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Aliases for ZC3H4 Gene

Aliases for ZC3H4 Gene

  • Zinc Finger CCCH-Type Containing 4 2 3 5
  • C19orf7 3 4
  • Zinc Finger CCCH Domain-Containing Protein 4 3
  • Chromosome 19 Open Reading Frame 7 2
  • KIAA1064 4

External Ids for ZC3H4 Gene

Previous HGNC Symbols for ZC3H4 Gene

  • C19orf7

Previous GeneCards Identifiers for ZC3H4 Gene

  • GC19M052260
  • GC19M047569
  • GC19M043991

Summaries for ZC3H4 Gene

Entrez Gene Summary for ZC3H4 Gene

  • This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]

GeneCards Summary for ZC3H4 Gene

ZC3H4 (Zinc Finger CCCH-Type Containing 4) is a Protein Coding gene. An important paralog of this gene is ZC3H6.

Additional gene information for ZC3H4 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZC3H4 Gene

Genomics for ZC3H4 Gene

GeneHancer (GH) Regulatory Elements for ZC3H4 Gene

Promoters and enhancers for ZC3H4 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
GH19I047105 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 618.9 +3.5 3455 9.2 CLOCK MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZC3H4 ENSG00000268810 BICRA C5AR2 PRKD2 CCDC9 NOP53-AS1 SNORD23 ENSG00000268746 DHX34
GH19I047225 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 286.1 -115.6 -115629 8.2 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 BBC3 ZC3H4 BICRA ENSG00000268810 NOP53-AS1 CCDC9 NOP53 SNORD23 PPP5D1 ENSG00000269124
GH19I047242 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 202.3 -130.0 -130039 2.5 CLOCK ZFP64 DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF143 ZNF548 MCM3 ZC3H4 BICRA ENSG00000268810 NOP53-AS1 CCDC9 NOP53 SLC1A5 SNORD23 ENSG00000268746 EHD2
GH19I047129 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 104.2 -17.6 -17589 2.9 HDGF PKNOX1 CLOCK MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 SAE1 ZC3H4 BICRA ENSG00000268810 NOP53-AS1 CCDC9 SNORD23 NOP53 MIR3190
GH19I047741 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 76.3 -630.2 -630169 5 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 NOP53 ZC3H4 BICRA SELENOW GRWD1 RASIP1 CA11 SNORD23 ZSWIM9 NOP53-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZC3H4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZC3H4 gene promoter:

Genomic Locations for ZC3H4 Gene

Genomic Locations for ZC3H4 Gene
chr19:47,064,187-47,113,752
(GRCh38/hg38)
Size:
49,566 bases
Orientation:
Minus strand
chr19:47,567,444-47,617,009
(GRCh37/hg19)

Genomic View for ZC3H4 Gene

Genes around ZC3H4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZC3H4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZC3H4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZC3H4 Gene

Proteins for ZC3H4 Gene

  • Protein details for ZC3H4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPT8-ZC3H4_HUMAN
    Recommended name:
    Zinc finger CCCH domain-containing protein 4
    Protein Accession:
    Q9UPT8
    Secondary Accessions:
    • Q9Y420

    Protein attributes for ZC3H4 Gene

    Size:
    1303 amino acids
    Molecular mass:
    140257 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA83016.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ZC3H4 Gene

neXtProt entry for ZC3H4 Gene

Post-translational modifications for ZC3H4 Gene

No Post-translational modifications

No data available for DME Specific Peptides for ZC3H4 Gene

Domains & Families for ZC3H4 Gene

Gene Families for ZC3H4 Gene

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

Protein Domains for ZC3H4 Gene

Suggested Antigen Peptide Sequences for ZC3H4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZC3H4: view

No data available for UniProtKB/Swiss-Prot for ZC3H4 Gene

Function for ZC3H4 Gene

Phenotypes From GWAS Catalog for ZC3H4 Gene

Gene Ontology (GO) - Molecular Function for ZC3H4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZC3H4: view
genes like me logo Genes that share phenotypes with ZC3H4: view

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZC3H4 Gene

Localization for ZC3H4 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 ZC3H4 gene
Compartment Confidence
nucleus 4
cytosol 3
cytoskeleton 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZC3H4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with ZC3H4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ZC3H4 Gene

Pathways & Interactions for ZC3H4 Gene

SuperPathways for ZC3H4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZC3H4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for ZC3H4 Gene

Drugs & Compounds for ZC3H4 Gene

No Compound Related Data Available

Transcripts for ZC3H4 Gene

Unigene Clusters for ZC3H4 Gene

Zinc finger CCCH-type containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZC3H4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c
SP1: - - - - - - - -
SP2:
SP3:
SP4: -
SP5:

Relevant External Links for ZC3H4 Gene

GeneLoc Exon Structure for
ZC3H4
ECgene alternative splicing isoforms for
ZC3H4

Expression for ZC3H4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZC3H4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZC3H4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.1), Lung (8.6), and CD8 Tcells (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZC3H4 Gene



Protein tissue co-expression partners for ZC3H4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZC3H4 Gene:

ZC3H4

SOURCE GeneReport for Unigene cluster for ZC3H4 Gene:

Hs.104661

Evidence on tissue expression from TISSUES for ZC3H4 Gene

  • Lung(5)
  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with ZC3H4: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZC3H4 Gene

Orthologs for ZC3H4 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZC3H4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZC3H4 33 34
  • 99.15 (n)
cow
(Bos Taurus)
Mammalia ZC3H4 33 34
  • 88.52 (n)
dog
(Canis familiaris)
Mammalia ZC3H4 33 34
  • 88.48 (n)
mouse
(Mus musculus)
Mammalia Zc3h4 33 16 34
  • 85.1 (n)
rat
(Rattus norvegicus)
Mammalia Zc3h4 33
  • 83.33 (n)
oppossum
(Monodelphis domestica)
Mammalia ZC3H4 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZC3H4 34
  • 60 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ZC3H4 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100145628 33
  • 63.81 (n)
Str.7732 33
zebrafish
(Danio rerio)
Actinopterygii zc3h4 34
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta su(s) 34
  • 12 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T26A8.4 34
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4406 34
  • 20 (a)
OneToMany
Species where no ortholog for ZC3H4 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)
  • 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)
  • 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 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)

Evolution for ZC3H4 Gene

ENSEMBL:
Gene Tree for ZC3H4 (if available)
TreeFam:
Gene Tree for ZC3H4 (if available)

Paralogs for ZC3H4 Gene

Paralogs for ZC3H4 Gene

(2) SIMAP similar genes for ZC3H4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with ZC3H4: view

Variants for ZC3H4 Gene

Sequence variations from dbSNP and Humsavar for ZC3H4 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000018053 -- 47,115,330(-) T/C upstream_transcript_variant
rs1000034897 -- 47,064,809(-) A/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000102632 -- 47,073,942(-) C/T intron_variant
rs1000106520 -- 47,065,055(-) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000147515 -- 47,111,123(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for ZC3H4 Gene

Variant ID Type Subtype PubMed ID
esv3644544 CNV loss 21293372
nsv1067417 CNV gain 25217958
nsv2512 CNV insertion 18451855
nsv472258 CNV novel sequence insertion 20440878
nsv833851 CNV loss 17160897

Variation tolerance for ZC3H4 Gene

Residual Variation Intolerance Score: 11% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.08; 68.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZC3H4 Gene

Human Gene Mutation Database (HGMD)
ZC3H4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZC3H4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZC3H4 Gene

Disorders for ZC3H4 Gene

Additional Disease Information for ZC3H4

No disorders were found for ZC3H4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZC3H4 Gene

Publications for ZC3H4 Gene

  1. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. (PMID: 20935630) Speliotes EK … Loos RJ (Nature genetics 2010) 3 44 58
  2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D … Nagase T (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 3 4 58

Products for ZC3H4 Gene

Sources for ZC3H4 Gene

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