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ZNF558 Gene

protein-coding   GIFtS: 47
GCID: GC19M008920

Zinc Finger Protein 558

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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 Protein 5581 2

External Ids:    HGNC: 264221   Entrez Gene: 1481562   Ensembl: ENSG000001677857   UniProtKB: Q96NG53   

Export aliases for ZNF558 gene to outside databases

Previous GC identifers: GC19M008782 GC19M008784 GC19M008497


(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 ZNF558 Gene:
ZNF558 (zinc finger protein 558) is a protein-coding gene. An important paralog of this gene is ZNF124.

UniProtKB/Swiss-Prot: ZN558_HUMAN, Q96NG5
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_000019.9  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZNF558 gene promoter:
         TBP   Bach1   p53   AML1a   LCR-F1   HNF-3beta   GATA-1   RORalpha2   RORalpha1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZNF558 promoter sequence
   Search Chromatin IP Primers for ZNF558

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZNF558


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

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

ZNF558 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF558 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M008920:  view genomic region     (about GC identifiers)

Start:
8,920,380 bp from pter      End:
8,943,004 bp from pter
Size:
22,625 bases      Orientation:
minus 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: ZN558_HUMAN, Q96NG5 (See protein sequence)
Recommended Name: Zinc finger protein 558  
Size: 402 amino acids; 45755 Da
Secondary accessions: A8K5F0

Explore the universe of human proteins at neXtProt for ZNF558: NX_Q96NG5

Explore proteomics data for ZNF558 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZNF558 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_653294.1  
    ENSEMBL proteins: 
     ENSP00000471277   ENSP00000301475   ENSP00000410703  
    Reactome Protein details: Q96NG5

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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:
    ZNF: Zinc fingers, C2H2-type

    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 Q96NG5

    ProtoNet protein and cluster: Q96NG5

    1 Blocks protein domain: IPB001909 KRAB box

    UniProtKB/Swiss-Prot: ZN558_HUMAN, Q96NG5
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 9 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    Find genes that share domains with ZNF558           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: ZN558_HUMAN, Q96NG5
    Function: May be involved in transcriptional regulation

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZNF558           About GenesLikeMe


    Animal Models:
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    miRNA
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    miRTarBase miRNAs that target ZNF558:
    hsa-mir-335-5p (MIRT017695), hsa-mir-181a-5p (MIRT025046)

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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
    ZN558_HUMAN, Q96NG5: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--

    Find genes that share ontologies with ZNF558           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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    SuperPaths for ZNF558 About    
    See pathways by source

    SuperPathContained pathways About
    1Gene Expression
    Generic Transcription Pathway0.40
    Gene Expression0.40


    Find genes that share SuperPaths with ZNF558           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1 Reactome Pathway for ZNF558
        Generic Transcription Pathway


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZNF558
    Interactions:

        Search GeneGlobe Interaction Network for ZNF558

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for ZNF558 (Q96NG53 ENSP000003014754) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOSC5Q9NQT43, ENSP000002212334I2D: score=3 STRING: ENSP00000221233
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0008150biological_process ND--

    Find genes that share ontologies with ZNF558           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 ZNF558 (ZN558)



    (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 ZNF558 gene: 
    NM_144693.1  

    Unigene Cluster for ZNF558:

    Zinc finger protein 558
    Hs.659797  [show with all ESTs]
    Unigene Representative Sequence: AK055494
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000601372 ENST00000301475(uc010xkh.1 uc002mkn.1 uc010dwg.1)
    ENST00000597304 ENST00000599938 ENST00000595786 ENST00000596172 ENST00000593891
    ENST00000444186
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat ZNF558

    Additional mRNA sequence: 

    AK055494.1 AK291265.1 AK301664.1 AK307200.1 BC064356.1 

    4 DOTS entries:

    DT.97864487  DT.40130364  DT.91973857  DT.92023390 

    Selected AceView cDNA sequences (see all 70):

    AI813807 AW440452 BM126757 BM677021 CB306785 CK003200 N74538 BP379004 
    AA366475 AA453272 AW440433 BI711389 AI693067 BQ575866 BM975824 BC064356 
    BX505367 AI373505 CK818802 AK055494 BI553017 BM127062 CF541232 BQ027277 

    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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    ZNF558 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGACAGCTCA
    ZNF558 Expression
    About this image

    ZNF558 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZNF558 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.659797
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF558

    (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 ZNF558 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zfp5581 , 5 zinc finger protein 5581, 5 82.26(n)1
    80.35(a)1
      9 (7.05 cM)5
    722301  NM_028935.11  NP_083211.11 
     184555755 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    25(a)
    1 → many
    GL344882.1(1643-15461)
    zebrafish
    (Danio rerio)
    Actinopterygii ZNF5576
    zinc finger protein 557
    20(a)
    1 → many
    15(997733-1002447) ENSDARG00000097394


    ENSEMBL Gene Tree for ZNF558 (if available)
    TreeFam Gene Tree for ZNF558 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZNF558 gene
    ZNF1242  ZNF1772  ZNF5572  ZNF3332  ZNF3172  ZNF8912  ZNF559-ZNF1772  
    Selected SIMAP similar genes for ZNF558 using alignment to 2 protein entries:     ZN558_HUMAN (see all proteins) (see all similar genes):
    kr-znf3    ZNF78L1    ZNF557    ZNF56    ZNF658    ZNF658B
    DKFZp686B16128    ZNF160    ZNF782    ZNF345    ZNF510    ZFP2
    ZNF    ZNF55    ZNF665    DKFZp686M04222    KIAA1829    ZFP3

    Find genes that share paralogs with ZNF558           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for ZNF558
    PGOHUM00000234389


    (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 ZNF558 (see all 420)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1819205491,2
    --8919892(+) AAAAGA/CAGCTC 1 -- ds50010--------
    rs1424682221,2
    C--8920039(+) AAAACC/TCGCCT 1 -- ds50010--------
    rs1479473501,2
    --8920125(+) TTAAAC/TGAATA 1 -- ds50010--------
    rs1176323761,2
    C,F--8920138(+) CTGAAG/AAGAAC 1 -- ds50011Minor allele frequency- A:0.03EA 120
    rs1148767181,2
    C,F--8920144(+) AGAACG/AGACAC 1 -- ds50011Minor allele frequency- A:0.06WA 118
    rs1418411851,2
    --8920145(+) GAACGA/GACACT 1 -- ds50010--------
    rs1156826131,2
    C,F--8920154(+) CTGGGA/CAAGAA 1 -- ds50011Minor allele frequency- C:0.03WA 118
    rs29677451,2
    C,F,O,A,H--8920167(-) AAATAA/CTGTTG 1 -- ds500136Minor allele frequency- C:0.35EA NA NS WA CSA 3412
    rs1848943711,2
    --8920189(+) ATAGAA/GAGAAA 1 -- ds50010--------
    rs2014395511,2
    --8920237(+) ATACC-/ACTACATT 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for ZNF558 (8920380 - 8943004 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for ZNF558:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2402CNV Loss18451855
    nsv171CNV Loss15895083
    dgv48n68CNV Gain17160897
    nsv911019CNV Gain21882294
    nsv833738CNV Gain17160897
    nsv833739CNV Gain+Loss17160897
    nsv428362CNV Gain+Loss18775914
    nsv469648CNV Complex16826518
    dgv1056e1CNV Complex17122850
    nsv483078CNV Complex15286789

    Site Specific Mutation Identification with PCR Assays
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    (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 ZNF558 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ZNF558)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    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. Interactome mapping suggests new mechanistic details underlying Alzheimer's disease. (PubMed id 21163940)1 Soler-LA^pez M....Aloy P. (Genome Res. 2011)
    4. A protein interaction framework for human mRNA degradation. (PubMed id 15231747)1 Lehner B. and Sanderson C.M. (Genome Res. 2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 148156 HGNC: 26422 AceView: ZNF558 Ensembl:ENSG00000167785 euGenes: HUgn148156
    ECgene: ZNF558 H-InvDB: ZNF558

    (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 ZNF558 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 ZNF558 gene:
    Search GeneIP for patents involving ZNF558

    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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