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RBBP6
    Names
    RB-binding Q-protein 1
    RING-type E3 ubiquitin transferase RBBP6
    p53-associated cellular protein of testis
    proliferation potential-related protein
    protein P2P-R
    retinoblastoma binding protein 6
    retinoblastoma-binding Q protein 1
    NP_008841.2
    NP_061173.1
    NP_116015.2

    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_006910.5 → NP_008841.2  E3 ubiquitin-protein ligase RBBP6 isoform 1

      See identical proteins and their annotated locations for NP_008841.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longest transcript and it encodes the longest isoform (1).
      Source sequence(s)
      AB112074, AC010321, AK026954, AL359564, BF727303, BI489954, BM314442
      Consensus CDS
      CCDS10621.1
      UniProtKB/Swiss-Prot
      Q147T5, Q15290, Q6DKH4, Q6P4C2, Q6YNC9, Q7Z6E8, Q7Z6E9, Q8N0V2, Q96PH3, Q9H3I8, Q9H5M5, Q9NPX4
      UniProtKB/TrEMBL
      A0A2R8Y880
      Related
      ENSP00000317872.4, ENST00000319715.10
      Conserved Domains (4) summary
      smart00184
      Location:259 → 299
      RING; Ring finger
      COG5222
      Location:2 → 322
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:156 → 176
      zf-CCHC_2; Zinc knuckle

    2. NM_018703.4 → NP_061173.1  E3 ubiquitin-protein ligase RBBP6 isoform 2

      See identical proteins and their annotated locations for NP_061173.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AB112075, AC010321, AK026954, AL359564, BF727303, BI489954, BM314442
      Consensus CDS
      CCDS10622.1
      UniProtKB/TrEMBL
      A0A2R8Y880
      Related
      ENSP00000316291.4, ENST00000348022.6
      Conserved Domains (4) summary
      smart00184
      Location:259 → 299
      RING; Ring finger
      COG5222
      Location:2 → 322
      COG5222; Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain
      pfam13696
      Location:156 → 176
      zf-CCHC_2; Zinc knuckle

    3. NM_032626.6 → NP_116015.2  E3 ubiquitin-protein ligase RBBP6 isoform 3

      See identical proteins and their annotated locations for NP_116015.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 3 which has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC010321, BF727303, BI489954, BM314442, CB529116
      Consensus CDS
      CCDS45444.1
      UniProtKB/Swiss-Prot
      Q7Z6E9
      Related
      ENSP00000390537.2, ENST00000452655.6
      Conserved Domains (1) summary
      pfam08783
      Location:4 → 75
      DWNN; DWNN domain

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      24539566..24572863
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      24816493..24849790
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z6E9.1 GenPept UniProtKB/Swiss-Prot:Q7Z6E9

    Gene LinkOut

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

    Chemical Information
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