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Aliases for ZIM3 Gene

Aliases for ZIM3 Gene

  • Zinc Finger Imprinted 3 2 3 5
  • Zinc Finger Protein 657 3 4
  • ZNF657 3 4

External Ids for ZIM3 Gene

Previous GeneCards Identifiers for ZIM3 Gene

  • GC19M058544
  • GC19M058099
  • GC19M062321
  • GC19M062337
  • GC19M057645
  • GC19M053958

Summaries for ZIM3 Gene

GeneCards Summary for ZIM3 Gene

ZIM3 (Zinc Finger Imprinted 3) is a Protein Coding gene. Among its related pathways are Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA binding transcription factor activity. An important paralog of this gene is ZNF793.

UniProtKB/Swiss-Prot for ZIM3 Gene

  • May be involved in transcriptional regulation.

Additional gene information for ZIM3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZIM3 Gene

Genomics for ZIM3 Gene

GeneHancer (GH) Regulatory Elements for ZIM3 Gene

Promoters and enhancers for ZIM3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I057190 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 11.2 -46.6 -46585 2 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 YY1 CBX5 ZNF207 ZNF143 KLF7 ZNF264 ZNF548 ZNF417 ZNF134 ZNF274 AURKC ZNF773 ZNF550 ZIM3 ZNF805
GH19I057103 Enhancer 0.9 Ensembl ENCODE 10.7 +41.1 41140 0.5 CTCF SAP130 ARID4B MAX MCM2 RAD21 CC2D1A ZNF335 GATAD1 PATZ1 ZIM3 AURKC ZNF805 LOC100419839 GC19M057058 GC19M057103
GH19I057099 Enhancer 0.8 ENCODE 11.1 +45.9 45874 0.2 ELF3 ARID4B ZNF48 ZSCAN9 RAD21 GTF3C2 ZNF143 THAP11 MIXL1 SMARCA5 ZIM3 ZIM2 PEG3 AURKC ZNF805 LOC100419839 GC19M057058
GH19I057095 Enhancer 0.6 ENCODE 11.1 +48.3 48254 2.5 SOX13 GATAD2A TFAP4 FOXA2 SAP130 TEAD1 FOXA3 KAT8 TEAD3 TGIF2 USP29 ZIM3 ZIM2 PEG3 AURKC ZNF805 ZNF418 ZNF814 ZNF417 LOC100128398
GH19I056698 Enhancer 0.4 dbSUPER 10 +445.4 445443 1.7 MXI1 RFX1 ZIM3 USP29 ZNF460-AS1 SMIM17 GC19P056696 OR5AH1P ENSG00000284729 LOC105372473 LOC105372472
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZIM3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ZIM3 Gene

Genomic Locations for ZIM3 Gene
11,107 bases
Minus strand

Genomic View for ZIM3 Gene

Genes around ZIM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZIM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZIM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZIM3 Gene

Proteins for ZIM3 Gene

  • Protein details for ZIM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger imprinted 3
    Protein Accession:
    Secondary Accessions:
    • Q14CA6

    Protein attributes for ZIM3 Gene

    472 amino acids
    Molecular mass:
    54498 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZIM3 Gene

Post-translational modifications for ZIM3 Gene

No Post-translational modifications

Other Protein References for ZIM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZIM3 Gene

Domains & Families for ZIM3 Gene

Gene Families for ZIM3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZIM3 Gene

Suggested Antigen Peptide Sequences for ZIM3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZIM3: view

Function for ZIM3 Gene

Molecular function for ZIM3 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transcriptional regulation.

Gene Ontology (GO) - Molecular Function for ZIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZIM3: view
genes like me logo Genes that share phenotypes with ZIM3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ZIM3 Gene

Localization for ZIM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZIM3 Gene

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 ZIM3 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for ZIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with ZIM3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ZIM3 Gene

Pathways & Interactions for ZIM3 Gene

SuperPathway Contained pathways
1 Gene Expression
genes like me logo Genes that share pathways with ZIM3: view

Pathways by source for ZIM3 Gene

2 Reactome pathways for ZIM3 Gene

Interacting Proteins for ZIM3 Gene

Gene Ontology (GO) - Biological Process for ZIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA --
genes like me logo Genes that share ontologies with ZIM3: view

No data available for SIGNOR curated interactions for ZIM3 Gene

Drugs & Compounds for ZIM3 Gene

No Compound Related Data Available

Transcripts for ZIM3 Gene

mRNA/cDNA for ZIM3 Gene

(1) REFSEQ mRNAs :
(3) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZIM3 Gene

No ASD Table

Relevant External Links for ZIM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZIM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZIM3 Gene

mRNA differential expression in normal tissues according to GTEx for ZIM3 Gene

This gene is overexpressed in Testis (x46.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZIM3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZIM3 Gene:


SOURCE GeneReport for Unigene cluster for ZIM3 Gene:

genes like me logo Genes that share expression patterns with ZIM3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZIM3 Gene

Orthologs for ZIM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZIM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZIM3 33 34
  • 98.87 (n)
(Mus musculus)
Mammalia Zfp819 34
  • 29 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 30 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG10543 35
  • 33 (a)
Species where no ortholog for ZIM3 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)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 ZIM3 Gene

Gene Tree for ZIM3 (if available)
Gene Tree for ZIM3 (if available)

Paralogs for ZIM3 Gene

Paralogs for ZIM3 Gene

(493) SIMAP similar genes for ZIM3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ZIM3: view

Variants for ZIM3 Gene

Sequence variations from dbSNP and Humsavar for ZIM3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000267113 -- 57,136,022(-) T/A/C coding_sequence_variant, synonymous_variant
rs1000576906 -- 57,133,598(-) A/G downstream_transcript_variant
rs1000754016 -- 57,138,442(-) G/A intron_variant
rs1000926292 -- 57,143,451(-) C/G intron_variant
rs1001581241 -- 57,140,743(-) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZIM3 Gene

Variant ID Type Subtype PubMed ID
nsv817876 CNV gain 17921354
nsv528378 CNV loss 19592680
nsv1064109 CNV gain 25217958
esv3893256 CNV loss 25118596
esv3644892 CNV gain 21293372
esv3556684 CNV deletion 23714750
esv2719067 CNV deletion 23290073
esv2280796 CNV deletion 18987734

Variation tolerance for ZIM3 Gene

Residual Variation Intolerance Score: 95.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.24; 92.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZIM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZIM3 Gene

Disorders for ZIM3 Gene

Additional Disease Information for ZIM3

No disorders were found for ZIM3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZIM3 Gene

Publications for ZIM3 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  2. Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain. (PMID: 11543637) Kim J … Stubbs L (Genomics 2001) 3 4 58
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for ZIM3 Gene

Sources for ZIM3 Gene

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