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    Clp1 cleavage factor polyribonucleotide kinase subunit 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311166, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Clp1provided by RGD
    Official Full Name
    cleavage factor polyribonucleotide kinase subunit 1provided by RGD
    Primary source
    RGD:1307679
    See related
    AllianceGenome:RGD:1307679
    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
    Heab; RGD1307679
    Summary
    Predicted to enable ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity and ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity. Predicted to be involved in cerebellar cortex development; negative regulation of gene expression; and tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of tRNA-intron endonuclease complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 10. Orthologous to human CLP1 (cleavage factor polyribonucleotide kinase subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 146.2), Thymus (RPKM 67.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Clp1 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (90213461..90217165, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (69806774..69818633, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (72125269..72137122, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene thioredoxin-related transmembrane protein 2 Neighboring gene mediator complex subunit 19 Neighboring gene zinc finger DHHC-type palmitoyltransferase 5 Neighboring gene uncharacterized LOC120101590 Neighboring gene yippee-like 4 Neighboring gene microRNA 130a Neighboring gene microRNA 3590

    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. Handling tRNA introns, archaeal way and eukaryotic way. Yoshihisa T. Front Genet, 2014. PMID 25071838, Free PMC Article
    2. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Schaffer AE, et al. Cell, 2014 Apr 24. PMID 24766810, Free PMC Article
    3. The human RNA kinase hClp1 is active on 3' transfer RNA exons and short interfering RNAs. Weitzer S, et al. Nature, 2007 May 10. PMID 17495927
    4. Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Karaca E, et al. Cell, 2014 Apr 24. PMID 24766809, Free PMC Article
    5. Pre-mRNA 3'-end processing complex assembly and function. Chan S, et al. Wiley Interdiscip Rev RNA, 2011 May-Jun. PMID 21957020, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC94928

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables polynucleotide 5'-hydroxyl-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in RISC complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in RISC complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cerebellar cortex development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cerebellar cortex development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in global gene silencing by mRNA cleavage ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in global gene silencing by mRNA cleavage ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mRNA 3'-end processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of mRNA cleavage factor complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of tRNA-intron endonuclease complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of tRNA-intron endonuclease complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    polyribonucleotide 5'-hydroxyl-kinase Clp1
    Names
    ATP/GTP-binding protein
    CLP1, cleavage and polyadenylation factor I subunit, homolog
    cleavage and polyadenylation factor I subunit 1
    polyadenylation factor Clp1
    polynucleotide kinase Clp1
    pre-mRNA cleavage complex II protein Clp1
    NP_001009599.1

    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_001009599.1 → NP_001009599.1  polyribonucleotide 5'-hydroxyl-kinase Clp1

      See identical proteins and their annotated locations for NP_001009599.1

      Status: PROVISIONAL

      Source sequence(s)
      BC087130
      UniProtKB/Swiss-Prot
      Q5PQL4
      Conserved Domains (2) summary
      COG5623
      Location:14 → 423
      CLP1; Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]
      pfam16575
      Location:121 → 306
      CLP1_P; mRNA cleavage and polyadenylation factor CLP1 P-loop

    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_086021.1 Reference GRCr8

      Range
      90213461..90217165 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5PQL4.1 GenPept UniProtKB/Swiss-Prot:Q5PQL4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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