Tut4 terminal uridylyl transferase 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tut4provided by RGD
Official Full Name: terminal uridylyl transferase 4provided by RGD
Primary source: RGD:1310138
See related: EnsemblRapid:ENSRNOG00000052062 AllianceGenome:RGD:1310138
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Zcchc11
Summary: Predicted to enable RNA uridylyltransferase activity and miRNA binding activity. Predicted to be involved in several processes, including RNA metabolic process; interleukin-6-mediated signaling pathway; and regulation of gene expression. Predicted to act upstream of or within negative regulation of NF-kappaB transcription factor activity and regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleolus. 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, Dec 2024]
Expression: Biased expression in Spleen (RPKM 134.8), Liver (RPKM 123.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q34

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (128354975..128535288)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (123201723..123306582)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (128063880..128168726)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA uridylyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA uridylyltransferase activity	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables uridylyltransferase activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in RNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
NOT involved_in histone mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in interleukin-6-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in miRNA catabolic process	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in oocyte maturation	ISO Inferred from Sequence Orthology more info
involved_in polyuridylation-dependent mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in pre-miRNA processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of lipopolysaccharide-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in transposable element silencing by mRNA destabilization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: terminal uridylyltransferase 4

Names: zinc finger CCHC-type containing 11; zinc finger, CCHC domain containing 11

NP_001101423.1

EC 2.7.7.52

XP_038965900.1

EC 2.7.7.52

XP_038965901.1

EC 2.7.7.52

XP_038965902.1

EC 2.7.7.52

XP_038965903.1

EC 2.7.7.52

XP_038965904.1

EC 2.7.7.52

XP_063143786.1

EC 2.7.7.52

XP_063143788.1

EC 2.7.7.52

XP_063143789.1

EC 2.7.7.52

XP_063143790.1

EC 2.7.7.52

XP_063143791.1

EC 2.7.7.52

XP_063143792.1

EC 2.7.7.52

XP_063143793.1

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_001107953.1 → NP_001101423.1 terminal uridylyltransferase 4 isoform 1

See identical proteins and their annotated locations for NP_001101423.1

Status: PROVISIONAL

Source sequence(s)

CH474008

UniProtKB/TrEMBL

A0A0G2JZ04, A6JYV0

Related

ENSRNOP00000070861.2, ENSRNOT00000079161.3

Conserved Domains (4) summary

cd05402
Location:832 → 940

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

pfam03828
Location:1015 → 1068

PAP_assoc; Cid1 family poly A polymerase

pfam07271
Location:1218 → 1406

Cytadhesin_P30; Cytadhesin P30/P32

cl11966
Location:398 → 462

NT_Pol-beta-like; Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins
NM_001429139.1 → NP_001416068.1 terminal uridylyltransferase 4 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

128354975..128535288

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287719.1 → XP_063143789.1 terminal uridylyltransferase 4 isoform X1
XM_063287722.1 → XP_063143792.1 terminal uridylyltransferase 4 isoform X4

UniProtKB/TrEMBL

A0A8I6GFX3

Related

ENSRNOP00000087360.1, ENSRNOT00000096908.2
XM_039109973.2 → XP_038965901.1 terminal uridylyltransferase 4 isoform X6

Related

ENSRNOP00000100961.1, ENSRNOT00000124337.1

Conserved Domains (5) summary

cd05402
Location:990 → 1108

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

COG5082
Location:1295 → 1384

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

COG5260
Location:948 → 1280

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

pfam03828
Location:650 → 699

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:287 → 618

TUTase; TUTase nucleotidyltransferase domain
XM_039109972.2 → XP_038965900.1 terminal uridylyltransferase 4 isoform X5

Conserved Domains (5) summary

cd05402
Location:990 → 1108

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

PTZ00368
Location:1299 → 1381

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

COG5260
Location:948 → 1280

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

pfam03828
Location:650 → 699

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:287 → 618

TUTase; TUTase nucleotidyltransferase domain
XM_039109974.2 → XP_038965902.1 terminal uridylyltransferase 4 isoform X7

Conserved Domains (5) summary

cd05402
Location:990 → 1108

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

PTZ00368
Location:1299 → 1381

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

COG5260
Location:948 → 1280

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

pfam03828
Location:650 → 699

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:287 → 618

TUTase; TUTase nucleotidyltransferase domain
XM_039109975.2 → XP_038965903.1 terminal uridylyltransferase 4 isoform X8

Conserved Domains (5) summary

cd05402
Location:990 → 1108

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

PTZ00368
Location:1299 → 1377

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

COG5260
Location:948 → 1280

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

pfam03828
Location:650 → 699

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:287 → 618

TUTase; TUTase nucleotidyltransferase domain
XM_039109976.2 → XP_038965904.1 terminal uridylyltransferase 4 isoform X9

Conserved Domains (5) summary

cd05402
Location:990 → 1108

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

PTZ00368
Location:1299 → 1377

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

COG5260
Location:948 → 1280

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

pfam03828
Location:650 → 699

PAP_assoc; Cid1 family poly A polymerase

pfam19088
Location:287 → 618

TUTase; TUTase nucleotidyltransferase domain
XM_063287718.1 → XP_063143788.1 terminal uridylyltransferase 4 isoform X1
XM_063287716.1 → XP_063143786.1 terminal uridylyltransferase 4 isoform X1
XM_063287720.1 → XP_063143790.1 terminal uridylyltransferase 4 isoform X2
XM_063287721.1 → XP_063143791.1 terminal uridylyltransferase 4 isoform X3
XM_063287723.1 → XP_063143793.1 terminal uridylyltransferase 4 isoform X10