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

    Gene ID: 291987, updated on 5-Mar-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
    Ensembl: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 transcription, DNA-templated. Predicted to be located in chromosome and fibrillar center. Predicted to be part of 90S preribosome; 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, Apr 2022]
    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
    • 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 IBA
    Inferred from Biological aspect of Ancestor
    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
      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
      Related
      ENSRNOP00000027553.4
      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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