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... See more...

Aliases for RBBP6 Gene

Aliases for RBBP6 Gene

  • RB Binding Protein 6, Ubiquitin Ligase 2 3 5
  • Proliferation Potential-Related Protein 2 3 4
  • Retinoblastoma-Binding Protein 6 2 3 4
  • P53-Associated Cellular Protein Of Testis 3 4
  • RING-Type E3 Ubiquitin Transferase RBBP6 3 4
  • Retinoblastoma-Binding Q Protein 1 3 4
  • E3 Ubiquitin-Protein Ligase RBBP6 3 4
  • Retinoblastoma Binding Protein 6 2 3
  • Protein P2P-R 3 4
  • RBQ-1 3 4
  • PACT 3 4
  • RB-Binding Q-Protein 1 3
  • EC 2.3.2.27 4
  • MY038 3
  • P2P-R 3
  • SNAMA 3
  • P2PR 4
  • RBQ1 4

External Ids for RBBP6 Gene

Previous GeneCards Identifiers for RBBP6 Gene

  • GC16P023966
  • GC16P024666
  • GC16P024494
  • GC16P024518
  • GC16P024517
  • GC16P024458
  • GC16P022641

Summaries for RBBP6 Gene

Entrez Gene Summary for RBBP6 Gene

  • 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]

GeneCards Summary for RBBP6 Gene

RBBP6 (RB Binding Protein 6, Ubiquitin Ligase) is a Protein Coding gene. Diseases associated with RBBP6 include Retinoblastoma and Esophageal Cancer. Among its related pathways are Class I MHC mediated antigen processing and presentation and Innate Immune System. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ligase activity. An important paralog of this gene is ZCCHC24.

UniProtKB/Swiss-Prot Summary for RBBP6 Gene

  • E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome (PubMed:18851979). May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth (By similarity). Regulates DNA-replication and the stability of chromosomal common fragile sites (CFSs) in a ZBTB38- and MCM10-dependent manner. Controls ZBTB38 protein stability and abundance via ubiquitination and proteasomal degradation, and ZBTB38 in turn negatively regulates the expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359).

Gene Wiki entry for RBBP6 Gene

Additional gene information for RBBP6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RBBP6 Gene

Genomics for RBBP6 Gene

GeneHancer (GH) Regulatory Elements for RBBP6 Gene

Promoters and enhancers for RBBP6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J024538 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 512.2 +3.7 3708 6.8 EP300 FOXK2 HNRNPK ZNF217 CTCF NRF1 USF1 POLR2G SP1 BCLAF1 RBBP6 lnc-TNRC6A-3 ARHGAP17 ENSG00000260751 DCTN5 hsa-miR-5095-190
GH16J024537 Promoter/Enhancer 1.1 EPDnew ENCODE 500.7 0.0 -19 0.2 POLR2G PHF8 TGIF2 SP2 POLR2A TBP POLR2H EHMT2 DRAP1 SUPT5H RBBP6 lnc-TNRC6A-3 ENSG00000260072
GH16J025256 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 198.1 +719.7 719708 4.4 EP300 ZBTB40 ZNF217 ZSCAN5C SIN3A NRF1 TCF12 MYC ZNF300 POLR2G ZKSCAN2 ZKSCAN2-DT piR-47474-003 RBBP6 ENSG00000261669 HMGN2P3 ENSG00000262587 LCMT1-AS2 SCML2P2 ARHGAP17
GH16J024540 Enhancer 0.6 Ensembl 500.7 -1.0 -992 0.2 SAP130 RXRA CEBPB NR2F6 HMG20A HNF4A KDM1A CEBPG RBPJ GATAD2A RBBP6 ENSG00000260072
GH16J024539 Enhancer 0.5 Ensembl 500.7 -1.4 -1393 0.2 CTCF SKI FOXA2 ZMYM3 NFIL3 ARID3A HLF RAD21 ZNF384 RBBP6 ENSG00000260072
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBBP6 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RBBP6

Top Transcription factor binding sites by QIAGEN in the RBBP6 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • Pax-4a

Genomic Locations for RBBP6 Gene

Genomic Locations for RBBP6 Gene
chr16:24,537,693-24,572,863
(GRCh38/hg38)
Size:
35,171 bases
Orientation:
Plus strand
chr16:24,549,014-24,584,184
(GRCh37/hg19)
Size:
35,171 bases
Orientation:
Plus strand

Genomic View for RBBP6 Gene

Genes around RBBP6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBBP6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBBP6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBBP6 Gene

Proteins for RBBP6 Gene

  • Protein details for RBBP6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z6E9-RBBP6_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RBBP6
    Protein Accession:
    Q7Z6E9
    Secondary Accessions:
    • Q147T5
    • Q15290
    • Q6DKH4
    • Q6P4C2
    • Q6YNC9
    • Q7Z6E8
    • Q8N0V2
    • Q96PH3
    • Q9H3I8
    • Q9H5M5
    • Q9NPX4

    Protein attributes for RBBP6 Gene

    Size:
    1792 amino acids
    Molecular mass:
    201564 Da
    Quaternary structure:
    • Interacts with p53/TP53 and RB1 (By similarity). Interacts also with MDM2 and YBX1. Interacts with NEK6. Interacts with ZBTB38.
    SequenceCaution:
    • Sequence=AAG43155.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305}; Sequence=AAH63524.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAL05625.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAL68925.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305}; Sequence=CAA59445.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RBBP6 Gene

    Alternative splice isoforms for RBBP6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBBP6 Gene

Post-translational modifications for RBBP6 Gene

No data available for DME Specific Peptides for RBBP6 Gene

Domains & Families for RBBP6 Gene

Gene Families for RBBP6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for RBBP6 Gene

Blocks:
  • Zn-finger, RING
  • C2HC-type zinc-finger signature
  • Zn-finger, modified RING
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RBBP6 Gene

GenScript: Design optimal peptide antigens:
  • p53-associated cellular protein of testis (RBBP6_HUMAN)
genes like me logo Genes that share domains with RBBP6: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RBBP6 Gene

Function for RBBP6 Gene

Molecular function for RBBP6 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome (PubMed:18851979). May play a role as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in increase of MDM2-mediated ubiquitination and degradation of p53/TP53; may function as negative regulator of p53/TP53, leading to both apoptosis and cell growth (By similarity). Regulates DNA-replication and the stability of chromosomal common fragile sites (CFSs) in a ZBTB38- and MCM10-dependent manner. Controls ZBTB38 protein stability and abundance via ubiquitination and proteasomal degradation, and ZBTB38 in turn negatively regulates the expression of MCM10 which plays an important role in DNA-replication (PubMed:24726359).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;.
GENATLAS Biochemistry:
RB1 binding nuclear protein (140kDa)

Enzyme Numbers (IUBMB) for RBBP6 Gene

Phenotypes From GWAS Catalog for RBBP6 Gene

Gene Ontology (GO) - Molecular Function for RBBP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22681889
GO:0004842 ubiquitin-protein transferase activity IDA 18851979
GO:0005515 protein binding IPI 18624398
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with RBBP6: view
genes like me logo Genes that share phenotypes with RBBP6: view

Animal Models for RBBP6 Gene

MGI Knock Outs for RBBP6:

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RBBP6 Gene

Localization for RBBP6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBBP6 Gene

Nucleus, nucleolus. Chromosome. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Colocalizes with mitotic chromosomes. Colocalizes with NEK6 in the centrosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RBBP6 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBBP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005730 nucleolus IEA --
GO:0005737 cytoplasm IEA --
GO:0005813 colocalizes_with centrosome IDA 20873783
genes like me logo Genes that share ontologies with RBBP6: view

Pathways & Interactions for RBBP6 Gene

genes like me logo Genes that share pathways with RBBP6: view

UniProtKB/Swiss-Prot Q7Z6E9-RBBP6_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RBBP6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination TAS --
GO:0001701 in utero embryonic development IEA --
GO:0006260 DNA replication IEA --
GO:0006275 regulation of DNA replication IMP 24726359
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with RBBP6: view

No data available for SIGNOR curated interactions for RBBP6 Gene

Drugs & Compounds for RBBP6 Gene

No Compound Related Data Available

Transcripts for RBBP6 Gene

mRNA/cDNA for RBBP6 Gene

3 REFSEQ mRNAs :
32 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RBBP6 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a ·
SP1: - - - - - -
SP2: - - - - - -
SP3: -
SP4: - - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - -
SP7:
SP8: -
SP9:
SP10: -
SP11: -
SP12:
SP13:
SP14:

ExUns: 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23a · 23b
SP1: - -
SP2: - - -
SP3: - - -
SP4: - - - - - - - - - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for RBBP6 Gene

GeneLoc Exon Structure for
RBBP6

Expression for RBBP6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RBBP6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RBBP6 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (62.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RBBP6 Gene



Protein tissue co-expression partners for RBBP6 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RBBP6

SOURCE GeneReport for Unigene cluster for RBBP6 Gene:

Hs.188553

mRNA Expression by UniProt/SwissProt for RBBP6 Gene:

Q7Z6E9-RBBP6_HUMAN
Tissue specificity: Highly expressed in the placenta and testis. Expressed at lower levels in the brain, heart, kidney, liver and lung. Overexpressed in esophageal cancer.

Evidence on tissue expression from TISSUES for RBBP6 Gene

  • Nervous system(4.6)
  • Kidney(4.4)
  • Liver(4.3)
  • Spleen(4.3)
  • Bone(4)
  • Lung(2)
genes like me logo Genes that share expression patterns with RBBP6: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBBP6 Gene

Orthologs for RBBP6 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RBBP6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RBBP6 31 30
  • 99.5 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RBBP6 31 30
  • 92.11 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RBBP6 31 30
  • 92.02 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rbbp6 30
  • 86.91 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 86 (a)
OneToMany
-- 31
  • 83 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 68 (a)
OneToMany
-- 31
  • 59 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Rbbp6 17 31 30
  • 85.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RBBP6 31
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves RBBP6 31
  • 94 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RBBP6 31
  • 71 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.34117 30
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75882 30
zebrafish
(Danio rerio)
Actinopterygii rbbp6 31
  • 50 (a)
OneToOne
Dr.18039 30
fruit fly
(Drosophila melanogaster)
Insecta snama 31
  • 24 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea rbpl-1 31
  • 23 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MPE1 33 31
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 52 (a)
OneToOne
Species where no ortholog for RBBP6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RBBP6 Gene

ENSEMBL:
Gene Tree for RBBP6 (if available)
TreeFam:
Gene Tree for RBBP6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RBBP6: view image

Paralogs for RBBP6 Gene

Paralogs for RBBP6 Gene

(2) SIMAP similar genes for RBBP6 Gene using alignment to 5 proteins:

  • RBBP6_HUMAN
  • H3BSK8_HUMAN
  • H3BUN0_HUMAN
  • I3L3Y2_HUMAN
  • L8E7X2_HUMAN

Pseudogenes.org Pseudogenes for RBBP6 Gene

genes like me logo Genes that share paralogs with RBBP6: view

Variants for RBBP6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RBBP6 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs16973796 - p.Asp43His
rs16973840 - p.Val555Ala
rs3743968 - p.Lys1208Ile

Additional dbSNP identifiers (rs#s) for RBBP6 Gene

Structural Variations from Database of Genomic Variants (DGV) for RBBP6 Gene

Variant ID Type Subtype PubMed ID
nsv1769 CNV deletion 18451855
nsv952957 CNV duplication 24416366

Variation tolerance for RBBP6 Gene

Residual Variation Intolerance Score: 1.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.15; 61.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RBBP6 Gene

Human Gene Mutation Database (HGMD)
RBBP6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBBP6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBBP6 Gene

Disorders for RBBP6 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RBBP6 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinoblastoma
  • rb1
esophageal cancer
  • esophageal cancer, somatic
waardenburg syndrome, type 4a
  • ws4a
- elite association - COSMIC cancer census association via MalaCards
Search RBBP6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RBBP6

genes like me logo Genes that share disorders with RBBP6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBBP6 Gene

Publications for RBBP6 Gene

  1. cDNA sequence and chromosomal localization of a novel human protein, RBQ-1 (RBBP6), that binds to the retinoblastoma gene product. (PMID: 8595913) Sakai Y … Taya Y (Genomics 1995) 2 3 4 23 54
  2. RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1. (PMID: 18851979) Chibi M … Pugh DJ (Journal of molecular biology 2008) 2 3 4 54
  3. DWNN, a novel ubiquitin-like domain, implicates RBBP6 in mRNA processing and ubiquitin-like pathways. (PMID: 16396680) Pugh DJ … Rees DJ (BMC structural biology 2006) 2 3 4 54
  4. Proliferation potential-related protein, an ideal esophageal cancer antigen for immunotherapy, identified using complementary DNA microarray analysis. (PMID: 15475430) Yoshitake Y … Nishimura Y (Clinical cancer research : an official journal of the American Association for Cancer Research 2004) 3 4 23 54
  5. The RBBP6/ZBTB38/MCM10 axis regulates DNA replication and common fragile site stability. (PMID: 24726359) Miotto B … Defossez PA (Cell reports 2014) 3 4 54

Products for RBBP6 Gene

Sources for RBBP6 Gene