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

Gene ID: 313481, updated on 11-Apr-2024

Summary

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Official Symbol
Tut4provided by RGD
Official Full Name
terminal uridylyl transferase 4provided by RGD
Primary source
RGD:1310138
See related
Ensembl: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 negative regulation of transposition, RNA-mediated. 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, Apr 2022]
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

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See Tut4 in Genome Data Viewer
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_086023.1Genomic Context describing neighboring genes Neighboring gene zyg-11 family member B, cell cycle regulator Neighboring gene cytochrome c oxidase assembly factor 7 Neighboring gene shisa like 2A Neighboring gene glutathione peroxidase 7 Neighboring gene ribosomal protein L9, pseudogene 7 Neighboring gene 40S ribosomal protein S27-like Neighboring gene small nucleolar RNA SNORA40 Neighboring gene uncharacterized LOC134486964 Neighboring gene RNA, U6 small nuclear 67 Neighboring gene pre-mRNA processing factor 38A Neighboring gene origin recognition complex, subunit 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. E2F1 and KIAA0191 expression predicts breast cancer patient survival. Hallett RM, et al. BMC Res Notes, 2011 Mar 31. PMID 21453498, Free PMC Article
  2. The long and short of microRNA. Yates LA, et al. Cell, 2013 Apr 25. PMID 23622238
  3. TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms. Kim B, et al. EMBO J, 2015 Jul 2. PMID 25979828, Free PMC Article
  4. miR-26a enhances miRNA biogenesis by targeting Lin28B and Zcchc11 to suppress tumor growth and metastasis. Fu X, et al. Oncogene, 2014 Aug 21. PMID 24056962, Free PMC Article
  5. mRNA 3' uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome. Morgan M, et al. Nature, 2017 Aug 17. PMID 28792939, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

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
  
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 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 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
XP_038965900.1
XP_038965901.1
XP_038965902.1
XP_038965903.1
XP_038965904.1
XP_063143786.1
XP_063143788.1
XP_063143789.1
XP_063143790.1
XP_063143791.1
XP_063143792.1
XP_063143793.1

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)

  1. 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, ENSRNOT00000079161.2
    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

  2. 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

  1. NC_086023.1 Reference GRCr8

    Range
    128354975..128535288
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063287719.1 → XP_063143789.1  terminal uridylyltransferase 4 isoform X1

  2. XM_063287722.1 → XP_063143792.1  terminal uridylyltransferase 4 isoform X4

    UniProtKB/TrEMBL
    A0A8I6GFX3

  3. XM_039109973.2 → XP_038965901.1  terminal uridylyltransferase 4 isoform X6

    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

  4. 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

  5. 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

  6. 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

  7. 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

  8. XM_063287718.1 → XP_063143788.1  terminal uridylyltransferase 4 isoform X1

  9. XM_063287716.1 → XP_063143786.1  terminal uridylyltransferase 4 isoform X1

  10. XM_063287720.1 → XP_063143790.1  terminal uridylyltransferase 4 isoform X2

  11. XM_063287721.1 → XP_063143791.1  terminal uridylyltransferase 4 isoform X3

  12. XM_063287723.1 → XP_063143793.1  terminal uridylyltransferase 4 isoform X10

Nucleotide Protein Strain
Heading Accession and Version

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