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Aliases for ZCCHC3 Gene

Aliases for ZCCHC3 Gene

  • Zinc Finger CCHC-Type Containing 3 2 3 5
  • C20orf99 3 4
  • Zinc Finger CCHC Domain-Containing Protein 3 3
  • Zinc Finger, CCHC Domain Containing 3 3
  • Chromosome 20 Open Reading Frame 99 2

External Ids for ZCCHC3 Gene

Previous HGNC Symbols for ZCCHC3 Gene

  • C20orf99

Previous GeneCards Identifiers for ZCCHC3 Gene

  • GC20P000227

Summaries for ZCCHC3 Gene

GeneCards Summary for ZCCHC3 Gene

ZCCHC3 (Zinc Finger CCHC-Type Containing 3) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding.

Additional gene information for ZCCHC3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZCCHC3 Gene

Genomics for ZCCHC3 Gene

Regulatory Elements for ZCCHC3 Gene

Enhancers for ZCCHC3 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
GH20H000266 1.5 FANTOM5 ENCODE 13 -30.0 -30044 1 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 C20orf96 ZCCHC3 NRSN2-AS1 DEFB129 DEFB128 NRSN2 ENSG00000272874 GC20P000265
GH20H000323 1.4 ENCODE dbSUPER 12.9 +29.5 29540 6 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 TBC1D20 DEFB129 ACTG1P3 ENSG00000272874 DEFB126 DEFB125 ZCCHC3 C20orf96 NRSN2 NRSN2-AS1
GH20H000330 1.4 Ensembl ENCODE dbSUPER 12.3 +33.9 33881 1 ELF3 ARID4B KLF17 THRB RAD21 RFX5 ZNF143 ZNF207 MIXL1 THAP11 ZCCHC3 C20orf96 RBCK1 TRIB3 DEFB132 DEFB129 GC20P000328 GC20M000330
GH20H000296 1.4 ENCODE dbSUPER 7.3 +2.9 2930 6 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 C20orf96 ZCCHC3 PSMF1 SOX12
GH20H000237 0.9 Ensembl ENCODE 10.1 -59.2 -59198 1 HDAC1 SMARCE1 MTA2 MAX JUNB BATF ZFHX2 EGR1 MTA1 RUNX3 DEFB128 NRSN2-AS1 C20orf96 ZCCHC3 NRSN2 DEFB129 DEFB132
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZCCHC3 on UCSC Golden Path with GeneCards custom track

Promoters for ZCCHC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for ZCCHC3 Gene

296,968 bp from pter
300,321 bp from pter
3,354 bases
Plus strand

Genomic View for ZCCHC3 Gene

Genes around ZCCHC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZCCHC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZCCHC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZCCHC3 Gene

Proteins for ZCCHC3 Gene

  • Protein details for ZCCHC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger CCHC domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q3B7J3
    • Q6NT79

    Protein attributes for ZCCHC3 Gene

    404 amino acids
    Molecular mass:
    43618 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ZCCHC3 Gene


neXtProt entry for ZCCHC3 Gene

Post-translational modifications for ZCCHC3 Gene

  • Ubiquitination at Lys45
  • Modification sites at PhosphoSitePlus

Other Protein References for ZCCHC3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ZCCHC3 Gene

Domains & Families for ZCCHC3 Gene

Gene Families for ZCCHC3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ZCCHC3 Gene


Suggested Antigen Peptide Sequences for ZCCHC3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZCCHC3: view

No data available for UniProtKB/Swiss-Prot for ZCCHC3 Gene

Function for ZCCHC3 Gene

Gene Ontology (GO) - Molecular Function for ZCCHC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZCCHC3: view
genes like me logo Genes that share phenotypes with ZCCHC3: view

Animal Model Products

CRISPR Products

miRNA for ZCCHC3 Gene

miRTarBase miRNAs that target ZCCHC3

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for ZCCHC3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZCCHC3 Gene

Localization for ZCCHC3 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 ZCCHC3 gene
Compartment Confidence
nucleus 3
plasma membrane 2
cytoskeleton 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for ZCCHC3 Gene

Pathways & Interactions for ZCCHC3 Gene

SuperPathways for ZCCHC3 Gene

No Data Available

Interacting Proteins for ZCCHC3 Gene

Selected Interacting proteins: Q9NUD5-ZCHC3_HUMAN for ZCCHC3 Gene via IID

Gene Ontology (GO) - Biological Process for ZCCHC3 Gene


No data available for Pathways by source and SIGNOR curated interactions for ZCCHC3 Gene

Drugs & Compounds for ZCCHC3 Gene

No Compound Related Data Available

Transcripts for ZCCHC3 Gene

mRNA/cDNA for ZCCHC3 Gene

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

Unigene Clusters for ZCCHC3 Gene

Zinc finger, CCHC domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for ZCCHC3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for ZCCHC3 Gene

No ASD Table

Relevant External Links for ZCCHC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZCCHC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZCCHC3 Gene

Protein differential expression in normal tissues from HIPED for ZCCHC3 Gene

This gene is overexpressed in Fetal testis (21.7), Heart (10.9), and Lung (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ZCCHC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZCCHC3 Gene:


SOURCE GeneReport for Unigene cluster for ZCCHC3 Gene:


Evidence on tissue expression from TISSUES for ZCCHC3 Gene

  • Liver(4.2)
genes like me logo Genes that share expression patterns with ZCCHC3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZCCHC3 Gene

Orthologs for ZCCHC3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ZCCHC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZCCHC3 33
  • 99.25 (n)
(Canis familiaris)
Mammalia ZCCHC3 33
  • 91.56 (n)
(Bos Taurus)
Mammalia ZCCHC3 33
  • 90.58 (n)
(Mus musculus)
Mammalia Zcchc3 33 16
  • 84.67 (n)
(Rattus norvegicus)
Mammalia Zcchc3 33
  • 84 (n)
Species where no ortholog for ZCCHC3 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)
  • oppossum (Monodelphis domestica)
  • 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 ZCCHC3 Gene

Gene Tree for ZCCHC3 (if available)
Gene Tree for ZCCHC3 (if available)

Paralogs for ZCCHC3 Gene Pseudogenes for ZCCHC3 Gene

genes like me logo Genes that share paralogs with ZCCHC3: view

No data available for Paralogs for ZCCHC3 Gene

Variants for ZCCHC3 Gene

Sequence variations from dbSNP and Humsavar for ZCCHC3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000529446 -- 299,101(+) TCTCT(C/T)CTTGC utr-variant-3-prime
rs1000967399 -- 297,158(+) GAAAA(G/T)GTACA upstream-variant-2KB
rs1001103162 -- 296,897(+) AAAAA(A/G)TAAAA upstream-variant-2KB
rs1001536440 -- 297,697(+) GAGAA(C/G)ATGGG reference, missense
rs1003377487 -- 300,646(+) TGAAC(C/T)CTGCC downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for ZCCHC3 Gene

Variant ID Type Subtype PubMed ID
dgv4219n100 CNV gain 25217958
dgv65n68 CNV loss 17160897
esv3893263 CNV loss 25118596
nsv469544 CNV loss 16826518

Variation tolerance for ZCCHC3 Gene

Residual Variation Intolerance Score: 18.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.78; 16.53% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZCCHC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZCCHC3 Gene

Disorders for ZCCHC3 Gene

Relevant External Links for ZCCHC3

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZCCHC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZCCHC3 Gene

Publications for ZCCHC3 Gene

  1. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4 60
  2. 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 60
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. Cold-inducible RBM3 inhibits PERK phosphorylation through cooperation with NF90 to protect cells from endoplasmic reticulum stress. (PMID: 26472337) Zhu X … Wellmann S (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2016) 3 60

Products for ZCCHC3 Gene

Sources for ZCCHC3 Gene

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