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

Gene ID: 5930, updated on 2-Nov-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
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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.

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