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Aliases for ZC3H3 Gene

Aliases for ZC3H3 Gene

  • Zinc Finger CCCH-Type Containing 3 2 3 5
  • Zinc Finger CCCH-Type Domain Containing 3 2 3
  • Smad-Interacting CPSF-Like Factor 3 4
  • ZC3HDC3 3 4
  • Zinc Finger CCCH Domain-Containing Protein 3 3
  • KIAA0150 4
  • SMICL 4

External Ids for ZC3H3 Gene

Previous HGNC Symbols for ZC3H3 Gene

  • ZC3HDC3

Previous GeneCards Identifiers for ZC3H3 Gene

  • GC08M144591
  • GC08M144519
  • GC08M139772

Summaries for ZC3H3 Gene

GeneCards Summary for ZC3H3 Gene

ZC3H3 (Zinc Finger CCCH-Type Containing 3) is a Protein Coding gene. An important paralog of this gene is CPSF4.

UniProtKB/Swiss-Prot for ZC3H3 Gene

  • Required for the export of polyadenylated mRNAs from the nucleus (PubMed:19364924). Enhances ACVR1B-induced SMAD-dependent transcription. Binds to single-stranded DNA but not to double-stranded DNA in vitro. Involved in RNA cleavage (By similarity).

Additional gene information for ZC3H3 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 ZC3H3 Gene

Genomics for ZC3H3 Gene

GeneHancer (GH) Regulatory Elements for ZC3H3 Gene

Promoters and enhancers for ZC3H3 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
GH08I143540 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 573.8 +0.8 836 2.2 PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 POLR2B ZNF766 ZC3H3 ENSG00000254144 GC08P143575 RN7SKP175 ENSG00000254859 GSDMD CPSF1 VPS28 ZNF623 SLC52A2
GH08I143552 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 26.5 -11.1 -11128 2.5 HDGF FOXA2 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A YY1 POLR2B GSDMD LOC105375796 ZC3H3 ENSG00000254859 NAPRT
GH08I143544 Enhancer 1.6 FANTOM5 Ensembl ENCODE 30.4 -4.9 -4867 6.2 HDGF PKNOX1 ARNT ARID4B IRF4 YY1 POLR2B ZNF766 CBX5 E2F8 ENSG00000254859 ZC3H3 GSDMD NAPRT TOP1MT GRINA SPATC1 PIR45502
GH08I142725 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.5 +815.0 815016 3.2 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 THEM6 ENSG00000253806 LOC100288181 LY6K JRK ZNF623 ZNF696 ENSG00000255050 ZC3H3 GLI4
GH08I143275 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 12.6 +263.2 263171 6.5 HDGF PKNOX1 CLOCK SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 MINCR ZNF623 GPAA1 PARP10 ENSG00000255050 ZNF707 ZFP41 EEF1D ZC3H3 RHPN1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZC3H3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZC3H3 gene promoter:

Genomic Locations for ZC3H3 Gene

Genomic Locations for ZC3H3 Gene
104,591 bases
Minus strand

Genomic View for ZC3H3 Gene

Genes around ZC3H3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZC3H3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZC3H3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZC3H3 Gene

Proteins for ZC3H3 Gene

  • Protein details for ZC3H3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger CCCH domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q14163
    • Q8N4E2
    • Q9BUS4

    Protein attributes for ZC3H3 Gene

    948 amino acids
    Molecular mass:
    101941 Da
    Quaternary structure:
    • Interacts with SMAD1, SMAD3, SMAD4, CPSF2 and CPSF3 (By similarity).

    Alternative splice isoforms for ZC3H3 Gene


neXtProt entry for ZC3H3 Gene

Post-translational modifications for ZC3H3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZC3H3 Gene

No data available for DME Specific Peptides for ZC3H3 Gene

Domains & Families for ZC3H3 Gene

Gene Families for ZC3H3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ZC3H3 Gene

Suggested Antigen Peptide Sequences for ZC3H3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZC3H3: view

No data available for UniProtKB/Swiss-Prot for ZC3H3 Gene

Function for ZC3H3 Gene

Molecular function for ZC3H3 Gene

UniProtKB/Swiss-Prot Function:
Required for the export of polyadenylated mRNAs from the nucleus (PubMed:19364924). Enhances ACVR1B-induced SMAD-dependent transcription. Binds to single-stranded DNA but not to double-stranded DNA in vitro. Involved in RNA cleavage (By similarity).

Phenotypes From GWAS Catalog for ZC3H3 Gene

Gene Ontology (GO) - Molecular Function for ZC3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IBA --
GO:0004521 endoribonuclease activity IBA --
GO:0046332 SMAD binding IEA --
genes like me logo Genes that share ontologies with ZC3H3: view

Phenotypes for ZC3H3 Gene

GenomeRNAi human phenotypes for ZC3H3:
genes like me logo Genes that share phenotypes with ZC3H3: view

miRNA for ZC3H3 Gene

miRTarBase miRNAs that target ZC3H3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZC3H3 Gene

Localization for ZC3H3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZC3H3 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 ZC3H3 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZC3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 16115198
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex IEA,IBA --
genes like me logo Genes that share ontologies with ZC3H3: view

Pathways & Interactions for ZC3H3 Gene

SuperPathways for ZC3H3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZC3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006378 mRNA polyadenylation IMP 19364924
GO:0006810 transport IEA --
GO:0010793 regulation of mRNA export from nucleus IMP 19364924
GO:0016973 poly(A)+ mRNA export from nucleus IMP 19364924
GO:0031124 mRNA 3-end processing IEA --
genes like me logo Genes that share ontologies with ZC3H3: view

No data available for Pathways by source and SIGNOR curated interactions for ZC3H3 Gene

Drugs & Compounds for ZC3H3 Gene

No Compound Related Data Available

Transcripts for ZC3H3 Gene

mRNA/cDNA for ZC3H3 Gene

Unigene Clusters for ZC3H3 Gene

Zinc finger CCCH-type containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H3 Gene

No ASD Table

Relevant External Links for ZC3H3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZC3H3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZC3H3 Gene

mRNA differential expression in normal tissues according to GTEx for ZC3H3 Gene

This gene is overexpressed in Whole Blood (x5.3).

Protein differential expression in normal tissues from HIPED for ZC3H3 Gene

This gene is overexpressed in Serum (52.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZC3H3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZC3H3 Gene:


SOURCE GeneReport for Unigene cluster for ZC3H3 Gene:


Evidence on tissue expression from TISSUES for ZC3H3 Gene

  • Bone marrow(4.2)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with ZC3H3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZC3H3 Gene

Orthologs for ZC3H3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ZC3H3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZC3H3 33 34
  • 98.66 (n)
(Canis familiaris)
Mammalia ZC3H3 33 34
  • 80.81 (n)
(Bos Taurus)
Mammalia ZC3H3 33 34
  • 79.8 (n)
(Mus musculus)
Mammalia Zc3h3 33 16 34
  • 77.02 (n)
Gm7353 34
  • 70 (a)
(Rattus norvegicus)
Mammalia Zc3h3 33
  • 76.55 (n)
(Monodelphis domestica)
Mammalia ZC3H3 34
  • 58 (a)
(Ornithorhynchus anatinus)
Mammalia ZC3H3 34
  • 51 (a)
(Gallus gallus)
Aves ZC3H3 33 34
  • 58.06 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia zc3h3 33
  • 55.82 (n)
Str.1164 33
(Danio rerio)
Actinopterygii zc3h3 33 34
  • 46.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta ZC3H3 34
  • 20 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YTH1 34
  • 25 (a)
Species where no ortholog for ZC3H3 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ZC3H3 Gene

Gene Tree for ZC3H3 (if available)
Gene Tree for ZC3H3 (if available)

Paralogs for ZC3H3 Gene

Paralogs for ZC3H3 Gene

genes like me logo Genes that share paralogs with ZC3H3: view

Variants for ZC3H3 Gene

Sequence variations from dbSNP and Humsavar for ZC3H3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000017760 -- 143,455,187(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000019482 -- 143,517,660(-) G/A intron_variant
rs1000021899 -- 143,545,507(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000026970 -- 143,530,204(-) C/T intron_variant
rs1000065577 -- 143,475,063(-) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZC3H3 Gene

Variant ID Type Subtype PubMed ID
dgv12409n54 CNV loss 21841781
dgv12410n54 CNV loss 21841781
dgv259n6 CNV deletion 16902084
dgv7336n100 CNV gain 25217958
dgv905n27 CNV loss 19166990
esv1005132 CNV deletion 20482838
esv1091073 CNV deletion 17803354
esv2611442 CNV deletion 19546169
esv2673374 CNV deletion 23128226
esv2738014 CNV deletion 23290073
esv2738015 CNV deletion 23290073
esv2738016 CNV deletion 23290073
esv29963 CNV loss 17803354
esv3385009 CNV duplication 20981092
esv3619111 CNV loss 21293372
esv998186 CNV deletion 20482838
nsv1110000 CNV deletion 24896259
nsv1143220 CNV tandem duplication 24896259
nsv1143375 CNV deletion 24896259
nsv1161809 CNV deletion 26073780
nsv465993 CNV loss 19166990
nsv470247 CNV loss 18288195
nsv475871 CNV novel sequence insertion 20440878
nsv516210 CNV loss 19592680
nsv612768 CNV loss 21841781
nsv612769 CNV loss 21841781
nsv612770 CNV loss 21841781
nsv612771 CNV loss 21841781
nsv612774 CNV loss 21841781
nsv612777 CNV gain 21841781
nsv612778 CNV gain 21841781
nsv824766 CNV gain 20364138
nsv831487 CNV gain 17160897
nsv950012 CNV deletion 24416366
nsv950013 CNV deletion 24416366

Variation tolerance for ZC3H3 Gene

Residual Variation Intolerance Score: 95.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 20.06; 99.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZC3H3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZC3H3 Gene

Disorders for ZC3H3 Gene

Additional Disease Information for ZC3H3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ZC3H3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZC3H3 Gene

Publications for ZC3H3 Gene

  1. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 8590280) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4 58
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 44 58
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 44 58
  4. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. (PMID: 19364924) Hurt JA … Silver PA (The Journal of cell biology 2009) 3 4 58
  5. 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

Products for ZC3H3 Gene

Sources for ZC3H3 Gene

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