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Utp4 UTP4 small subunit processome component [ Rattus norvegicus (Norway rat) ]

Gene ID: 291987, updated on 14-Nov-2024

Summary

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Official Symbol
Utp4provided by RGD
Official Full Name
UTP4 small subunit processome componentprovided by RGD
Primary source
RGD:1311341
See related
EnsemblRapid:ENSRNOG00000020333 AllianceGenome:RGD:1311341
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Naic; Cirh1a; Cirhin; Tex292; Teg-292
Summary
Predicted to be involved in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and regulation of DNA-templated transcription. Predicted to be located in chromosome and fibrillar center. Predicted to be part of small-subunit processome and t-UTP complex. Human ortholog(s) of this gene implicated in cholestasis and primary biliary cholangitis. Orthologous to human UTP4 (UTP4 small subunit processome component). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 107.5), Kidney (RPKM 94.2) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Utp4 in Genome Data Viewer
Location:
19q12
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (51696437..51730323)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (34790962..34820558)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (39087995..39116124)

Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene transport and golgi organization 6 homolog Neighboring gene hyaluronan synthase 3 Neighboring gene chromosome transmission fidelity factor 8 Neighboring gene DERPC proline and glycine rich nuclear protein Neighboring gene syntrophin, beta 2 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC134483350 Neighboring gene vacuolar protein sorting 4 homolog A

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 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. Nucleolar localization of cirhin, the protein mutated in North American Indian childhood cirrhosis. Yu B, et al. Exp Cell Res, 2005 Dec 10. PMID 16225863
  2. Cirhin up-regulates a canonical NF-kappaB element through strong interaction with Cirip/HIVEP1. Yu B, et al. Exp Cell Res, 2009 Nov 1. PMID 19732766
  3. Interaction, mobility, and phosphorylation of human orthologues of WD repeat-containing components of the yeast SSU processome t-UTP sub-complex. Sato M, et al. Biochem Cell Biol, 2013 Dec. PMID 24219289
  4. NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. Freed EF, et al. PLoS Genet, 2012. PMID 22916032, Free PMC Article
  5. Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells. Prieto JL, et al. Genes Dev, 2007 Aug 15. PMID 17699751, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC95114

Gene Ontology Provided by RGD

Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in maturation of SSU-rRNA ISO
Inferred from Sequence Orthology
more info
  
involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in ribosomal small subunit biogenesis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of 90S preribosome IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome ISO
Inferred from Sequence Orthology
more info
  
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of small-subunit processome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of small-subunit processome ISO
Inferred from Sequence Orthology
more info
  
part_of t-UTP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of t-UTP complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
U3 small nucleolar RNA-associated protein 4 homolog
Names
UTP4 small subunit (SSU) processome component
cirrhosis, autosomal recessive 1A (cirhin)
testis-expressed gene 292

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_001009640.1 → NP_001009640.1  U3 small nucleolar RNA-associated protein 4 homolog

    See identical proteins and their annotated locations for NP_001009640.1

    Status: PROVISIONAL

    Source sequence(s)
    BC088461
    UniProtKB/TrEMBL
    A6IYY1, Q5I0C9
    Related
    ENSRNOP00000112370.1, ENSRNOT00000166964.1
    Conserved Domains (2) summary
    sd00039
    Location:21 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:16 → 306
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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_086037.1 Reference GRCr8

    Range
    51696437..51730323
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006255563.5 → XP_006255625.1  U3 small nucleolar RNA-associated protein 4 homolog isoform X1

    See identical proteins and their annotated locations for XP_006255625.1

    UniProtKB/TrEMBL
    A6IYY1, Q5I0C9
    Conserved Domains (2) summary
    sd00039
    Location:21 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:16 → 306
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. XM_006255562.3 → XP_006255624.1  U3 small nucleolar RNA-associated protein 4 homolog isoform X1

    See identical proteins and their annotated locations for XP_006255624.1

    UniProtKB/TrEMBL
    A6IYY1, Q5I0C9
    Conserved Domains (2) summary
    sd00039
    Location:21 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:16 → 306
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
Nucleotide Protein Strain
Heading Accession and Version

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