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ZDBF2 Gene

protein-coding   GIFtS: 43
GCID: GC02P207139

Zinc Finger, DBF-Type Containing 2

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(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
Zinc Finger, DBF-Type Containing 21 2
DBF4-Type Zinc Finger-Containing Protein 22
Zinc Finger DBF-Type Containing 2 Vesion 12
Zinc Finger DBF-Type Containing 2 Vesion 22
KIAA15713

External Ids:    HGNC: 293131   Entrez Gene: 576832   Ensembl: ENSG000002041867   UniProtKB: Q9HCK13   

Export aliases for ZDBF2 gene to outside databases

Previous GC identifers: GC02P206848 GC02P198990


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ZDBF2 Gene:
ZDBF2 (zinc finger, DBF-type containing 2) is a protein-coding gene. GO annotations related to this gene include nucleic acid binding.


(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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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZDBF2 gene promoter:
         SRF   Sox5   USF1   p300   Brachyury   SRF (504 AA)   IRF-1   Evi-1   USF-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ZDBF2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZDBF2


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

Entrez Gene cytogenetic band: 2q33.3   Ensembl cytogenetic band:  2q33.3   HGNC cytogenetic band: 2q33.3

ZDBF2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZDBF2 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P207139:  view genomic region     (about GC identifiers)

Start:
207,139,387 bp from pter      End:
207,179,148 bp from pter
Size:
39,762 bases      Orientation:
plus strand

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ZDBF2_HUMAN, Q9HCK1 (See protein sequence)
Recommended Name: DBF4-type zinc finger-containing protein 2  
Size: 2354 amino acids; 265618 Da
Sequence caution: Sequence=BAC85454.1; Type=Erroneous initiation;
Secondary accessions: Q6ZNP7 Q6ZSN8

Explore the universe of human proteins at neXtProt for ZDBF2: NX_Q9HCK1

Explore proteomics data for ZDBF2 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys2133
  • Modification sites at PhosphoSitePlus

  • See ZDBF2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001272478.1  NP_065974.1  

    ENSEMBL proteins: 
     ENSP00000363545  

    ZDBF2 Human Recombinant Protein Products:

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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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    HGNC Gene Families:
    ZDBF: Zinc fingers, DBF-type

    1 InterPro protein domain:
     IPR006572 Znf_DBF

    Graphical View of Domain Structure for InterPro Entry Q9HCK1

    ProtoNet protein and cluster: Q9HCK1

    UniProtKB/Swiss-Prot: ZDBF2_HUMAN, Q9HCK1
    Similarity: Contains 1 DBF4-type zinc finger


    Find genes that share domains with ZDBF2           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with ZDBF2           About GenesLikeMe


    Animal Models:
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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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    plasma membrane1

    (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 ZDBF2
    Interactions:

        Search GeneGlobe Interaction Network for ZDBF2

    1 Interacting protein for ZDBF2 (Q9HCK13) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP1CAP621363I2D: score=1 
    About this table

    (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 ZDBF2



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ZDBF2 gene (2 alternative transcripts): 
    NM_001285549.1  NM_020923.2  

    Unigene Cluster for ZDBF2:

    Zinc finger, DBF-type containing 2
    Hs.110489  [show with all ESTs]
    Unigene Representative Sequence: NM_020923
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000374423(uc002vbp.2)
    miRNA
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    hsa-miR-944 hsa-miR-410 hsa-miR-105 hsa-miR-3658 hsa-miR-3613-3p hsa-miR-186 hsa-miR-23a hsa-miR-3143
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      QuantiFast Probe-based Assays in human, mouse, rat ZDBF2

    Additional mRNA sequence: 

    AB046791.2 AK024339.1 AK127271.1 AK130893.1 

    2 DOTS entries:

    DT.206131  DT.100741554 

    17 AceView cDNA sequences:

    AI128443 AU137494 BX093847 AI151388 AI128504 CB160399 AK002005 BC028329 
    BX113617 BE535795 T58264 AI653148 AU157195 T54342 BE734382 T85180 
    T84296 

    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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    ZDBF2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAAACTAAT
    ZDBF2 Expression
    About this image


    ZDBF2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Pancreas (Endocrine System)    fully expand to see all 4 entries
             Endocrine Progenitor Cells Ventral Pancreatic Bud
     
     Heart (Cardiovascular System)
             Cardiac Fibroblasts Myocardium
     
     Fibroblasts
             Cardiac Fibroblasts Myocardium
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
    ZDBF2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZDBF2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.110489
        Custom PCR Arrays for ZDBF2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZDBF2

    (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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    This gene was present in the common ancestor of chordates.

    Orthologs for ZDBF2 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zdbf21 , 5 zinc finger, DBF-type containing 21, 5 70.16(n)1
    50.58(a)1
      1 (32.31 cM)5
    738841  NM_001285936.11  NP_001272865.11 
     632732655 
    chicken
    (Gallus gallus)
    Aves ZDBF26
    zinc finger, DBF-type containing 2
    28(a)
    1 ↔ 1
    7(12036611-12047108)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    31(a)
    14(a)
    many → 1
    many → 1
    GL343208.1(540160-551525)
    GL343208.1(538657-538878)


    ENSEMBL Gene Tree for ZDBF2 (if available)
    TreeFam Gene Tree for ZDBF2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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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    Selected SNPs for ZDBF2 (see all 886)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs802329841,2
    F--207137706(+) CAATGG/TTGTTA 1 -- us2k11Minor allele frequency- T:0.01EA 120
    rs1845152701,2
    --207137756(+) CTATCA/GAGAAT 1 -- us2k10--------
    rs1907901381,2
    --207137768(+) ATATCC/GAAGTT 1 -- us2k10--------
    rs748674231,2
    C,F--207137823(+) CATATA/GTGGGT 1 -- us2k12Minor allele frequency- G:0.06CSA WA 120
    rs1414119261,2
    --207137966(+) TTCTCC/TAGGCA 1 -- us2k10--------
    rs1470180101,2
    C--207137967(+) TCTCCA/GGGCAA 1 -- us2k10--------
    rs67292751,2
    C,F--207138034(+) TAATTC/TCCTTC 1 -- us2k1 tfbs3 trp31Minor allele frequency- T:0.04WA 118
    rs67293741,2
    C,F--207138073(+) ATGCAC/TTTATC 1 -- us2k11Minor allele frequency- T:0.02WA 118
    rs729489321,2
    C--207138127(+) AATACA/G/TTGGAG 1 -- us2k14NA WA EA 360
    rs1390211001,2
    --207138133(+) TGGAGA/GTAATG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZDBF2 (207139387 - 207179148 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for ZDBF2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv875738CNV Gain21882294
    nsv834516CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for ZDBF2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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 ZDBF2 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with ZDBF2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10997877)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 2000)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Protein phosphatase 1I^ isoforms linked interactions in the brain. (PubMed id 23080069)1 Esteves S.L....da Cruz e Silva E.F. (J. Mol. Neurosci. 2013)
    4. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (Nat. Methods 2013)
    5. Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc. (PubMed id 23764515)1 Kobayashi H....Kono T. (Epigenetics 2013)
    6. The SOX2-interactome in brain cancer cells identifies the requirement of MSI2 and USP9X for the growth of brain tumor cells. (PubMed id 23667531)1 Cox J.L....Rizzino A. (PLoS ONE 2013)
    7. Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. (PubMed id 22688191)1 Bergen S.E....Sullivan P.F. (Mol. Psychiatry 2012)
    8. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    9. Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. (PubMed id 19200453)1 Kobayashi H....Kono T. (Genomics 2009)
    10. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)

    (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: 57683 HGNC: 29313 AceView: KIAA1571 Ensembl:ENSG00000204186 euGenes: HUgn57683
    ECgene: ZDBF2 H-InvDB: ZDBF2

    (According to HUGE)
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    HUGE: KIAA1571

    (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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    NameDescription
    PharmGKB entry for ZDBF2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ZDBF2 gene:
    Search GeneIP for patents involving ZDBF2

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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