Aliases for ZIM3 Gene

Aliases for ZIM3 Gene

  • Zinc Finger Imprinted 3 2 3 4 5
  • ZNF657 2 3 4
  • Zinc Finger Protein 657 3 4
  • Zinc Finger Protein 264 3
  • ZNF264 3
  • ZIM3 5

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. Diseases associated with ZIM3 include Coloboma, Ocular, With Or Without Hearing Impairment, Cleft Lip/Palate, And/Or Mental Retardation and Squamous Cell Papilloma. Among its related pathways are Gene Expression and Herpes simplex virus 1 infection. 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 ZNF568.

UniProtKB/Swiss-Prot Summary for ZIM3 Gene

Additional gene information for ZIM3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZIM3 Gene

Genomics for ZIM3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ZIM3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J057190 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 11.2 -46.7 -46699 3.4 GATAD2A IKZF1 ZNF692 POLR2A BACH1 LARP7 GABPA ZNF143 ZSCAN4 RBFOX2 ZNF264 ZNF548 ZNF417 ZNF134 ZNF274 AURKC ENSG00000268379 ZNF773 ZNF550 ZIM3
GH19J057099 Enhancer 1 Ensembl ENCODE 11.1 +45.9 45857 0.5 GATAD2A CTCF ZBTB33 RCOR2 JUND ZNF143 RXRB REST RAD21 IRF2 RF00017-3091 piR-41306-137 ZIM3 PEG3 ZIM2 AURKC ZNF805 RF00017-3090 USP29
GH19J057095 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 11.1 +48.3 48295 2.5 GATAD2A ZNF7 RBFOX2 RXRB SOX13 CEBPB ZKSCAN8 TGIF2 FOXA2 KAT7 USP29 ZIM3 PEG3 ZIM2 AURKC ZNF805 ZNF418 ZNF814 ZNF417 ENSG00000176593
GH19J057103 Enhancer 0.7 ENCODE 10.7 +41.0 41034 0.2 CTCF PRDM10 ZNF143 PATZ1 REST RAD21 IRF2 TRIM22 GABPA SCRT2 ZIM3 AURKC ZNF805 piR-41306-137 LOC100419839 USP29 ZIM2
GH19J057104 Promoter 0.5 CraniofacialAtlas 10.7 +41.5 41469 0.2 CTCF DMAP1 ZIM3 AURKC ZNF805 piR-41306-137 LOC100419839 USP29 ZIM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZIM3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZIM3

Genomic Locations for ZIM3 Gene

Genomic Locations for ZIM3 Gene
chr19:57,134,096-57,145,202
(GRCh38/hg38)
Size:
11,107 bases
Orientation:
Minus strand
chr19:57,645,464-57,656,570
(GRCh37/hg19)
Size:
11,107 bases
Orientation:
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:
    Q96PE6-ZIM3_HUMAN
    Recommended name:
    Zinc finger imprinted 3
    Protein Accession:
    Q96PE6
    Secondary Accessions:
    • Q14CA6

    Protein attributes for ZIM3 Gene

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

neXtProt entry for ZIM3 Gene

Post-translational modifications for ZIM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

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

Protein Domains for ZIM3 Gene

InterPro:
Blocks:
  • C2H2-type zinc finger signature
  • KRAB box
ProtoNet:

Suggested Antigen Peptide Sequences for ZIM3 Gene

GenScript: Design optimal peptide antigens:
  • Zinc finger, imprinted 3 (Q6NTE1_HUMAN)
  • Zinc finger protein 657 (ZIM3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96PE6

UniProtKB/Swiss-Prot:

ZIM3_HUMAN :
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
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.

Phenotypes From GWAS Catalog for ZIM3 Gene

Gene Ontology (GO) - Molecular Function for ZIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
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

miRNA for ZIM3 Gene

miRTarBase miRNAs that target ZIM3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZIM3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , 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

COMPARTMENTS
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 4
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for ZIM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

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

Pathways by source for ZIM3 Gene

2 Reactome pathways for ZIM3 Gene
1 KEGG pathway 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:0006355 regulation of transcription, DNA-templated IEA --
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 :
4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZIM3

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

No ASD Table

Relevant External Links for ZIM3 Gene

GeneLoc Exon Structure for
ZIM3

Expression for ZIM3 Gene

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZIM3

SOURCE GeneReport for Unigene cluster for ZIM3 Gene:

Hs.348622
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
Chimpanzee
(Pan troglodytes)
Mammalia ZIM3 30 31
  • 98.87 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Zfp819 31
  • 29 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 30 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG10543 32
  • 33 (a)
Species where no ortholog for ZIM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for ZIM3 (if available)
TreeFam:
Gene Tree for ZIM3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZIM3: view image

Paralogs for ZIM3 Gene

Paralogs for ZIM3 Gene

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

  • ZIM3_HUMAN
  • L8E933_HUMAN
  • Q6NTE1_HUMAN
genes like me logo Genes that share paralogs with ZIM3: view

Variants for ZIM3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZIM3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs10407445 - p.Arg7Lys
rs2370134 - p.Glu28Lys
rs35202951 - p.Gly205Arg
rs4801200 - p.Leu69Met
rs4801433 - p.Ile379Val

Additional dbSNP identifiers (rs#s) for ZIM3 Gene

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

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

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
ZIM3

SNP Genotyping and Copy Number Assay Products

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

Disorders for ZIM3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ZIM3 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search ZIM3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with ZIM3: view

No data available for 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
  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
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. (PMID: 29987050) Xiao T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2018) 3
  5. La-related Protein 1 (LARP1) Represses Terminal Oligopyrimidine (TOP) mRNA Translation Downstream of mTOR Complex 1 (mTORC1). (PMID: 25940091) Fonseca BD … Damgaard CK (The Journal of biological chemistry 2015) 3

Products for ZIM3 Gene

Sources for ZIM3 Gene