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    Rtraf RNA transcription, translation and transport factor [ Rattus norvegicus (Norway rat) ]

    Gene ID: 302247, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Rtrafprovided by RGD
    Official Full Name
    RNA transcription, translation and transport factorprovided by RGD
    Primary source
    RGD:1304704
    See related
    EnsemblRapid:ENSRNOG00000000340 AllianceGenome:RGD:1304704
    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
    LRRGT00192; RGD1304704
    Summary
    Predicted to enable RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Predicted to be involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to be located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Predicted to be part of tRNA-splicing ligase complex. Orthologous to human RTRAF (RNA transcription, translation and transport factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Muscle (RPKM 682.8), Kidney (RPKM 665.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rtraf in Genome Data Viewer
    Location:
    15p16
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (4482699..4507115)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (4447243..4457973)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (4882925..4893890)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 2 Neighboring gene uncharacterized LOC102554918 Neighboring gene nidogen 2 Neighboring gene uncharacterized LOC102555049

    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. A novel ninein-interaction protein, CGI-99, blocks ninein phosphorylation by GSK3beta and is highly expressed in brain tumors. Howng SL, et al. FEBS Lett, 2004 May 21. PMID 15147888
    2. hCLE/CGI-99, a human protein that interacts with the influenza virus polymerase, is a mRNA transcription modulator. Pérez-González A, et al. J Mol Biol, 2006 Oct 6. PMID 16950395
    3. hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. Pérez-González A, et al. PLoS One, 2014. PMID 24608264, Free PMC Article
    4. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. Popow J, et al. Nature, 2014 Jul 3. PMID 24870230, Free PMC Article
    5. Landscape of the hnRNP K protein-protein interactome. Mikula M, et al. Proteomics, 2006 Apr. PMID 16518874

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of protein kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    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
    		  
    Component Evidence Code Pubs
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of tRNA-splicing ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of tRNA-splicing ligase complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    RNA transcription, translation and transport factor protein
    Names
    UPF0568 protein C14orf166 homolog

    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_001395114.1 → NP_001382043.1  RNA transcription, translation and transport factor protein

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A8I6AA36, A6KKK9, F7EMB2
      Related
      ENSRNOP00000070052.1, ENSRNOT00000092002.3
      Conserved Domains (1) summary
      pfam10036
      Location:8 → 243
      RLL; Putative carnitine deficiency-associated protein

    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_086033.1 Reference GRCr8

      Range
      4482699..4507115
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063274191.1 → XP_063130261.1  RNA transcription, translation and transport factor protein isoform X1

      UniProtKB/TrEMBL
      A6KKK9, F7EMB2
      Related
      ENSRNOP00000049155.2, ENSRNOT00000049255.5

    2. XM_006251638.5 → XP_006251700.1  RNA transcription, translation and transport factor protein isoform X2

      UniProtKB/TrEMBL
      A0A8I6AA36, A0A8I6GBA2
      Related
      ENSRNOP00000084953.1, ENSRNOT00000101009.2
      Conserved Domains (1) summary
      pfam10036
      Location:5 → 220
      RLL; Putative carnitine deficiency-associated protein

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001047874.1: Suppressed sequence

      Description
      NM_001047874.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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