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    Rnaseh1 ribonuclease H1 [ Mus musculus (house mouse) ]

    Gene ID: 19819, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Rnaseh1provided by MGI
    Official Full Name
    ribonuclease H1provided by MGI
    Primary source
    MGI:MGI:1335073
    See related
    Ensembl:ENSMUSG00000020630 AllianceGenome:MGI:1335073
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    This gene encodes an endonuclease that specifically degrades the RNA of RNA-DNA hybrids and is necessary for DNA replication and repair. This enzyme is present in both mitochondria and nuclei, which are resulted from translation of a single mRNA with two in-frame initiation start codons. The use of the first start codon produces the mitochondrial isoform and the use of the second start codon produces the nuclear isoform. The production of the mitochondrial isoform is modulated by an upstream open reading frame (uORF) which encodes 7aa in mouse. An alternately spliced transcript variant has been found which is a candidate for nonsense-mediated mRNA decay (NMD). [provided by RefSeq, Nov 2013]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 8.3), limb E14.5 (RPKM 7.2) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    12 A2; 12 10.99 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (28699600..28709591)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (28649601..28659592)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3049 Neighboring gene ribosomal protein S7 Neighboring gene predicted gene, 53713 Neighboring gene microRNA 6937 Neighboring gene acireductone dioxygenase 1 Neighboring gene trafficking protein particle complex 12 Neighboring gene STARR-seq mESC enhancer starr_31820 Neighboring gene predicted gene, 31269

    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. Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion. Misic J, et al. Nucleic Acids Res, 2022 Aug 26. PMID 35947649, Free PMC Article
    2. Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination. Lai F, et al. Mol Cell, 2020 Mar 5. PMID 31924447
    3. Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication. Holmes JB, et al. Proc Natl Acad Sci U S A, 2015 Jul 28. PMID 26162680, Free PMC Article
    4. Eukaryotic RNases H1 act processively by interactions through the duplex RNA-binding domain. Gaidamakov SA, et al. Nucleic Acids Res, 2005. PMID 15831789, Free PMC Article
    5. Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function. Lima WF, et al. Nucleic Acids Res, 2016 Jun 20. PMID 27131367, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion.
      Title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion.
    2. RNase H1 is necessary for the activity of DNA-like ASOs. During liver regeneration, a clone of hepatocytes that expressed RNase H1 developed and partially restored mitochondrial and liver function.
      Title: Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function.
    3. the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication
      Title: Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication.
    4. translational organization of RNase H1 allows tight control of expression of RNase H1 in mitochondria, where its excess or absence can lead to cell death, without affecting the expression of the nuclear RNase H1
      Title: An upstream open reading frame and the context of the two AUG codons affect the abundance of mitochondrial and nuclear RNase H1.
    5. RNase H1 is involved in generation of mitochondrial DNA
      Title: Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    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-DNA hybrid ribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA-DNA hybrid ribonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA-DNA hybrid ribonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA-DNA hybrid ribonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA replication, removal of RNA primer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within mitochondrial DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ribonuclease H1
    Names
    RNase H1
    NP_001273794.1
    NP_035405.2

    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_001286865.1 → NP_001273794.1  ribonuclease H1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes two isoforms due to the use of alternative translation initiation codons. The longer isoform (1) is derived from the upstream AUG start codon, while the shorter isoform (2) is derived from the downstream AUG start codon. This RefSeq represents the shorter isoform (2), which is a nuclear protein (see details in PMID: 20823270).
      Source sequence(s)
      AI390696, BM943446, BY274268, CA554498, DV662103
      UniProtKB/Swiss-Prot
      O70338, Q8VCR6
      Conserved Domains (2) summary
      cd09280
      Location:114 → 255
      RNase_HI_eukaryote_like; Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts
      pfam01693
      Location:3 → 44
      Cauli_VI; Caulimovirus viroplasmin

    2. NM_011275.3 → NP_035405.2  ribonuclease H1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes two isoforms due to the use of alternative translation initiation codons. The longer isoform (1) is derived from the upstream AUG start codon, while the shorter isoform (2) is derived from the downstream AUG start codon. This RefSeq represents the longer isoform (1), which is a mitochondrial protein (see details in PMID: 20823270).
      Source sequence(s)
      AI390696, BM943446, BY274268, CA554498, DV662103
      Consensus CDS
      CCDS25852.1
      UniProtKB/Swiss-Prot
      O70338, Q8VCR6
      UniProtKB/TrEMBL
      E9QLN8
      Related
      ENSMUSP00000020959.8, ENSMUST00000020959.9
      Conserved Domains (2) summary
      cd09280
      Location:140 → 281
      RNase_HI_eukaryote_like; Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts
      pfam01693
      Location:29 → 70
      Cauli_VI; Caulimovirus viroplasmin

    RNA

    1. NR_104608.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon and has an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI390696, AK011680, BG084607, BY274268, CJ073105
      Related
      ENSMUST00000223322.2

    2. NR_186048.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC136986

    3. NR_186049.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC136986

    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_000078.7 Reference GRCm39 C57BL/6J

      Range
      28699600..28709591
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001780439.1 RNA Sequence

    2. XR_004937465.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O70338.1 GenPept UniProtKB/Swiss-Prot:O70338

    Gene LinkOut

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

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