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    Upf1 UPF1 regulator of nonsense transcripts homolog (yeast) [ Mus musculus (house mouse) ]

    Gene ID: 19704, updated on 26-Sep-2022

    Summary

    Official Symbol
    Upf1provided by MGI
    Official Full Name
    UPF1 regulator of nonsense transcripts homolog (yeast)provided by MGI
    Primary source
    MGI:MGI:107995
    See related
    Ensembl:ENSMUSG00000058301 AllianceGenome:MGI:107995
    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
    NORF1; Rent1; Upflp; PNORF-1; B430202H16Rik
    Summary
    Predicted to enable RNA helicase activity; chromatin binding activity; and nucleic acid binding activity. Acts upstream of or within dosage compensation by inactivation of X chromosome. Predicted to be located in chromatin; chromosome, telomeric region; and nucleoplasm. Predicted to be part of exon-exon junction complex and supraspliceosomal complex. Predicted to be active in cytoplasm. Is expressed in cerebral cortex ventricular layer; embryo; and oocyte. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thymus adult (RPKM 29.6), adrenal adult (RPKM 22.9) and 28 other tissues See more
    Orthologs
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    Genomic context

    See Upf1 in Genome Data Viewer
    Location:
    8 B3.3; 8 34.15 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (70784143..70806418, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (70331493..70353423, complement)

    Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene homer scaffolding protein 3 Neighboring gene DEAD box helicase 49 Neighboring gene coatomer protein complex, subunit epsilon Neighboring gene ceramide synthase 1 Neighboring gene growth differentiation factor 1 Neighboring gene predicted gene, 51533 Neighboring gene cartilage oligomeric matrix protein Neighboring gene CREB regulated transcription coactivator 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables double-stranded DNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables telomeric DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in 3'-UTR-mediated mRNA destabilization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA duplex unwinding ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA replication ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell cycle phase transition ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to interleukin-1 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to lipopolysaccharide ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in histone mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of telomere maintenance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of translational termination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in telomere maintenance via semi-conservative replication ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of exon-exon junction complex 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
     
    part_of supraspliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    regulator of nonsense transcripts 1
    Names
    ATP-dependent helicase RENT1
    regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog)
    NP_001116301.1
    NP_109605.2
    XP_006509667.1
    XP_006509668.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001122829.2NP_001116301.1  regulator of nonsense transcripts 1 isoform a

      See identical proteins and their annotated locations for NP_001116301.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC158553, BC052149, BC056442, BE456815
      Consensus CDS
      CCDS52572.1
      UniProtKB/Swiss-Prot
      Q99PR4, Q9EPU0
      UniProtKB/TrEMBL
      A0A6P5QCC0, A0A8C6IN75
      Related
      ENSMUSP00000075089.7, ENSMUST00000075666.8
      Conserved Domains (2) summary
      COG1112
      Location:140915
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      cd18039
      Location:476709
      DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
    2. NM_030680.3NP_109605.2  regulator of nonsense transcripts 1 isoform b

      See identical proteins and their annotated locations for NP_109605.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) is shorter compared to isoform a.
      Source sequence(s)
      AC158553, BC052149, BE456815, BQ771453
      Consensus CDS
      CCDS90409.1
      UniProtKB/Swiss-Prot
      Q9EPU0
      UniProtKB/TrEMBL
      A0A6P5Q5D6
      Related
      ENSMUSP00000148927.2, ENSMUST00000215817.2
      Conserved Domains (2) summary
      COG1112
      Location:140904
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      cd18039
      Location:465698
      DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000074.7 Reference GRCm39 C57BL/6J

      Range
      70784143..70806418 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006509604.5XP_006509667.1  regulator of nonsense transcripts 1 isoform X1

      See identical proteins and their annotated locations for XP_006509667.1

      UniProtKB/Swiss-Prot
      Q99PR4, Q9EPU0
      UniProtKB/TrEMBL
      A0A6P5QCC0, A0A8C6IN75
      Conserved Domains (2) summary
      COG1112
      Location:140915
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      cd18039
      Location:476709
      DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1
    2. XM_006509605.5XP_006509668.1  regulator of nonsense transcripts 1 isoform X1

      See identical proteins and their annotated locations for XP_006509668.1

      UniProtKB/Swiss-Prot
      Q99PR4, Q9EPU0
      UniProtKB/TrEMBL
      A0A6P5QCC0, A0A8C6IN75
      Conserved Domains (2) summary
      COG1112
      Location:140915
      DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
      cd18039
      Location:476709
      DEXXQc_UPF1; DEXXQ-box helicase domain of UPF1