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Aliases for ZCCHC11 Gene

Aliases for ZCCHC11 Gene

  • Zinc Finger CCHC-Type Containing 11 2 3 5
  • Zinc Finger CCHC Domain-Containing Protein 11 3 4
  • TUTase 4 3 4
  • TUT4 3 4
  • Zinc Finger, CCHC Domain Containing 11 3
  • PAP Associated Domain Containing 3 3
  • Terminal Uridylyltransferase 4 3
  • EC 2.7.7.52 4
  • KIAA0191 4
  • TUTase4 2
  • PAPD3 3

External Ids for ZCCHC11 Gene

Previous GeneCards Identifiers for ZCCHC11 Gene

  • GC01M052259
  • GC01M052601
  • GC01M052661
  • GC01M052888
  • GC01M051004

Summaries for ZCCHC11 Gene

Entrez Gene Summary for ZCCHC11 Gene

  • ZCCHC11 is an RNA uridyltransferase (EC 2.7.7.52) that uses UTP to add uridines to the 3-prime end of substrate RNA molecules (Jones et al., 2009 [PubMed 19701194]).[supplied by OMIM, Jan 2011]

GeneCards Summary for ZCCHC11 Gene

ZCCHC11 (Zinc Finger CCHC-Type Containing 11) is a Protein Coding gene. Diseases associated with ZCCHC11 include Perlman Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotidyltransferase activity. An important paralog of this gene is ZCCHC6.

UniProtKB/Swiss-Prot for ZCCHC11 Gene

  • Uridylyltransferase that mediates the terminal uridylation of mRNAs with short (less than 25 nucleotides) poly(A) tails, hence facilitating global mRNA decay (PubMed:25480299). Involved in microRNA (miRNA)-induced gene silencing through uridylation of deadenylated miRNA targets. Also acts as a suppressor of miRNA biogenesis by mediating the terminal uridylation of some miRNA precursors, including that of let-7 (pre-let-7), miR107, miR-143 and miR-200c. Uridylated miRNAs are not processed by Dicer and undergo degradation. Degradation of pre-let-7 contributes to the maintenance of embryonic stem (ES) cell pluripotency (By similarity). Does not bind RNA directly, but recruited to RNA targets by RNA-binding protein LIN28A. Also catalyzes the 3 uridylation of miR-26A, a miRNA that targets IL6 transcript. This abrogates the silencing of IL6 transcript, hence promoting cytokine expression (By similarity). May also suppress Toll-like receptor-induced NF-kappa-B activation via binding to T2BP. Does not play a role in replication-dependent histone mRNA degradation. Due to functional redundancy between ZCCHC6 and ZCCHC11, the identification of the specific role of each of these proteins is difficult.

Additional gene information for ZCCHC11 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZCCHC11 Gene

Genomics for ZCCHC11 Gene

GeneHancer (GH) Regulatory Elements for ZCCHC11 Gene

Promoters and enhancers for ZCCHC11 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
GH01I052550 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 583.3 +0.6 588 5.6 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 POLR2B CBX5 ZNF207 ZCCHC11 ENSG00000272371 MAGOH ENSG00000266993 CC2D1B RPS13P2 ENSG00000230953 GPX7 C1orf123 PRPF38A
GH01I051874 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 52.1 +676.0 676020 5.3 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC NRDC ENSG00000266993 ZCCHC11 PRPF38A CC2D1B ZFYVE9 LINC01562 TXNDC12 RPS13P2 KTI12
GH01I052631 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.2 -81.9 -81865 8.1 HDGF PKNOX1 YBX1 IRF4 ZNF766 ZNF207 ATF7 RUNX3 RXRA CAVIN1 SHISAL2A ZCCHC11 GPX7 MAGOH PRPF38A ENSG00000230953 ENSG00000272100 CC2D1B ENSG00000266993 ORC1
GH01I052697 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 28.3 -144.7 -144662 2.2 HDGF FOXA2 PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A DMAP1 COA7 GC01P052696 ZCCHC11 MAGOH KTI12 PRPF38A ENSG00000230953 ENSG00000272100 ENSG00000266993 ZFYVE9
GH01I052364 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 24.7 +187.8 187821 3.2 HDGF PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 YY1 CC2D1B PRPF38A ZCCHC11 MAGOH ENSG00000230953 ENSG00000266993 ORC1 LOC100190934 RPS13P2 GPX7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZCCHC11 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZCCHC11 gene promoter:

Genomic Locations for ZCCHC11 Gene

Genomic Locations for ZCCHC11 Gene
chr1:52,408,282-52,553,487
(GRCh38/hg38)
Size:
145,206 bases
Orientation:
Minus strand
chr1:52,873,954-53,019,159
(GRCh37/hg19)

Genomic View for ZCCHC11 Gene

Genes around ZCCHC11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZCCHC11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZCCHC11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZCCHC11 Gene

Proteins for ZCCHC11 Gene

  • Protein details for ZCCHC11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5TAX3-TUT4_HUMAN
    Recommended name:
    Terminal uridylyltransferase 4
    Protein Accession:
    Q5TAX3
    Secondary Accessions:
    • A2RRP0
    • B7Z8J5
    • D3DQ35
    • Q12764
    • Q5TAX2
    • Q5TAX4
    • Q86XZ3

    Protein attributes for ZCCHC11 Gene

    Size:
    1644 amino acids
    Molecular mass:
    185166 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Interacts with LIN28A in the presence of pre-let-7 RNA. Interacts with T2BP.
    SequenceCaution:
    • Sequence=CAI23477.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for ZCCHC11 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZCCHC11 Gene

Post-translational modifications for ZCCHC11 Gene

  • Ubiquitination at isoforms=2680, posLast=10001000, isoforms=1036, and posLast=12601260

No data available for DME Specific Peptides for ZCCHC11 Gene

Domains & Families for ZCCHC11 Gene

Gene Families for ZCCHC11 Gene

Suggested Antigen Peptide Sequences for ZCCHC11 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5TAX3

UniProtKB/Swiss-Prot:

TUT4_HUMAN :
  • Belongs to the DNA polymerase type-B-like family.
Family:
  • Belongs to the DNA polymerase type-B-like family.
genes like me logo Genes that share domains with ZCCHC11: view

Function for ZCCHC11 Gene

Molecular function for ZCCHC11 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
UTP + RNA(n) = diphosphate + RNA(n+1).
UniProtKB/Swiss-Prot Function:
Uridylyltransferase that mediates the terminal uridylation of mRNAs with short (less than 25 nucleotides) poly(A) tails, hence facilitating global mRNA decay (PubMed:25480299). Involved in microRNA (miRNA)-induced gene silencing through uridylation of deadenylated miRNA targets. Also acts as a suppressor of miRNA biogenesis by mediating the terminal uridylation of some miRNA precursors, including that of let-7 (pre-let-7), miR107, miR-143 and miR-200c. Uridylated miRNAs are not processed by Dicer and undergo degradation. Degradation of pre-let-7 contributes to the maintenance of embryonic stem (ES) cell pluripotency (By similarity). Does not bind RNA directly, but recruited to RNA targets by RNA-binding protein LIN28A. Also catalyzes the 3 uridylation of miR-26A, a miRNA that targets IL6 transcript. This abrogates the silencing of IL6 transcript, hence promoting cytokine expression (By similarity). May also suppress Toll-like receptor-induced NF-kappa-B activation via binding to T2BP. Does not play a role in replication-dependent histone mRNA degradation. Due to functional redundancy between ZCCHC6 and ZCCHC11, the identification of the specific role of each of these proteins is difficult.

Enzyme Numbers (IUBMB) for ZCCHC11 Gene

Phenotypes From GWAS Catalog for ZCCHC11 Gene

Gene Ontology (GO) - Molecular Function for ZCCHC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IDA 22658674
GO:0005515 protein binding IPI 19703396
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with ZCCHC11: view
genes like me logo Genes that share phenotypes with ZCCHC11: view

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZCCHC11 Gene

Localization for ZCCHC11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZCCHC11 Gene

Nucleus. Cytoplasm. Note=Mainly cytoplasmic (PubMed:19703396, PubMed:25480299). Translocates into the cytoplasm following treatment of the cell with LPS (PubMed:16643855).

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 ZCCHC11 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZCCHC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA,HDA 22664934
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 19703396
GO:0005829 cytosol IDA,TAS --
genes like me logo Genes that share ontologies with ZCCHC11: view

Pathways & Interactions for ZCCHC11 Gene

SuperPathways for ZCCHC11 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZCCHC11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening TAS --
GO:0001816 cytokine production IEA --
GO:0010586 miRNA metabolic process ISS --
GO:0010587 miRNA catabolic process IMP 19703396
GO:0019827 stem cell population maintenance IMP 19703396
genes like me logo Genes that share ontologies with ZCCHC11: view

No data available for Pathways by source and SIGNOR curated interactions for ZCCHC11 Gene

Drugs & Compounds for ZCCHC11 Gene

(1) Drugs for ZCCHC11 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine triphosphate Experimental, Investigational Pharma 0

(1) Additional Compounds for ZCCHC11 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with ZCCHC11: view

Transcripts for ZCCHC11 Gene

Unigene Clusters for ZCCHC11 Gene

Zinc finger, CCHC domain containing 11:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZCCHC11 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^
SP1: - -
SP2:
SP3:
SP4:
SP5: -
SP6:
SP7: - - - -
SP8:
SP9:
SP10: -
SP11:
SP12:
SP13: - -
SP14:

ExUns: 21a · 21b ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b · 29c · 29d ^ 30 ^ 31 ^ 32a · 32b ^ 33 ^ 34 ^ 35a · 35b · 35c · 35d
SP1: -
SP2: -
SP3: - -
SP4: - -
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for ZCCHC11 Gene

GeneLoc Exon Structure for
ZCCHC11
ECgene alternative splicing isoforms for
ZCCHC11

Expression for ZCCHC11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZCCHC11 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ZCCHC11 Gene

This gene is overexpressed in Plasma (22.1), Monocytes (17.8), and Neutrophil (13.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZCCHC11 Gene



Protein tissue co-expression partners for ZCCHC11 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZCCHC11 Gene:

ZCCHC11

SOURCE GeneReport for Unigene cluster for ZCCHC11 Gene:

Hs.655407

Evidence on tissue expression from TISSUES for ZCCHC11 Gene

  • Bone marrow(4.2)
  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with ZCCHC11: view

Primer Products

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 ZCCHC11 Gene

Orthologs for ZCCHC11 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZCCHC11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZCCHC11 33 34
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia ZCCHC11 33 34
  • 92.76 (n)
cow
(Bos Taurus)
Mammalia LOC528986 33
  • 92.69 (n)
ZCCHC11 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Zcchc11 33 16 34
  • 89.11 (n)
rat
(Rattus norvegicus)
Mammalia Zcchc11 33
  • 88.51 (n)
oppossum
(Monodelphis domestica)
Mammalia ZCCHC11 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia ZCCHC11 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZCCHC11 33 34
  • 73.79 (n)
lizard
(Anolis carolinensis)
Reptilia ZCCHC11 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zcchc11 33
  • 65.48 (n)
Str.15797 33
zebrafish
(Danio rerio)
Actinopterygii LOC795358 33
  • 64.94 (n)
zcchc11 34
  • 47 (a)
OneToOne
Dr.17857 33
fruit fly
(Drosophila melanogaster)
Insecta mkg-p 34
  • 15 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea pup-2 34
  • 26 (a)
ManyToMany
cid-1 34
  • 20 (a)
ManyToMany
Y34F4.3 34
  • 20 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5065 34
  • 41 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4240 33
Species where no ortholog for ZCCHC11 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)
  • 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 ZCCHC11 Gene

ENSEMBL:
Gene Tree for ZCCHC11 (if available)
TreeFam:
Gene Tree for ZCCHC11 (if available)

Paralogs for ZCCHC11 Gene

Paralogs for ZCCHC11 Gene

genes like me logo Genes that share paralogs with ZCCHC11: view

Variants for ZCCHC11 Gene

Sequence variations from dbSNP and Humsavar for ZCCHC11 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000027586 -- 52,517,129(-) C/T intron_variant
rs1000029564 -- 52,553,171(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000034878 -- 52,510,864(-) C/G intron_variant
rs1000037070 -- 52,426,172(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000048446 -- 52,425,357(-) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for ZCCHC11 Gene

Variant ID Type Subtype PubMed ID
esv3586051 CNV loss 21293372
esv988243 CNV insertion 20482838
nsv1137759 CNV deletion 24896259

Variation tolerance for ZCCHC11 Gene

Residual Variation Intolerance Score: 2.47% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZCCHC11 Gene

Human Gene Mutation Database (HGMD)
ZCCHC11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZCCHC11

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZCCHC11 Gene

Disorders for ZCCHC11 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ZCCHC11 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
perlman syndrome
  • nephroblastoma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ZCCHC11

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ZCCHC11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ZCCHC11 Gene

Publications for ZCCHC11 Gene

  1. Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 8724849) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 2 3 4 58
  2. Uridylation by TUT4 and TUT7 marks mRNA for degradation. (PMID: 25480299) Lim J … Kim VN (Cell 2014) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. (PMID: 19703396) Heo I … Kim VN (Cell 2009) 3 4 58

Products for ZCCHC11 Gene

Sources for ZCCHC11 Gene

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