Free for academic non-profit institutions. Other users need a Commercial license

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).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZC3H3 Gene

Genomics for ZC3H3 Gene

Regulatory Elements for ZC3H3 Gene

Enhancers for ZC3H3 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
GH08F143544 1 FANTOM5 ENCODE 30.4 -4.9 -4864 6.2 HDGF PKNOX1 ARNT CREB3L1 ARID4B YY1 FOS KLF13 SP5 JUNB ENSG00000254859 ZC3H3 GSDMD NAPRT C8orf82 MAF1 HSF1 TOP1MT GRINA SPATC1
GH08F143552 0.6 ENCODE 26.4 -11.1 -11129 2.5 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A YY1 ZNF143 FOS KLF13 ZC3H3 GSDMD ENSG00000254859 NAPRT LOC105375796
GH08F143540 0.2 ENCODE 23.8 +0.8 836 2.2 PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF207 ENSG00000254859 GSDMD ZC3H3 FAM83H-AS1 GC08P143564 GC08P143506
GH08F143914 1.3 FANTOM5 Ensembl ENCODE 15.5 -394.9 -394886 45.2 MLX CREB3L1 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 SP3 ZNF251 ZNF250 ZNF517 LRRC14 PLEC LOC105375803 ZNF696 ZNF623 VPS28 COMMD5
GH08F144184 1.3 Ensembl ENCODE 12.1 -643.1 -643067 1.4 HDGF PKNOX1 BHLHE40 RELA ARID3A IKZF1 CTBP2 NBN SPI1 ZC3H3 BOP1 HSF1 ENSG00000254690 DGAT1 MIR6848 WDR97 ZNF251 ENSG00000255224 PIR45617
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ZC3H3 on UCSC Golden Path with GeneCards custom track

Promoters for ZC3H3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001446380 745 1801 PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF207

Genomic Location for ZC3H3 Gene

Chromosome:
8
Start:
143,437,655 bp from pter
End:
143,542,245 bp from pter
Size:
104,591 bases
Orientation:
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:
    Q8IXZ2-ZC3H3_HUMAN
    Recommended name:
    Zinc finger CCCH domain-containing protein 3
    Protein Accession:
    Q8IXZ2
    Secondary Accessions:
    • Q14163
    • Q8N4E2
    • Q9BUS4

    Protein attributes for ZC3H3 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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

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

Q8IXZ2

UniProtKB/Swiss-Prot:

ZC3H3_HUMAN :
  • Contains 5 C3H1-type zinc fingers.
Similarity:
  • Contains 5 C3H1-type zinc fingers.
genes like me logo Genes that share domains with ZC3H3: view

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).

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

Animal Model Products

miRNA for ZC3H3 Gene

miRTarBase miRNAs that target ZC3H3

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

COMPARTMENTS
Jensen Localization Image for ZC3H3 Gene COMPARTMENTS Subcellular localization image for ZC3H3 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

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

Transcripts for ZC3H3 Gene

mRNA/cDNA for ZC3H3 Gene

Unigene Clusters for ZC3H3 Gene

Zinc finger CCCH-type containing 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for ZC3H3 Gene

GeneLoc Exon Structure for
ZC3H3
ECgene alternative splicing isoforms for
ZC3H3

Expression for ZC3H3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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:

ZC3H3

SOURCE GeneReport for Unigene cluster for ZC3H3 Gene:

Hs.521915
genes like me logo Genes that share expression patterns with ZC3H3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt 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
chimpanzee
(Pan troglodytes)
Mammalia ZC3H3 34 35
  • 98.66 (n)
dog
(Canis familiaris)
Mammalia ZC3H3 34 35
  • 80.81 (n)
cow
(Bos Taurus)
Mammalia ZC3H3 34 35
  • 79.8 (n)
mouse
(Mus musculus)
Mammalia Zc3h3 34 16 35
  • 77.02 (n)
Gm7353 35
  • 70 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Zc3h3 34
  • 76.55 (n)
oppossum
(Monodelphis domestica)
Mammalia ZC3H3 35
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZC3H3 35
  • 51 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZC3H3 34 35
  • 58.06 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia zc3h3 34
  • 55.82 (n)
Str.1164 34
zebrafish
(Danio rerio)
Actinopterygii zc3h3 34 35
  • 46.73 (n)
fruit fly
(Drosophila melanogaster)
Insecta ZC3H3 35
  • 20 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YTH1 35
  • 25 (a)
OneToMany
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

ENSEMBL:
Gene Tree for ZC3H3 (if available)
TreeFam:
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 Sequence Context AA Info Type
rs10081449 -- 143,538,845(+) GGCCT(A/C/T)GAGGG nc-transcript-variant, reference, synonymous-codon
rs10081594 -- 143,538,640(+) GCCCA(C/G/T)GGCCA nc-transcript-variant, reference, missense
rs10089146 -- 143,444,099(+) cctcc(C/T)gagta intron-variant
rs10098046 -- 143,535,753(+) GACTG(A/G)GCACA intron-variant
rs10098442 -- 143,497,694(+) TCACA(A/C)CTGCC 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)

Relevant External Links for ZC3H3 Gene

Human Gene Mutation Database (HGMD)
ZC3H3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZC3H3

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

Disorders for ZC3H3 Gene

Relevant External Links for ZC3H3

Genetic Association Database (GAD)
ZC3H3
Human Genome Epidemiology (HuGE) Navigator
ZC3H3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ZC3H3

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 Res. 1995) 2 3 4 64
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 46 64
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2010) 3 46 64
  4. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. (PMID: 19364924) Hurt J.A. … Silver P.A. (J. Cell Biol. 2009) 3 4 64
  5. 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

Products for ZC3H3 Gene

Sources for ZC3H3 Gene

Content
Loading form....