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ZNF408 Gene

protein-coding   GIFtS: 48
GCID: GC11P046722

Zinc Finger Protein 408

  See ZNF408-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
Zinc Finger Protein 4081 2
PR Domain Zinc Finger Protein 172 3
PFM143
PRDM173

External Ids:    HGNC: 200411   Entrez Gene: 797972   Ensembl: ENSG000001752137   UniProtKB: Q9H9D43   

Export aliases for ZNF408 gene to outside databases

Previous GC identifers: GC11P047600 GC11P046753 GC11P046686 GC11P046678 GC11P046428


(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 ZNF408 Gene:
ZNF408 (zinc finger protein 408) is a protein-coding gene. Diseases associated with ZNF408 include exudative vitreoretinopathy. GO annotations related to this gene include identical protein binding.

UniProtKB/Swiss-Prot: ZN408_HUMAN, Q9H9D4
Function: May be involved in transcriptional regulation




(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_000011.9  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZNF408 gene promoter:
         AREB6   CREB   deltaCREB   ATF-2   Lmo2   Nkx2-5   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZNF408 promoter sequence
   Search Chromatin IP Primers for ZNF408

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZNF408


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

Entrez Gene cytogenetic band: 11p11.2   Ensembl cytogenetic band:  11p11.2   HGNC cytogenetic band: 11p11.2

ZNF408 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF408 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P046722:  view genomic region     (about GC identifiers)

Start:
46,722,317 bp from pter      End:
46,727,466 bp from pter
Size:
5,150 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: ZN408_HUMAN, Q9H9D4 (See protein sequence)
Recommended Name: Zinc finger protein 408  
Size: 720 amino acids; 78439 Da

Explore the universe of human proteins at neXtProt for ZNF408: NX_Q9H9D4

Explore proteomics data for ZNF408 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZNF408 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001171680.1  NP_079017.1  

    ENSEMBL proteins: 
     ENSP00000309606  

    ZNF408 Human Recombinant Protein Products:

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    Search eBioscience for ELISAs for ZNF408 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    3 InterPro protein domains:
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9H9D4

    ProtoNet protein and cluster: Q9H9D4

    UniProtKB/Swiss-Prot: ZN408_HUMAN, Q9H9D4
    Similarity: Contains 10 C2H2-type zinc fingers


    Find genes that share domains with ZNF408           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZN408_HUMAN, Q9H9D4
    Function: May be involved in transcriptional regulation

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding IPI14667819
    GO:0042802identical protein binding IPI15231747
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZNF408           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZNF408
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    miRNA
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    miRTarBase miRNAs that target ZNF408:
    hsa-mir-339-5p (MIRT042778)

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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ZNF408

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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
    ZN408_HUMAN, Q9H9D4: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with ZNF408           About GenesLikeMe


    (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 ZNF408
    Interactions:

        Search GeneGlobe Interaction Network for ZNF408

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for ZNF408 (Q9H9D41, 2, 3 ENSP000003096064) via UniProtKB, MINT, STRING, and/or I2D (see all 47)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000224979Q9Y3331, 2, 3, ENSP000004140064EBI-347633,EBI-347416 MINT-62595 MINT-62769 MINT-62693 I2D: score=4 STRING: ENSP00000414006
    ENSG00000236826Q9Y3331, 2, 3, ENSP000004146344EBI-347633,EBI-347416 MINT-62595 MINT-62769 MINT-62693 I2D: score=4 STRING: ENSP00000414634
    LSM2Q9Y3331, 2, 3, ENSP000003648134EBI-347633,EBI-347416 MINT-62595 MINT-62769 MINT-62693 I2D: score=4 STRING: ENSP00000364813
    ENSG00000172850Q9Y3331, 2, 3EBI-347633,EBI-347416 MINT-62595 MINT-62769 MINT-62693 I2D: score=4 
    ENSG00000225998Q9Y3331, 2, 3EBI-347633,EBI-347416 MINT-62595 MINT-62769 MINT-62693 I2D: score=4 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

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

    Find genes that share ontologies with ZNF408           About GenesLikeMe



    (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 ZNF408 (ZN408)



    (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 ZNF408 gene (2 alternative transcripts): 
    NM_001184751.1  NM_024741.2  

    Unigene Cluster for ZNF408:

    Zinc finger protein 408
    Hs.656931  [show with all ESTs]
    Unigene Representative Sequence: NM_024741
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000311764(uc001nde.2 uc010rgw.2) ENST00000531866 ENST00000526410
    ENST00000534481 ENST00000527008
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ZNF408
      QuantiFast Probe-based Assays in human, mouse, rat ZNF408

    Additional mRNA sequence: 

    AF346626.1 AK022889.1 AK302180.1 BC013355.2 BC015708.2 

    5 DOTS entries:

    DT.308775  DT.120706588  DT.120706600  DT.102841102  DT.99945789 

    Selected AceView cDNA sequences (see all 121):

    AW246726 BQ671338 AA639997 AI816535 BM828902 AF346626 BC013355 BQ707434 
    CA447608 CR603963 CD632274 AK022889 BU173878 BM680571 BX353915 BM808352 
    BQ670029 AI242496 BF061011 BM674741 AU279752 NM_024741 H63042 BC015708 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for ZNF408    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5
    SP1:                    -     -           -           -                     
    SP2:                          -           -           -                     
    SP3:                    -     -           -                                 
    SP4:                    -     -                                             
    SP5:                                      -                                 


    ECgene alternative splicing isoforms for ZNF408

    (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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    ZNF408 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCCTCGGCG
    ZNF408 Expression
    About this image

    ZNF408 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZNF408 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.656931
        Custom PCR Arrays for ZNF408
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF408

    (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 ZNF408 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zfp4081 , 5 zinc finger protein 4081, 5 76.99(n)1
    69.18(a)1
      2 (50.63 cM)5
    3814101  NM_001033451.21  NP_001028623.11 
     916436695 
    lizard
    (Anolis carolinensis)
    Reptilia ZNF4086
    zinc finger protein 408
    57(a)
    1 ↔ 1
    1(43109050-43110444)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia znf4081 zinc finger protein 408 56.28(n)
    52.95(a)
      100493930  XM_004913389.1  XP_004913446.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7934211 zinc finger protein 408-like 50.65(n)
    47.26(a)
      793421  XM_001333131.2  XP_001333167.1 


    ENSEMBL Gene Tree for ZNF408 (if available)
    TreeFam Gene Tree for ZNF408 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZNF408 gene
    Selected SIMAP similar genes for ZNF408 using alignment to 1 protein entry:     ZN408_HUMAN(see all similar genes):
    ZNF    ZNF697    ZNF709    ZNF323    ZNF844    ZNF157
    ZNF37A    ZNF419    ZNF558    ZNF565    ZNF589    ZNF92
    ZNF32    ZNF345    ZNF561    ZNF702P    ZNF75A    ZNF416

    Find genes that share paralogs with ZNF408           About GenesLikeMe



    (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 ZNF408 (see all 159)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1997490921,2
    C--46724242(+) TTGTTG/TGTTTA 2 -- int11Minor allele frequency- T:0.00EU 1323
    rs42974191,2
    C,F--46724289(-) TCACAG/CGCACA 4 /A syn1 ese36Minor allele frequency- C:0.10NA WA EU 6061
    rs799283461,2
    C,F--46724438(+) ACGGCG/ATCCTT 2 -- int11Minor allele frequency- A:0.03EA 120
    rs1402015021,2
    C,F--46724598(+) AGAGGC/TTTCAT 4 L F mis11Minor allele frequency- T:0.00NA 4550
    rs1498468661,2
    C,F--46724643(+) AACTGC/TTGCTG 4 L syn11Minor allele frequency- T:0.00NA 4428
    rs1480555281,2
    C--46724717(+) GTAGC-/AGTGG 
     TGACAGA
    AGTGG
    2 -- cds10--------
    rs1457221871,2
    C,F--46724722(+) AGTGGT/AGACAG 4 /E /V mis11Minor allele frequency- A:0.00NA 4382
    rs773737521,2
    C--46724724(+) TGGTGA/G/TCAGAA 6 T A S mis10--------
    rs3762203071,2
    C--46724728(+) GACAGA/CAGTGG 4 E A mis10--------
    rs1426287771,2
    C--46724801(+) ATGTGA/TCAAAT 2 -- int10--------

    HapMap Linkage Disequilibrium report for ZNF408 (46722317 - 46727466 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for ZNF408: --
    Human Gene Mutation Database (HGMD): ZNF408
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZNF408
    DNA2.0 Custom Variant and Variant Library Synthesis for ZNF408

    (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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    1 disease for ZNF408:    
    About MalaCards
    exudative vitreoretinopathy


    Find genes that share disorders with ZNF408           About GenesLikeMe

    Genetic Association Database (GAD): ZNF408

    Export disorders for ZNF408 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 ZNF408 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with ZNF408)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. (PubMed id 19801982)1, 4 Rivadeneira F....Uitterlinden A.G. (Nat. Genet. 2009)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. A protein interaction framework for human mRNA degradation. (PubMed id 15231747)1, 3 Lehner B. and Sanderson C.M. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature. (PubMed id 23716654)1 Collin R.W....Cremers F.P. (Proc. Natl. Acad. Sci. U.S.A. 2013)
    6. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. (PubMed id 22504420)1 Estrada K....Rivadeneira F. (Nat. Genet. 2012)
    7. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (Cell 2010)
    8. Protein microarray analysis identifies human cellular prion protein interactors. (PubMed id 18482256)1 Satoh J....Tabunoki H. (Neuropathol. Appl. Neurobiol. 2009)
    9. An empirical framework for binary interactome mapping. (PubMed id 19060904)1 Venkatesan K....Vidal M. (Nat. Methods 2009)
    10. A protein-protein interaction network of transcription factors acting during liver cell proliferation. (PubMed id 18255255)1 Gao J....Yu Y. (Genomics 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: 79797 HGNC: 20041 AceView: ZNF408 Ensembl:ENSG00000175213 euGenes: HUgn79797
    ECgene: ZNF408 H-InvDB: ZNF408

    (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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    NameDescription
    PharmGKB entry for ZNF408 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 ZNF408 gene:
    Search GeneIP for patents involving ZNF408

    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
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