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Aliases for TUT4 Gene

Aliases for TUT4 Gene

  • Terminal Uridylyl Transferase 4 2 3
  • Zinc Finger CCHC-Type Containing 11 2 3 5
  • Zinc Finger CCHC Domain-Containing Protein 11 3 4
  • TUTase 4 3 4
  • ZCCHC11 3 5
  • 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
  • TENT3A 3
  • PAPD3 3

External Ids for TUT4 Gene

Previous HGNC Symbols for TUT4 Gene

  • ZCCHC11

Summaries for TUT4 Gene

Entrez Gene Summary for TUT4 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 TUT4 Gene

TUT4 (Terminal Uridylyl Transferase 4) is a Protein Coding gene. An important paralog of this gene is TUT7.

UniProtKB/Swiss-Prot for TUT4 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 TUT4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TUT4 Gene

Genomics for TUT4 Gene

GeneHancer (GH) Regulatory Elements for TUT4 Gene

Promoters and enhancers for TUT4 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
GH01J052631 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 670.6 -81.9 -81865 8.1 HDGF PKNOX1 YBX1 IRF4 ZNF766 ZNF207 ATF7 RUNX3 RXRA CAVIN1 TUT4 SHISAL2A GPX7 MAGOH ENSG00000230953 CC2D1B ENSG00000266993 ORC1 ECHDC2 RPS13P2
GH01J052550 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 696.2 +0.6 588 5.6 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 POLR2B CBX5 ZNF207 TUT4 ENSG00000272371 ENSG00000228838 PRPF38A MAGOH ENSG00000266993 CC2D1B RPS13P2 ENSG00000230953 GPX7
GH01J051874 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 41.6 +676.0 676020 5.3 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC NRDC ENSG00000266993 TUT4 PRPF38A KTI12 SLC25A6P3 GAPDHP51 TXNDC12-AS1 CC2D1B TXNDC12
GH01J052032 Promoter/Enhancer 1.6 Ensembl ENCODE 56 +520.1 520091 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 KTI12 ENSG00000223390 TUT4 PRPF38A ENSG00000266993 CC2D1B TXNDC12 BTF3L4 ENSG00000272100 ORC1
GH01J052364 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 37.7 +187.8 187821 3.2 HDGF PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 YY1 CC2D1B PRPF38A TUT4 MAGOH ENSG00000230953 ENSG00000266993 ORC1 LOC100190934 RPS13P2 GPX7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TUT4 on UCSC Golden Path with GeneCards custom track

Genomic Locations for TUT4 Gene

Genomic Locations for TUT4 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)
Size:
145,206 bases
Orientation:
Minus strand

Genomic View for TUT4 Gene

Genes around TUT4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TUT4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TUT4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TUT4 Gene

Proteins for TUT4 Gene

  • Protein details for TUT4 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 TUT4 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 TUT4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TUT4 Gene

Post-translational modifications for TUT4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TUT4 Gene

Domains & Families for TUT4 Gene

Suggested Antigen Peptide Sequences for TUT4 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 TUT4: view

Function for TUT4 Gene

Molecular function for TUT4 Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
UTP + RNA(n) = diphosphate + RNA(n+1).

Enzyme Numbers (IUBMB) for TUT4 Gene

Phenotypes From GWAS Catalog for TUT4 Gene

Gene Ontology (GO) - Molecular Function for TUT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 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 TUT4: view
genes like me logo Genes that share phenotypes with TUT4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TUT4

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TUT4 Gene

Localization for TUT4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TUT4 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 TUT4 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 TUT4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 22664934
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA,IDA 19703396
GO:0005829 cytosol TAS,IDA --
genes like me logo Genes that share ontologies with TUT4: view

Pathways & Interactions for TUT4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TUT4 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 TUT4: view

No data available for Pathways by source and SIGNOR curated interactions for TUT4 Gene

Drugs & Compounds for TUT4 Gene

(1) Drugs for TUT4 Gene - From: HMDB

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

(1) Additional Compounds for TUT4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
14000-31-8
genes like me logo Genes that share compounds with TUT4: view

Transcripts for TUT4 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TUT4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TUT4 Gene

No ASD Table

Relevant External Links for TUT4 Gene

GeneLoc Exon Structure for
TUT4
ECgene alternative splicing isoforms for
TUT4

Expression for TUT4 Gene

NURSA nuclear receptor signaling pathways regulating expression of TUT4 Gene:

TUT4

Evidence on tissue expression from TISSUES for TUT4 Gene

  • Bone marrow(4.2)
  • Nervous system(2.9)
No Expression Related Data Available

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TUT4 Gene

Orthologs for TUT4 Gene

This gene was present in the common ancestor of animals.

Orthologs for TUT4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZCCHC11 34 33
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ZCCHC11 34 33
  • 92.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LOC528986 33
  • 92.69 (n)
ZCCHC11 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Zcchc11 34 33
  • 89.11 (n)
OneToOne
Tut4 16
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 34 33
  • 73.79 (n)
OneToOne
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
Cin.4240 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4240 33
Species where no ortholog for TUT4 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 TUT4 Gene

ENSEMBL:
Gene Tree for TUT4 (if available)
TreeFam:
Gene Tree for TUT4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TUT4: view image

Paralogs for TUT4 Gene

Paralogs for TUT4 Gene

genes like me logo Genes that share paralogs with TUT4: view

Variants for TUT4 Gene

Sequence variations from dbSNP and Humsavar for TUT4 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 TUT4 Gene

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

Variation tolerance for TUT4 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 TUT4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TUT4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TUT4 Gene

Disorders for TUT4 Gene

Additional Disease Information for TUT4

No disorders were found for TUT4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TUT4 Gene

Publications for TUT4 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. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. (PMID: 19703396) Heo I … Kim VN (Cell 2009) 3 4 58
  4. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. (PMID: 18172165) Mullen TE … Marzluff WF (Genes & development 2008) 3 4 58
  5. A novel Zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling. (PMID: 16643855) Minoda Y … Yoshimura A (Biochemical and biophysical research communications 2006) 3 4 58

Products for TUT4 Gene

Sources for TUT4 Gene

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