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RBAK-RBAKDN Gene

protein-coding   GIFtS: 22
GCID: GC07P005025

RBAK-RBAKDN Readthrough

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RBAK-RBAKDN Readthrough1 2     hRBaK3
RBAK-LOC3894582     RB-Associated KRAB Repressor3
RBAK-LOC389458 Readthrough2     Zinc Finger Protein 7693
ZNF7693     

External Ids:    HGNC: 429711   Entrez Gene: 1005339522   Ensembl: ENSG000002729687   UniProtKB: A6NC623   UniProtKB: Q9NYW83   

Export aliases for RBAK-RBAKDN gene to outside databases

Previous GC identifer: GC07P005024


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RBAK-RBAKDN Gene:
This locus represents naturally occurring read-through transcription between the neighboring RBAK (RB-associated
KRAB zinc finger) and LOC389458 (hypothetical LOC389458) genes on chromosome 7. The read-through transcript
encodes a protein that shares sequence identity with the upstream gene product but its C-terminal region is
distinct due to frameshifts relative to the downstream gene. (provided by RefSeq, Mar 2011)

GeneCards Summary for RBAK-RBAKDN Gene:
RBAK-RBAKDN (RBAK-RBAKDN readthrough) is a protein-coding gene. Diseases associated with RBAK-RBAKDN include retinoblastoma. An important paralog of this gene is ZNF175.

UniProtKB/Swiss-Prot: RBAK_HUMAN, Q9NYW8
Function: May repress E2F-dependent transcription. May promote AR-dependent transcription




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for RBAK-RBAKDN
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RBAK-RBAKDN

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBAK-RBAKDN


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Ensembl cytogenetic band:  7p22.1   HGNC cytogenetic band: 7p22.1

RBAK-RBAKDN Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBAK-RBAKDN gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P005025:  view genomic region     (about GC identifiers)

Start:
5,023,349 bp from pter      End:
5,112,854 bp from pter
Size:
89,506 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 5,131,807-5,159,209     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: YG007_HUMAN, A6NC62 (See protein sequence)
Recommended Name: Putative uncharacterized protein LOC389458  
Size: 111 amino acids; 12297 Da
Caution: Product of a dubious gene prediction
Secondary accessions: Q8N0T3

UniProtKB/Swiss-Prot: RBAK_HUMAN, Q9NYW8 (See protein sequence)

Recommended Name: RB-associated KRAB zinc finger protein  
Size: 714 amino acids; 82995 Da
Subunit: Interacts with AR and RB1. May also interact with other nuclear hormone receptors such as NR3C1/GR
Secondary accessions: A6NDF2 A8KAK4 B2RN44 B9EGS1 F8W6M7
Alternative splicing: 2 isoforms:  Q9NYW8-1   Q9NYW8-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RBAK-RBAKDN: NX_Q9NYW8

Explore proteomics data for RBAK-RBAKDN at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RBAK-RBAKDN Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001191442.1  
    ENSEMBL proteins: 
     ENSP00000385560   ENSP00000380112  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR001909 Krueppel-associated_box
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry A6NC62
    Graphical View of Domain Structure for InterPro Entry Q9NYW8

    ProtoNet protein and cluster: A6NC62

    UniProtKB/Swiss-Prot: RBAK_HUMAN, Q9NYW8
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 16 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    RBAK-RBAKDN for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RBAK_HUMAN, Q9NYW8
    Function: May repress E2F-dependent transcription. May promote AR-dependent transcription

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0008270zinc ion binding ----
         
    RBAK-RBAKDN for ontologies           About GeneDecksing


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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RBAK_HUMAN, Q9NYW8: Nucleus

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus ----

    RBAK-RBAKDN for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RBAK-RBAKDN
    Interactions:

        Search GeneGlobe Interaction Network for RBAK-RBAKDN

    3 Interacting proteins for RBAK-RBAKDN (Q9NYW83) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARP102753I2D: score=1 
    RB1P064003I2D: score=1 
    SUMO1P631653I2D: score=1 
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated ----
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0045892negative regulation of transcription, DNA-templated ----

    RBAK-RBAKDN for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RBAK-RBAKDN (RBAK)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RBAK-RBAKDN gene: 
    NM_001204513.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000407184(uc003snr.3) ENST00000396904(uc021zzc.1)
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    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    RBAK-RBAKDN Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RBAK-RBAKDN Protein Expression

    UniProtKB/Swiss-Prot: RBAK_HUMAN, Q9NYW8
    Tissue specificity: Expressed in bone, brain, heart, kidney, liver, lung, pancreas and placenta

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RBAK-RBAKDN

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    ENSEMBL Gene Tree for RBAK-RBAKDN (if available)
    TreeFam Gene Tree for RBAK-RBAKDN (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RBAK-RBAKDN gene
    ZNF1752  ZNF6742  ZNF4872  ZNF5102  ZIM32  ZNF6142  ZNF1572  ZNF262  
    ZNF6132  ZNF812  ZNF6492  ENSG000002673602  ZNF7822  ZNF7932  ZNF252  ZNF5682  
    ENSG000002365752  ENSG000002296312  ZNF5672  ZNF1822  ZNF37A2  ZNF2482  ZNF3002  ZNF3822  
    Selected SIMAP similar genes for RBAK-RBAKDN using alignment to 1 protein entry:     I3L0D1_HUMAN(see all similar genes):
    POM121C    ZNF133    ZNF81    ZNF283    ZNF573    ZNF780A
    ZNF250    ZNF420    PMS2P3    ZNF300P1    ZNF527    ZNF615
    MGC12518    ZNF33B    ZNF569    ZNF718    ZNF33A    ZNF300

    RBAK-RBAKDN for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    3 SNPs for RBAK-RBAKDN    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs733166461,2
    C,F--5109637(+) GTCTAA/CTTTTT 1 -- int12Minor allele frequency- C:0.05WA 120
    rs1501283641,2
    --5109644(+) TTTTTA/TATTTT 1 -- int10--------
    rs352435481,2
    C--5109657(+) TCGTAG/AAGACA 1 -- int11Minor allele frequency- A:0.50NA 2

    HapMap Linkage Disequilibrium report for RBAK-RBAKDN (5023349 - 5112854 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for RBAK-RBAKDN: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RBAK-RBAKDN
    DNA2.0 Custom Variant and Variant Library Synthesis for RBAK-RBAKDN

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    1 disease for RBAK-RBAKDN:    
    About MalaCards
    retinoblastoma


    RBAK-RBAKDN for disorders           About GeneDecksing


    Export disorders for RBAK-RBAKDN gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RBAK-RBAKDN gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RBAK-RBAKDN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1, 2 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The retinoblastoma protein-associated transcription repressor RBaK interacts with the androgen receptor and enhances its transcriptional activity. (PubMed id 14664718)2 Hofman K.... Heyns W. (J. Mol. Endocrinol. 2003)
    5. The DNA sequence of human chromosome 7. (PubMed id 12853948)2 Hillier L.W.... Wilson R.K. (Nature 2003)
    6. Cloning and characterization of a novel Kruppel-associated box family transcriptional repressor that interacts with the retinoblastoma gene product, RB. (PubMed id 10702291)2 Skapek S.X....Lee E.Y.-H.P. (J. Biol. Chem. 2000)
    7. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 100533952 HGNC: 42971 Ensembl:ENSG00000272968 euGenes: HUgn100533952 ECgene: RBAK-RBAKDN
    H-InvDB: RBAK-RBAKDN

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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      --

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RBAK-RBAKDN gene:
    Search GeneIP for patents involving RBAK-RBAKDN

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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