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    Rtraf RNA transcription, translation and transport factor [ Mus musculus (house mouse) ]

    Gene ID: 68045, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Rtrafprovided by MGI
    Official Full Name
    RNA transcription, translation and transport factorprovided by MGI
    Primary source
    MGI:MGI:1915295
    See related
    Ensembl:ENSMUSG00000021807 AllianceGenome:MGI:1915295
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    2700060E02Rik
    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. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and respiratory system. Orthologous to human RTRAF (RNA transcription, translation and transport factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta adult (RPKM 51.4), CNS E11.5 (RPKM 47.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rtraf in Genome Data Viewer
    Location:
    14 10.95 cM; 14 A3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (19861470..19873891, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (19811402..19823823, complement)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene prostaglandin D receptor pseudogene Neighboring gene predicted gene, 29899 Neighboring gene STARR-seq mESC enhancer starr_36077 Neighboring gene STARR-seq mESC enhancer starr_36080 Neighboring gene nidogen 2 Neighboring gene STARR-positive B cell enhancer ABC_E9891 Neighboring gene DNA segment, Chr 14, ERATO Doi 670, expressed Neighboring gene STARR-seq mESC enhancer starr_36086 Neighboring gene guanine nucleotide binding protein (G protein), gamma 2 Neighboring gene STARR-seq mESC enhancer starr_36089

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. Cassar PA, et al. EMBO Rep, 2015 Oct. PMID 26265008, Free PMC Article
    2. Comprehensive interactome of Otx2 in the adult mouse neural retina. Fant B, et al. Genesis, 2015 Nov. PMID 26426291
    3. Insights into specificity, redundancy and new cellular functions of C/EBPa and C/EBPb transcription factors through interactome network analysis. Cirilli M, et al. Biochim Biophys Acta Gen Subj, 2017 Feb. PMID 27746211
    4. Elucidation of the 14-3-3ζ interactome reveals critical roles of RNA-splicing factors during adipogenesis. Mugabo Y, et al. J Biol Chem, 2018 May 4. PMID 29530978, Free PMC Article
    5. Prosaposin facilitates sortilin-independent lysosomal trafficking of progranulin. Zhou X, et al. J Cell Biol, 2015 Sep 14. PMID 26370502, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2) 

    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 MGI

    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 binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase II complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II complex binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of protein kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of protein kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    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 centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitotic spindle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    part_of tRNA-splicing ligase complex ISS
    Inferred from Sequence or Structural Similarity
    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_026528.3 → NP_080804.1  RNA transcription, translation and transport factor protein

      See identical proteins and their annotated locations for NP_080804.1

      Status: VALIDATED

      Source sequence(s)
      AK012486, AK160555
      Consensus CDS
      CCDS26839.1
      UniProtKB/Swiss-Prot
      Q9CQE8
      UniProtKB/TrEMBL
      Q4VA29
      Related
      ENSMUSP00000022341.6, ENSMUST00000022341.7
      Conserved Domains (1) summary
      pfam10036
      Location:8 → 243
      RLL; Putative carnitine deficiency-associated protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000080.7 Reference GRCm39 C57BL/6J

      Range
      19861470..19873891 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CQE8.1 GenPept UniProtKB/Swiss-Prot:Q9CQE8

    Gene LinkOut

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

    Chemical Information
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