Tut4 terminal uridylyl transferase 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tut4provided by MGI
Official Full Name: terminal uridylyl transferase 4provided by MGI
Primary source: MGI:MGI:2445126
See related: Ensembl:ENSMUSG00000034610 AllianceGenome:MGI:2445126
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PPAPD3; Tent3a; Zcchc11; mKIAA0191; 6030404K05Rik; 9230115F04Rik
Summary: Enables RNA uridylyltransferase activity and miRNA binding activity. Involved in several processes, including RNA metabolic process; interleukin-6-mediated signaling pathway; and positive regulation of interleukin-6 production. Acts upstream of or within negative regulation of NF-kappaB transcription factor activity and regulation of lipopolysaccharide-mediated signaling pathway. Located in cytoplasm and nucleus. Is expressed in 1-cell stage embryo; 2-cell stage embryo; primary oocyte; and secondary oocyte. Human ortholog(s) of this gene implicated in liver benign neoplasm. Orthologous to human TUT4 (terminal uridylyl transferase 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 17.3), limb E14.5 (RPKM 15.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 C7; 4 50.55 cM

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (108316607..108416612)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (108459410..108559415)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication.
Title: TUT4/7-mediated uridylation of a coronavirus subgenomic RNAs delays viral replication.
We conclude that the Zcchc11-mediated terminal uridylation of mature miRNAs is pervasive and physiologically significant, especially important in the neonatal period for fostering IGF-1 expression and enhancing postnatal growth and survival
Title: Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival.
Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells
Title: Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells.
Zcchc11 fine tunes IL-6 production by uridylating miR-26a.
Title: Zcchc11-dependent uridylation of microRNA directs cytokine expression.
We propose that ZCCHC11 is a unique TLR signal regulator, which interacts with TIFA after LPS treatment and suppresses the TRAF6-dependent activation of NF-kappaB.
Title: A novel Zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (5) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

13.MMHAP54FLE1.seq (e-PCR)
- UniSTS:123172

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA uridylyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA uridylyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA uridylyltransferase activity	ISO Inferred from Sequence Orthology more info
enables RNA uridylyltransferase activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables uridylyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables uridylyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA 3' uridylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA 3' uridylation	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA 3' uridylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA 3'-end processing	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA 3'-end processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in interleukin-6-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in miRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in miRNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in miRNA metabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of NF-kappaB transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in oocyte maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in polyuridylation-dependent mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pre-miRNA processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of lipopolysaccharide-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in retrotransposon silencing by mRNA destabilization	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: terminal uridylyltransferase 4

Names: TUTase 4; zinc finger CCHC domain-containing protein 11; zinc finger, CCHC domain containing 11

NP_001366592.1

EC 2.7.7.52

NP_001366593.1

EC 2.7.7.52

NP_001366594.1

EC 2.7.7.52

NP_780681.2

EC 2.7.7.52

XP_006503043.1

EC 2.7.7.52

XP_006503046.1

EC 2.7.7.52

XP_017175628.1

EC 2.7.7.52

XP_030109297.1

EC 2.7.7.52

XP_036019916.1

EC 2.7.7.52

XP_036019917.1

EC 2.7.7.52

XP_036019918.1

EC 2.7.7.52

XP_036019919.1

EC 2.7.7.52

XP_036019920.1

EC 2.7.7.52

XP_036019921.1

EC 2.7.7.52

XP_036019922.1

EC 2.7.7.52

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001379663.1 → NP_001366592.1 terminal uridylyltransferase 4 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL626783, AL627238

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

COG5082
Location:1293 → 1382

AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
NM_001379664.1 → NP_001366593.1 terminal uridylyltransferase 4 isoform 2

Status: VALIDATED

Source sequence(s)

AL626783, AL627238

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1297 → 1379

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
NM_001379665.1 → NP_001366594.1 terminal uridylyltransferase 4 isoform 4

Status: VALIDATED

Source sequence(s)

AL626783, AL627238

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1297 → 1375

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
NM_175472.4 → NP_780681.2 terminal uridylyltransferase 4 isoform 3

See identical proteins and their annotated locations for NP_780681.2

Status: VALIDATED

Source sequence(s)

AL626783, AL627238

Consensus CDS

CCDS18451.1

UniProtKB/Swiss-Prot

A2A8R8, B2RX14, Q3UYT6, Q5DU43

Related

ENSMUSP00000044836.6, ENSMUST00000043368.12

Conserved Domains (5) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1297 → 1375

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

108316607..108416612

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164023.1 → XP_036019916.1 terminal uridylyltransferase 4 isoform X1

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

COG5082
Location:1304 → 1393

AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_036164025.1 → XP_036019918.1 terminal uridylyltransferase 4 isoform X3

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

COG5082
Location:1304 → 1393

AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_036164024.1 → XP_036019917.1 terminal uridylyltransferase 4 isoform X2

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1308 → 1390

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_036164026.1 → XP_036019919.1 terminal uridylyltransferase 4 isoform X4

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1308 → 1390

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_036164027.1 → XP_036019920.1 terminal uridylyltransferase 4 isoform X5

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1308 → 1386

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_036164028.1 → XP_036019921.1 terminal uridylyltransferase 4 isoform X6

Conserved Domains (6) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1308 → 1386

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1289

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 621

TUTase; TUTase nucleotidyltransferase domain
XM_017320139.3 → XP_017175628.1 terminal uridylyltransferase 4 isoform X7

UniProtKB/TrEMBL

A2A8R7

Related

ENSMUSP00000095538.3, ENSMUST00000097925.9

Conserved Domains (5) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

COG5082
Location:1293 → 1382

AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase
XM_006502980.4 → XP_006503043.1 terminal uridylyltransferase 4 isoform X8

Conserved Domains (5) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1297 → 1379

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase
XM_030253437.2 → XP_030109297.1 terminal uridylyltransferase 4 isoform X9

UniProtKB/Swiss-Prot

A2A8R8, B2RX14, Q3UYT6, Q5DU43

Conserved Domains (5) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

PTZ00368
Location:1297 → 1375

PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

COG5260
Location:946 → 1278

TRF4; DNA polymerase sigma [Replication, recombination and repair]

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase
XM_036164029.1 → XP_036019922.1 terminal uridylyltransferase 4 isoform X10

UniProtKB/TrEMBL

A0A0A0MQJ6

Conserved Domains (4) summary

cd05402
Location:988 → 1106

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:285 → 620

TUTase; TUTase nucleotidyltransferase domain
XM_006502983.5 → XP_006503046.1 terminal uridylyltransferase 4 isoform X11

UniProtKB/TrEMBL

A0A0A0MQJ6

Related

ENSMUSP00000120172.2, ENSMUST00000155068.2

Conserved Domains (3) summary

cd05402
Location:395 → 507

NT_PAP_TUTase; Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases

TIGR00600
Location:2 → 366

rad2; DNA excision repair protein (rad2)

pfam03828
Location:648 → 697

PAP_assoc; Cid1 family poly A polymerase