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Aliases for ZNF397 Gene

Aliases for ZNF397 Gene

  • Zinc Finger Protein 397 2 3 5
  • Zinc Finger Protein 47 2 3 4
  • Zinc Finger And SCAN Domain-Containing Protein 15 3 4
  • ZSCAN15 3 4
  • ZNF47 3 4

External Ids for ZNF397 Gene

Previous HGNC Symbols for ZNF397 Gene

  • ZNF47

Previous GeneCards Identifiers for ZNF397 Gene

  • GC18P032855
  • GC18P032640
  • GC18P031072
  • GC18P031073
  • GC18P031074
  • GC18P032820
  • GC18P029679

Summaries for ZNF397 Gene

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 transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is ZKSCAN8.

UniProtKB/Swiss-Prot for ZNF397 Gene

  • Isoform 3 acts as a DNA-dependent transcriptional repressor.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNF397 Gene

Genomics for ZNF397 Gene

Regulatory Elements for ZNF397 Gene

Enhancers for ZNF397 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH18F035495 1.2 ENCODE 32.5 +256.3 256328 3.1 CREB3L1 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 TBX21 ENSG00000268573 ZNF397 ZNF396 ENSG00000267583 C18orf21 ELP2 INO80C ENSG00000267140 ENSG00000279074
GH18F035289 1.1 ENCODE 26.7 +49.6 49577 2.3 HDGF PKNOX1 ARNT CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF397 ELP2 ZNF24 ZSCAN30 ZNF271P GC18M035301 PIR53427
GH18F035343 1.5 FANTOM5 ENCODE 14.9 +104.2 104172 3.4 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF396 ZNF397 MAPRE2 ZNF24 ZNF271P GC18M035337
GH18F035613 1.2 Ensembl ENCODE 13.8 +376.5 376535 8.3 PKNOX1 TBL1XR1 INSM2 FEZF1 RAD21 ZBTB40 ZNF366 CBX5 RCOR1 ETV6 ENSG00000268573 GALNT1 ZNF397 SLC39A6 ENSG00000266965 LOC105372065
GH18F035037 1.4 FANTOM5 ENCODE 10.6 -199.7 -199722 6.6 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 MAPRE2 ENSG00000268573 ENSG00000267583 ZSCAN30 ZNF397 ENSG00000267397 ZNF24 ENSG00000280096
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZNF397 on UCSC Golden Path with GeneCards custom track

Promoters for ZNF397 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for ZNF397 Gene

35,240,718 bp from pter
35,267,133 bp from pter
26,416 bases
Plus strand

Genomic View for ZNF397 Gene

Genes around ZNF397 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF397 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF397 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF397 Gene

Proteins for ZNF397 Gene

  • Protein details for ZNF397 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 397
    Protein Accession:
    Secondary Accessions:
    • Q9BRM2

    Protein attributes for ZNF397 Gene

    534 amino acids
    Molecular mass:
    61139 Da
    Quaternary structure:
    • Isoforms 1 and 3 can both homo- and hetero-associate. Homo-association of isoform 1 is dependent on the presence of the SCAN domain.

    Alternative splice isoforms for ZNF397 Gene


neXtProt entry for ZNF397 Gene

Post-translational modifications for ZNF397 Gene

  • Ubiquitination at Lys 225
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ZNF397 Gene

Domains & Families for ZNF397 Gene

Gene Families for ZNF397 Gene

Suggested Antigen Peptide Sequences for ZNF397 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 SCAN box domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 9 C2H2-type zinc fingers.
  • Contains 1 SCAN box domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 9 C2H2-type zinc fingers.
genes like me logo Genes that share domains with ZNF397: view

Function for ZNF397 Gene

Molecular function for ZNF397 Gene

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

Gene Ontology (GO) - Molecular Function for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA,IBA --
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNF397: view
genes like me logo Genes that share phenotypes with ZNF397: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNF397 Gene

Localization for ZNF397 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF397 Gene

Isoform 1: Nucleus.
Isoform 3: Nucleus. Cytoplasm.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZNF397 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IBA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ZNF397: view

Pathways & Interactions for ZNF397 Gene

SuperPathways for ZNF397 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZNF397 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with ZNF397: view

No data available for Pathways by source and SIGNOR curated interactions for ZNF397 Gene

Transcripts for ZNF397 Gene

Unigene Clusters for ZNF397 Gene

Zinc finger protein 397:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF397 Gene

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

Relevant External Links for ZNF397 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF397 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZNF397 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZNF397 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (52.2) and Blymphocyte (16.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZNF397 Gene

Protein tissue co-expression partners for ZNF397 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZNF397 Gene:


SOURCE GeneReport for Unigene cluster for ZNF397 Gene:


mRNA Expression by UniProt/SwissProt for ZNF397 Gene:

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.
genes like me logo Genes that share expression patterns with ZNF397: view

Primer Products

No data available for mRNA differential expression in normal tissues for ZNF397 Gene

Orthologs for ZNF397 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ZNF397 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF397 34 35
  • 99.75 (n)
(Canis familiaris)
Mammalia ZNF397 34 35
  • 90.83 (n)
(Mus musculus)
Mammalia Zfp397 34 16 35
  • 87.07 (n)
(Bos Taurus)
Mammalia ZNF397 34
  • 86.87 (n)
(Rattus norvegicus)
Mammalia Zfp397 34
  • 86.19 (n)
(Monodelphis domestica)
Mammalia -- 35
  • 38 (a)
-- 35
  • 37 (a)
Species where no ortholog for ZNF397 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for ZNF397 Gene

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

Paralogs for ZNF397 Gene

(490) SIMAP similar genes for ZNF397 Gene using alignment to 5 proteins: Pseudogenes for ZNF397 Gene

genes like me logo Genes that share paralogs with ZNF397: view

Variants for ZNF397 Gene

Sequence variations from dbSNP and Humsavar for ZNF397 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs1054890 -- 35,243,941(+) TCATG(C/T)TAATT intron-variant
rs1060178 -- 35,248,583(+) cacct(A/G)taatg intron-variant, utr-variant-3-prime
rs1060758 -- 35,246,672(+) GGGCT(G/T)GTGTG intron-variant, utr-variant-3-prime
rs1060760 -- 35,246,697(+) CTTCG(A/T)CTCAG intron-variant, utr-variant-3-prime
rs1062236 -- 35,245,573(+) ATGTA(A/T)GTGGG intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for ZNF397 Gene

Variant ID Type Subtype PubMed ID
esv3642197 CNV gain 21293372
esv3390534 CNV insertion 20981092
esv3305949 CNV mobile element insertion 20981092

Variation tolerance for ZNF397 Gene

Gene Damage Index Score: 0.56; 12.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZNF397 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF397 Gene

Disorders for ZNF397 Gene

Relevant External Links for ZNF397

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZNF397 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZNF397 Gene

Publications for ZNF397 Gene

  1. Identification and characterization of two novel human SCAN domain- containing zinc finger genes ZNF396 and ZNF397. (PMID: 12801647) Wu Y. … Zhao S. (Gene 2003) 3 4 22 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  4. System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability. (PMID: 25755297) Xiao Z. … Vertegaal A.C. (Mol. Cell. Proteomics 2015) 4 64
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64

Products for ZNF397 Gene

Sources for ZNF397 Gene

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