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ZNF397 Gene

protein-coding   GIFtS: 50
GCID: GC18P032820

Zinc Finger Protein 397

(Previous name: zinc finger protein 47)
(Previous symbol: ZNF47)
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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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

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   
ORGUL members:         

Export aliases for ZNF397 gene to outside databases

Previous GC identifers: GC18P032855 GC18P032640 GC18P031072 GC18P031073 GC18P031074 GC18P029679


(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 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. GO annotations related to this gene include 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000018.9  NT_010966.15  NC_018929.2  
Regulatory elements:
   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 Chromatin IP Primers for ZNF397

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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
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: 

  • Ubiquitination2 at Lys225, Lys395
  • Modification sites at PhosphoSitePlus

  • See ZNF397 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    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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    (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

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

    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


    Find genes that share domains with ZNF397           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: ZN397_HUMAN, Q8NF99
    Function: Isoform 3 acts as a DNA-dependent transcriptional repressor

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with ZNF397           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ZNF397

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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
    ZN397_HUMAN, Q8NF99: Isoform 1: Nucleus
    ZN397_HUMAN, Q8NF99: Isoform 3: Nucleus. Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    cytoskeleton1
    plasma membrane1

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

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

    Find genes that share ontologies with ZNF397           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 ZNF397
    Interactions:

        Search GeneGlobe Interaction Network 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): 2 biological process terms:    About this table

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

    Find genes that share ontologies with ZNF397           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
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    Browse Tocris compounds for 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,
    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 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
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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 

    Selected AceView cDNA sequences (see all 118):

    CR623021 AA082541 BG992967 BF061611 NM_032347 AW675257 CR624709 BC006172 
    AI247860 AA805259 AI824163 AI217495 CR624700 BM718848 BX385438 BI334756 
    BM975019 BQ718552 CF594063 BQ185707 AA923414 CB988334 AI096382 AW119198 

    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™, 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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    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


    ZNF397 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Eye (Sensory Organs)
             Retina
    ZNF397 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZNF397 Protein Expression

    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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    (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 human and mouse.

    Orthologs for ZNF397 gene from Selected 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)
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    Paralogs for ZNF397 gene
    ZNF4462  ZSCAN92  ZKSCAN12  ZNF5002  ZNF2132  ZNF2322  ZSCAN302  ZNF1742  
    ZNF32  ZKSCAN42  ZNF3962  ZSCAN122  ZNF3942  ZSCAN212  ZSCAN232  ZNF1652  
    ZSCAN162  ZKSCAN82  ZSCAN222  ZSCAN312  ZNF242  ZKSCAN32  ZNF182  
    Selected 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

    Find genes that share paralogs with ZNF397           About GenesLikeMe


    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), 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 ZNF397 (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZNF397
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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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    OMIM gene information: 609601    OMIM disorders: --


    Find genes that share disorders with ZNF397           About GenesLikeMe


    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)
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    PubMed articles for ZNF397 gene, integrated from 10 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. (Gene 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. (Genome Res. 2004)
    3. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. 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)
    6. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (Cell 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. (Chromosoma 2008)
    8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 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. (Genome Res. 2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84307 HGNC: 18818 AceView: ZNF397 Ensembl:ENSG00000186812 euGenes: HUgn84307
    ECgene: ZNF397 H-InvDB: ZNF397

    (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 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

    GeneCards and IP:
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