Human Gene RBBP6 (uc002dmh.3)
  Description: Homo sapiens retinoblastoma binding protein 6 (RBBP6), transcript variant 1, mRNA.
RefSeq Summary (NM_006910): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:24,550,908-24,584,183 Size: 33,276 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr16:24,551,948-24,583,766 Size: 31,819 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:24,550,908-24,584,183)mRNA (may differ from genome)Protein (1792 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RBBP6_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase RBBP6; EC=6.3.2.-; AltName: Full=Proliferation potential-related protein; AltName: Full=Protein P2P-R; AltName: Full=Retinoblastoma-binding Q protein 1; Short=RBQ-1; AltName: Full=Retinoblastoma-binding protein 6; AltName: Full=p53-associated cellular protein of testis;
FUNCTION: E3 ubiquitin-protein ligase which promotes ubiquitination of YBX1, leading to its degradation by the proteasome. 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.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with p53/TP53 and RB1 (By similarity). Interacts also with MDM2 and YBX1. Interacts with NEK6.
INTERACTION: Q16629:SRSF7; NbExp=3; IntAct=EBI-2117026, EBI-398885;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Chromosome. Cytoplasm, cytoskeleton, centrosome. Note=Colocalizes with mitotic chromosomes. Co-localizes with NEK6 in the centrosome.
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.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. Phosphorylated by NEK6.
SIMILARITY: Contains 1 CCHC-type zinc finger.
SIMILARITY: Contains 1 DWNN domain.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAG43155.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=AAH63524.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAL05625.1; Type=Frameshift; Positions=198; Sequence=AAL68925.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAB15600.1; Type=Erroneous initiation; Sequence=CAA59445.1; Type=Frameshift; Positions=198, 1048, 1098;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RBBP6
CDC HuGE Published Literature: RBBP6
Positive Disease Associations: Brain structure , Stroke , von Willebrand Factor
Related Studies:
  1. Brain structure
    Stein ,et al. Neuroimage 2010, Voxelwise Genome-Wide Association Study , NeuroImage 2010 . [PubMed 20171287]
  2. Stroke
    , , . [PubMed 0]
  3. von Willebrand Factor
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RBBP6
Diseases sorted by gene-association score: retinoblastoma (9), esophageal cancer (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 26.32 RPKM in Testis
Total median expression: 578.91 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -522.501040-0.502 Picture PostScript Text
3' UTR -93.20417-0.224 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR014891 - DWNN_domain
IPR001878 - Znf_CCHC
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00098 - Zinc knuckle
PF04564 - U-box domain
PF08783 - DWNN domain
PF13696 - Zinc knuckle

SCOP Domains:
57756 - Retrovirus zinc finger-like domains
57850 - RING/U-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2C7H - NMR MuPIT 2YSA - NMR MuPIT 2YUR - NMR MuPIT 3ZTG - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q7Z6E9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0019901 protein kinase binding
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0001701 in utero embryonic development
GO:0006260 DNA replication
GO:0006275 regulation of DNA replication
GO:0006397 mRNA processing
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 cellular response to DNA damage stimulus
GO:0016567 protein ubiquitination
GO:0035264 multicellular organism growth
GO:0048568 embryonic organ development
GO:0061053 somite development

Cellular Component:
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016607 nuclear speck
GO:0032991 macromolecular complex
GO:0005813 centrosome


-  Descriptions from all associated GenBank mRNAs
  AK303040 - Homo sapiens cDNA FLJ59289 partial cds, highly similar to Retinoblastoma-binding protein 6.
BC051317 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:6214974), with apparent retained intron.
AF063596 - Homo sapiens brain my038 protein mRNA, complete cds.
BC101139 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014931), complete cds.
BC101140 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014932), complete cds.
BC101141 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014933), complete cds.
BC101142 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014935), complete cds.
BC114353 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014936), complete cds.
BC114354 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014937), complete cds.
BC118667 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014938), complete cds.
BC139830 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:40014940), complete cds.
JD260402 - Sequence 241426 from Patent EP1572962.
BC029352 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:4593989), complete cds.
BC063524 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:4369701), partial cds.
AB112074 - Homo sapiens RBBP6 mRNA for retinoblastoma binding protein 6 isoform 1, complete cds.
AB112075 - Homo sapiens RBBP6 mRNA for retinoblastoma binding protein 6 isoform 2, complete cds.
BC172357 - Synthetic construct Homo sapiens clone IMAGE:100069051, MGC:199062 retinoblastoma binding protein 6 (RBBP6) mRNA, encodes complete protein.
HQ447789 - Synthetic construct Homo sapiens clone IMAGE:100071130; CCSB013195_01 retinoblastoma binding protein 6 (RBBP6) gene, encodes complete protein.
KJ891985 - Synthetic construct Homo sapiens clone ccsbBroadEn_01379 RBBP6 gene, encodes complete protein.
BX648661 - Homo sapiens mRNA; cDNA DKFZp686P0638 (from clone DKFZp686P0638).
AK023612 - Homo sapiens cDNA FLJ13550 fis, clone PLACE1007111.
AY072922 - Homo sapiens p53-associated cellular protein PACT (PACT) mRNA, complete cds.
X85133 - H.sapiens RBQ-1 mRNA.
AF352051 - Homo sapiens proliferation potential-related protein mRNA, complete cds.
BC029649 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:5140877), partial cds.
AF116625 - Homo sapiens PRO1155 mRNA, complete cds.
BC030964 - Homo sapiens, clone IMAGE:4272381, mRNA.
BC015318 - Homo sapiens, clone IMAGE:4415312, mRNA, partial cds.
JD328094 - Sequence 309118 from Patent EP1572962.
AK026954 - Homo sapiens cDNA: FLJ23301 fis, clone HEP11120.
AL359564 - Homo sapiens mRNA; cDNA DKFZp761B2423 (from clone DKFZp761B2423).
BC073938 - Homo sapiens retinoblastoma binding protein 6, mRNA (cDNA clone IMAGE:5229358), partial cds.
JD235286 - Sequence 216310 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7Z6E9 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: My038, NM_006910, NP_008841, P2PR, PACT, Q147T5, Q15290, Q6DKH4, Q6P4C2, Q6YNC9, Q7Z6E8, Q7Z6E9, Q8N0V2, Q96PH3, Q9H3I8, Q9H5M5, Q9NPX4, RBBP6_HUMAN, RBQ1
UCSC ID: uc002dmh.3
RefSeq Accession: NM_006910
Protein: Q7Z6E9 (aka RBBP6_HUMAN)
CCDS: CCDS10621.1, CCDS10622.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006910.4
exon count: 18CDS single in 3' UTR: no RNA size: 6853
ORF size: 5379CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 10911.50frame shift in genome: no % Coverage: 99.75
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.