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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ZNF397 Gene

protein-coding   GIFtS: 48
GCID: GC18P032820

Zinc Finger Protein 397

(Previous name: zinc finger protein 47)
(Previous symbol: ZNF47)
Microbiology & Infectious Diseases Congress
  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)
About This Section

Aliases
Zinc Finger Protein 3971 2
Zinc Finger Protein 471 2 3
ZNF471 2 3
Zinc Finger And SCAN Domain-Containing Protein 152 3
ZSCAN152 3

External Ids:    HGNC: 188181   Entrez Gene: 843072   Ensembl: ENSG000001868127   OMIM: 6096015   UniProtKB: Q8NF993   

Export aliases for ZNF397 gene to outside databases

Previous GC identifers: GC18P032855 GC18P032640 GC18P031072 GC18P031073 GC18P031074 GC18P029679


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for ZNF397 Gene:
This gene encodes a protein with a N-terminal SCAN domain, and the longer isoform contains nine C2H2-type zinc
finger repeats in the C-terminal domain. The protein localizes to centromeres during interphase and early
prophase, and different isoforms can repress or activate transcription in transfection studies. Multiple
transcript variants encoding different isoforms have been found for this gene. Additional variants have been
described, but their biological validity has not been determined. (provided by RefSeq, Oct 2009)

GeneCards Summary for ZNF397 Gene: 
ZNF397 (zinc finger protein 397) is a protein-coding gene. Diseases associated with ZNF397 include prostatitis. GO annotations related to this gene include DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ZNF446.

UniProtKB/Swiss-Prot: ZN397_HUMAN, Q8NF99
Function: Isoform 3 acts as a DNA-dependent transcriptional repressor




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000018.9  NC_018929.2  NT_010966.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZNF397 gene promoter:
         HEN1   STAT5A   Tal-1beta   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZNF397 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZNF397

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZNF397


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

Entrez Gene cytogenetic band: 18q12.2   Ensembl cytogenetic band:  18q12.2   HGNC cytogenetic band: 18p12

ZNF397 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF397 gene location

GeneLoc information about chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18P032820:  view genomic region     (about GC identifiers)

Start:
32,820,994 bp from pter      End:
32,847,097 bp from pter
Size:
26,104 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ZN397_HUMAN, Q8NF99 (See protein sequence)
Recommended Name: Zinc finger protein 397  
Size: 534 amino acids; 61139 Da
Subunit: Isoforms 1 and 3 can both homo- and hetero-associate. Homo-association of isoform 1 is dependent on the
presence of the SCAN domain
Subcellular location: Isoform 1: Nucleus
Subcellular location: Isoform 3: Nucleus. Cytoplasm
Secondary accessions: Q9BRM2
Alternative splicing: 3 isoforms:  Q8NF99-1   Q8NF99-2   Q8NF99-3   (Ref.1 (AAN65175) sequence differs from that shown due to a frameshift in position 194)

Explore the universe of human proteins at neXtProt for ZNF397: NX_Q8NF99

Explore proteomics data for ZNF397 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8NF99

  • ZNF397 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    ZNF397 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001128650.1  NP_115723.1  

    ENSEMBL proteins: 
     ENSP00000472393   ENSP00000466317   ENSP00000331577   ENSP00000261333   ENSP00000347850  
     ENSP00000466760   ENSP00000468413   ENSP00000464808  

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    Cloud-Clone Corp. Proteins for ZNF397 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    ZNF397 for ontologies           About GeneDecksing



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

    5 InterPro protein domains:
     IPR015880 Znf_C2H2-like
     IPR008916 Retrov_capsid_C
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2
     IPR003309 Tscrpt_reg_SCAN

    Graphical View of Domain Structure for InterPro Entry Q8NF99

    ProtoNet protein and cluster: Q8NF99

    2 Blocks protein domains:
    IPB003309 Transcriptional regulator SCAN
    IPB007086 C2H2-type zinc finger signature


    UniProtKB/Swiss-Prot: ZN397_HUMAN, Q8NF99
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 9 C2H2-type zinc fingers
    Similarity: Contains 1 SCAN box domain


    ZNF397 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZN397_HUMAN, Q8NF99
    Function: Isoform 3 acts as a DNA-dependent transcriptional repressor

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0008270zinc ion binding ----
    GO:0046872metal ion binding IEA--
         
    ZNF397 for ontologies           About GeneDecksing


    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidZNF397 3' UTR sequence
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZNF397

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for ZNF397 (Q8NF993 ENSP000003315774) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SCAND1P570863, ENSP000003019954I2D: score=1 STRING: ENSP00000301995
    ZNF396Q96N953, ENSP000003023104I2D: score=1 STRING: ENSP00000302310
    ZNF446Q9NWS93, ENSP000003365654I2D: score=1 STRING: ENSP00000336565
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0016032viral process ----

    ZNF397 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ZNF397 (ZN397)

    Search CenterWatch for drugs/clinical trials and news about ZNF397 / ZN397

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ZNF397 gene (2 alternative transcripts): 
    NM_001135178.2  NM_032347.2  

    Unigene Cluster for ZNF397:

    Zinc finger protein 397
    Hs.591061  [show with all ESTs]
    Unigene Representative Sequence: NM_001135178
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000589630 ENST00000601719 ENST00000591206 ENST00000330501(uc010dmp.3)
    ENST00000589420 ENST00000261333(uc002kyi.3 uc002kyj.3 uc010dmq.3 uc010dmr.3)
    ENST00000355632 ENST00000585800 ENST00000592264 ENST00000588119 ENST00000590470
    ENST00000591505
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    hsa-miR-4324 hsa-miR-544b hsa-miR-3613-3p hsa-miR-3662 hsa-miR-496 hsa-miR-378* hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidZNF397 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AF533250.2 AK027384.1 AK123116.1 AK311533.1 AY157641.2 BC006172.1 

    15 DOTS entries:

    DT.100781947  DT.100778175  DT.121090876  DT.95265247  DT.311540  DT.95265250  DT.101970029  DT.121090851 
    DT.91696052  DT.95265245  DT.95265246  DT.99966060  DT.121090854  DT.95090370  DT.95110056 

    24/118 AceView cDNA sequences (see all 118):

    CR624709 BG992967 AI824163 NM_032347 AI217495 BF061611 AA082541 BC006172 
    AW675257 CR623021 CR624700 BM718848 BX385438 AI247860 AA805259 AA325908 
    BQ188266 BX441885 CB988334 CD109801 BX099644 BX364251 AI244547 AW450538 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for ZNF397    About this scheme

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


    ECgene alternative splicing isoforms for ZNF397

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ZNF397 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    ZNF397 Expression
    About this image


    See ZNF397 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZNF397

    SOURCE GeneReport for Unigene cluster: Hs.591061

    UniProtKB/Swiss-Prot: ZN397_HUMAN, Q8NF99
    Tissue specificity: Expressed strongly in testis, moderately in skeletal muscle, pancreas and prostate, and weakly
    in heart, placenta, liver, kidney, spleen, thymus and small intestine

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    In Situ
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    (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)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for ZNF397 gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zfp3971 , 5 zinc finger protein 3971, 5 87.07(n)1
    84.79(a)1
      18 (12.44 cM)5
    692561  NM_027007.21  NP_081283.21 
     239546885 


    ENSEMBL Gene Tree for ZNF397 (if available)
    TreeFam Gene Tree for ZNF397 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZNF397 gene
    ZNF4462  ZSCAN92  ZKSCAN12  ZNF2322  ZSCAN302  ZNF1742  ZNF32  ZKSCAN42  
    ZNF3962  ZSCAN122  ZNF3942  ZSCAN232  ZSCAN212  ZNF1652  ZSCAN162  ZKSCAN82  
    ZSCAN222  ZSCAN312  ZNF242  ZKSCAN32  ZNF182  
    18/488 SIMAP similar genes for ZNF397 using alignment to 5 protein entries:     ZN397_HUMAN (see all proteins) (see all similar genes):
    LOC100128510    ZFP41    ZNF724P    HZF30    SCAND1    ZIK1
    ZNF211    ZNF283    DKFZp666C237    ZFS-1    ZNF331    ZNF776
    zf30    DKFZp686L0787    HZF36    ZFP1    ZNF493    ZNF550

    ZNF397 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for ZNF397
    PGOHUM00000233500


    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/403 SNPs in ZNF397 are shown (see all 403)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 18 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs572437351,2
    C--29688646(+) AAAAA-/CACTGA 1 -- int10--------
    rs1500142521,2
    --32812432(+) AAGGTA/GTGTTA 2 -- us2k10--------
    rs1491399911,2
    C--32812628(+) CACCAG/TGTAAG 2 -- us2k10--------
    rs561608521,2
    C,F--32812658(+) TGAATG/AGAGAG 2 -- us2k14Minor allele frequency- A:0.27NA EA 244
    rs784565971,2
    C,F--32812724(+) AGCAAT/GTTGAG 2 -- us2k11Minor allele frequency- G:0.11WA 118
    rs1160073471,2
    F--32812758(+) CCCAGT/CTAAGT 2 -- us2k11Minor allele frequency- C:0.01WA 118
    rs1438880511,2
    C--32813381(+) TTCACA/CGACTA 2 -- us2k10--------
    rs1468879291,2
    --32813688(+) GGAAAA/GGAACT 2 -- us2k10--------
    rs2010601141,2
    C--32813714(+) TCTGA-/GGTTTT 2 -- us2k10--------
    rs1134976511,2
    C,F--32813715(+) CTGAGG/TTTTTT 2 -- us2k12Minor allele frequency- T:0.50NA WA 4

    HapMap Linkage Disequilibrium report for ZNF397 (32820994 - 32847097 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for ZNF397:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv270226CNV Insertion20981092

    SABiosciences Cancer Mutation PCR Assays
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    (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.)
    About This Section
    OMIM gene information: 609601    OMIM disorders: --

    2 diseases for ZNF397:    About MalaCards
    prostatitis    


    ZNF397 for disorders           About GeneDecksing


    Export disorders for ZNF397 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)
    About This Section

    PubMed articles for ZNF397 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with ZNF397)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of two novel human SCAN domain- containing zinc finger genes ZNF396 and ZNF397. (PubMed id 12801647)1, 2, 9 Wu Y.... Zhao S. (2003)
    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. (2004)
    3. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    6. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (2010)
    7. ZNF397, a new class of interphase to early prophase-specific, SCAN-zinc-finger, mammalian centromere protein. (PubMed id 18369653)1 Bailey S.L....Kalitsis P. (2008)
    8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84307 HGNC: 18818 AceView: ZNF397 Ensembl:ENSG00000186812 euGenes: HUgn84307
    ECgene: ZNF397 H-InvDB: ZNF397

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ZNF397 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 ZNF397 gene:
    Search GeneIP for patents involving ZNF397

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