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Aliases for ZCCHC9 Gene

Aliases for ZCCHC9 Gene

  • Zinc Finger CCHC-Type Containing 9 2 3 5
  • Protein Phosphatase 1, Regulatory Subunit 41 2 3
  • Zinc Finger CCHC Domain-Containing Protein 9 3
  • Zinc Finger, CCHC Domain Containing 9 3
  • PPP1R41 3

External Ids for ZCCHC9 Gene

Previous GeneCards Identifiers for ZCCHC9 Gene

  • GC05P080682
  • GC05P080633
  • GC05P075807
  • GC05P080597

Summaries for ZCCHC9 Gene

GeneCards Summary for ZCCHC9 Gene

ZCCHC9 (Zinc Finger CCHC-Type Containing 9) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding.

UniProtKB/Swiss-Prot for ZCCHC9 Gene

  • May down-regulate transcription mediated by NF-kappa-B and the serum response element.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZCCHC9 Gene

Genomics for ZCCHC9 Gene

Regulatory Elements for ZCCHC9 Gene

Enhancers for ZCCHC9 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
GH05F081352 0.2 ENCODE 16.6 +52.4 52412 2.2 ELF3 ATF1 MLX ARID4B THRB ZSCAN9 RAD21 RARA YY1 SLC30A9 ZCCHC9 CKMT2-AS1 ACOT12 CKMT2 GC05M081320
GH05F081848 0.4 Ensembl 16.5 +547.0 547018 0.8 ZNF341 IKZF1 HMBOX1 ZNF140 ZCCHC9 CKMT2-AS1 ENSG00000249483 SSBP2
GH05F080487 0.8 ENCODE 16.5 -812.6 -812629 3.7 ARID4B SIN3A GLI4 DMAP1 ZNF48 ZNF2 YY1 SLC30A9 GLIS2 KLF7 ZCCHC9 CKMT2-AS1 ZFYVE16 DHFR LOC105379049 RPS27AP9
GH05F082274 0.4 ENCODE 15.6 +973.3 973277 1.4 PKNOX1 SIN3A CHD7 ZNF48 CHAMP1 CCNT2 POLR2A ZNF202 PAF1 SMAD5 ATP6AP1L ZCCHC9 CKMT2-AS1 GC05P082278 ENSG00000251374
GH05F081267 0.8 Ensembl ENCODE 11.3 -32.4 -32365 2.5 MXI1 PKNOX1 MLX KLF17 MAX PATZ1 SCRT2 PRDM10 FOS TCF7L2 CKMT2-AS1 ZCCHC9 CKMT2 ENSG00000248794
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ZCCHC9 on UCSC Golden Path with GeneCards custom track

Promoters for ZCCHC9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001411155 17 2801 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3

Genomic Location for ZCCHC9 Gene

81,301,583 bp from pter
81,313,344 bp from pter
11,762 bases
Plus strand

Genomic View for ZCCHC9 Gene

Genes around ZCCHC9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZCCHC9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZCCHC9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZCCHC9 Gene

Proteins for ZCCHC9 Gene

  • Protein details for ZCCHC9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger CCHC domain-containing protein 9
    Protein Accession:
    Secondary Accessions:
    • B2RAE7
    • Q9H027

    Protein attributes for ZCCHC9 Gene

    271 amino acids
    Molecular mass:
    30477 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZCCHC9 Gene

Post-translational modifications for ZCCHC9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ZCCHC9 Gene

No data available for DME Specific Peptides for ZCCHC9 Gene

Domains & Families for ZCCHC9 Gene

Protein Domains for ZCCHC9 Gene


Suggested Antigen Peptide Sequences for ZCCHC9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 4 CCHC-type zinc fingers.
  • Contains 4 CCHC-type zinc fingers.
genes like me logo Genes that share domains with ZCCHC9: view

Function for ZCCHC9 Gene

Molecular function for ZCCHC9 Gene

UniProtKB/Swiss-Prot Function:
May down-regulate transcription mediated by NF-kappa-B and the serum response element.

Gene Ontology (GO) - Molecular Function for ZCCHC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
GO:0044822 poly(A) RNA binding IDA 22658674
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZCCHC9: view
genes like me logo Genes that share phenotypes with ZCCHC9: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZCCHC9 Gene

Localization for ZCCHC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZCCHC9 Gene

Nucleus, nucleolus. Nucleus. Note=Expressed throughout the nucleus and concentrated mainly in the nucleolus. {ECO:0000269 PubMed:18721783}.

Subcellular locations from

Jensen Localization Image for ZCCHC9 Gene COMPARTMENTS Subcellular localization image for ZCCHC9 gene
Compartment Confidence
nucleus 5
cytosol 1
extracellular 1
golgi apparatus 1
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for ZCCHC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with ZCCHC9: view

Pathways & Interactions for ZCCHC9 Gene

SuperPathways for ZCCHC9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZCCHC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0010923 negative regulation of phosphatase activity IDA 19389623
genes like me logo Genes that share ontologies with ZCCHC9: view

No data available for Pathways by source and SIGNOR curated interactions for ZCCHC9 Gene

Transcripts for ZCCHC9 Gene

Unigene Clusters for ZCCHC9 Gene

Zinc finger, CCHC domain containing 9:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZCCHC9 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b
SP1: - - - -
SP3: - - - - -
SP5: - - - - -
SP6: -
SP7: - -

Relevant External Links for ZCCHC9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZCCHC9 Gene

mRNA expression in normal human tissues for ZCCHC9 Gene

Protein differential expression in normal tissues from HIPED for ZCCHC9 Gene

This gene is overexpressed in Lung (67.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZCCHC9 Gene

Protein tissue co-expression partners for ZCCHC9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZCCHC9 Gene:


SOURCE GeneReport for Unigene cluster for ZCCHC9 Gene:

genes like me logo Genes that share expression patterns with ZCCHC9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for ZCCHC9 Gene

Orthologs for ZCCHC9 Gene

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

Orthologs for ZCCHC9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZCCHC9 34 35
  • 99.75 (n)
(Bos Taurus)
Mammalia ZCCHC9 34 35
  • 91.02 (n)
-- 35
  • 79 (a)
(Canis familiaris)
Mammalia ZCCHC9 34 35
  • 90.77 (n)
(Mus musculus)
Mammalia Zcchc9 34 16 35
  • 82.9 (n)
(Rattus norvegicus)
Mammalia Zcchc9 34
  • 82.9 (n)
(Monodelphis domestica)
Mammalia -- 35
  • 81 (a)
-- 35
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia ZCCHC9 35
  • 76 (a)
(Gallus gallus)
Aves ZCCHC9 34 35
  • 67.8 (n)
(Anolis carolinensis)
Reptilia ZCCHC9 35
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zcchc9 34
  • 63.21 (n)
Str.11804 34
(Danio rerio)
Actinopterygii zcchc9 34 35
  • 57.67 (n)
zgc56467 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13811 34
(Caenorhabditis elegans)
Secernentea F07E5.5 35
  • 22 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC683.02c 34
  • 52.07 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4394 34
Species where no ortholog for ZCCHC9 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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 ZCCHC9 Gene

Gene Tree for ZCCHC9 (if available)
Gene Tree for ZCCHC9 (if available)

Paralogs for ZCCHC9 Gene Pseudogenes for ZCCHC9 Gene

genes like me logo Genes that share paralogs with ZCCHC9: view

No data available for Paralogs for ZCCHC9 Gene

Variants for ZCCHC9 Gene

Sequence variations from dbSNP and Humsavar for ZCCHC9 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs10036022 -- 81,301,451(+) TTGAA(C/T)TCTTC nc-transcript-variant, upstream-variant-2KB
rs10041138 -- 81,309,981(+) AAAGA(A/G)TTTTT intron-variant, utr-variant-3-prime
rs10052929 -- 81,302,186(+) GATAA(C/T)TTAGG intron-variant, upstream-variant-2KB
rs10514218 -- 81,308,914(+) GTATT(A/G)TCAAC intron-variant, downstream-variant-500B
rs1055383 -- 81,308,611(+) CCCGC(C/T)GCCCT downstream-variant-500B, reference, synonymous-codon, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for ZCCHC9 Gene

Variant ID Type Subtype PubMed ID
esv3890664 CNV gain 25118596
nsv598750 CNV gain 21841781

Variation tolerance for ZCCHC9 Gene

Residual Variation Intolerance Score: 86% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.52; 64.65% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZCCHC9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZCCHC9 Gene

Disorders for ZCCHC9 Gene

Relevant External Links for ZCCHC9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZCCHC9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZCCHC9 Gene

Publications for ZCCHC9 Gene

  1. A nuclear localized protein ZCCHC9 is expressed in cerebral cortex and suppresses the MAPK signal pathway. (PMID: 18721783) Zhou A. … Zhang J. (J Genet Genomics 2008) 2 3 4 22 64
  2. 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
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64
  5. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H. … Mohammed S. (J. Proteome Res. 2013) 4 64

Products for ZCCHC9 Gene

Sources for ZCCHC9 Gene

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