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RNASEH1 ribonuclease H1 [ Homo sapiens (human) ]

Gene ID: 246243, updated on 5-Mar-2024

Summary

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Official Symbol
RNASEH1provided by HGNC
Official Full Name
ribonuclease H1provided by HGNC
Primary source
HGNC:HGNC:18466
See related
Ensembl:ENSG00000171865 MIM:604123; AllianceGenome:HGNC:18466
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNH1; H1RNA; PEOB2
Summary
This gene encodes an endonuclease that specifically degrades the RNA of RNA-DNA hybrids and plays a key role in DNA replication and repair. Alternate in-frame start codon initiation results in the production of alternate isoforms that are directed to the mitochondria or to the nucleus. The production of the mitochondrial isoform is modulated by an upstream open reading frame (uORF). Mutations in this gene have been found in individuals with progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 2. Alternative splicing results in additional coding and non-coding transcript variants. Pseudogenes of this gene have been defined on chromosomes 2 and 17. [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in brain (RPKM 5.7), endometrium (RPKM 5.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p25.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (3531813..3558333, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3554342..3580861, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3579403..3605923, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene acireductone dioxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11111 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3522968-3523489 Neighboring gene uncharacterized LOC124907725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3523490-3524010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15230 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:3583482-3584681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15231 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11115 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3607689-3608586 Neighboring gene RNASEH1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15233 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3615875-3616480 Neighboring gene uncharacterized LOC124907726 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3616481-3617087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:3617088-3617693 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3622403-3622978

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A pan-cancer analysis of RNASEH1, a potential regulator of the tumor microenvironment. Yi C, et al. Clin Transl Oncol, 2023 Aug. PMID 37022517
  2. A non-coding RNASEH1 gene variant associates with type 1 diabetes and interacts with HLA tagSNPs in families from Colombia. Gomez-Lopera N, et al. Pediatr Diabetes, 2020 Nov. PMID 32447804
  3. RNase H1 directs origin-specific initiation of DNA replication in human mitochondria. Posse V, et al. PLoS Genet, 2019 Jan. PMID 30605451, Free PMC Article
  4. RNASEH1 gene variants are associated with autoimmune type 1 diabetes in Colombia. Pineda-Trujillo N, et al. J Endocrinol Invest, 2018 Jul. PMID 29204916
  5. Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria. Akman G, et al. Proc Natl Acad Sci U S A, 2016 Jul 26. PMID 27402764, Free PMC Article

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNase H1 facilitates recombinase recruitment by degrading DNA-RNA hybrids during meiosis.
    Title: RNase H1 facilitates recombinase recruitment by degrading DNA-RNA hybrids during meiosis.
  2. A pan-cancer analysis of RNASEH1, a potential regulator of the tumor microenvironment.
    Title: A pan-cancer analysis of RNASEH1, a potential regulator of the tumor microenvironment.
  3. BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance.
    Title: BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance.
  4. A non-coding RNASEH1 gene variant associates with type 1 diabetes and interacts with HLA tagSNPs in families from Colombia.
    Title: A non-coding RNASEH1 gene variant associates with type 1 diabetes and interacts with HLA tagSNPs in families from Colombia.
  5. Progressive External Ophthalmoplegia in Polish Patients-From Clinical Evaluation to Genetic Confirmation.
    Title: Progressive External Ophthalmoplegia in Polish Patients-From Clinical Evaluation to Genetic Confirmation.
  6. The protein-protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1.
    Title: Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1.
  7. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutatio
    Title: A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL.
  8. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria.
    Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria.
  9. RNASEH1 gene variants associate with susceptibility/protection to T1 Diabetes in Colombia.
    Title: RNASEH1 gene variants are associated with autoimmune type 1 diabetes in Colombia.
  10. Studies indicate that ribonuclease H1 is essential for mitochondrial DNA replication.
    Title: Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria.
Submit: New GeneRIF Correction See all GeneRIFs (28)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • AC108488.4

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables RNA nuclease activity TAS
Traceable Author Statement
more info
 PubMed 
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 magnesium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA replication, removal of RNA primer IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in RNA catabolic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ribonuclease H1
Names
ribonuclease H type II
NP_001273763.1
NP_001273766.1
NP_001365200.1
NP_001365201.1
NP_001365202.1
NP_002927.2

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.

Genomic

  1. NG_051310.1 RefSeqGene

    Range
    5039..21942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1090

mRNA and Protein(s)

  1. NM_001286834.3 → NP_001273763.1  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)
    AC108488
    Conserved Domains (2) summary
    cd09280
    Location:115 → 256
    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_001286837.3 → NP_001273766.1  ribonuclease H1 isoform 3

    See identical proteins and their annotated locations for NP_001273766.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the 5' region, which results in translation initiation at a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC108488, AK075490, AK096913, BC002973, DA532761, DA612116
    UniProtKB/TrEMBL
    B3KUD4
    Conserved Domains (1) summary
    cd09280
    Location:24 → 165
    RNase_HI_eukaryote_like; Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts

  3. NM_001378271.1 → NP_001365200.1  ribonuclease H1 isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC108488
    Conserved Domains (2) summary
    cd09280
    Location:141 → 259
    RNase_HI_eukaryote_like; Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts
    pfam01693
    Location:28 → 70
    Cauli_VI; Caulimovirus viroplasmin

  4. NM_001378272.1 → NP_001365201.1  ribonuclease H1 isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AC108488
    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:28 → 70
    Cauli_VI; Caulimovirus viroplasmin

  5. NM_001378273.1 → NP_001365202.1  ribonuclease H1 isoform 6 precursor

    Status: REVIEWED

    Source sequence(s)
    AC108488
    Conserved Domains (2) summary
    cd09280
    Location:141 → 277
    RNase_HI_eukaryote_like; Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts
    pfam01693
    Location:28 → 70
    Cauli_VI; Caulimovirus viroplasmin

  6. NM_002936.6 → NP_002927.2  ribonuclease H1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002927.2

    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 longer isoform (1), which is a mitochondrial protein (see details in PMID: 20823270).
    Source sequence(s)
    AC108488
    Consensus CDS
    CCDS1647.1
    UniProtKB/Swiss-Prot
    B3KQU4, O60523, O60857, O60930, Q57Z93, Q5U0C1, Q6FHD4
    UniProtKB/TrEMBL
    E5KN15
    Related
    ENSP00000313350.3, ENST00000315212.4
    Conserved Domains (2) summary
    cd09280
    Location:141 → 282
    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_148532.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  2. NR_148533.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  3. NR_148534.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  4. NR_165465.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  5. NR_165466.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  6. NR_165467.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

  7. NR_165468.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC108488

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    3531813..3558333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    3554342..3580861 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60930.2 GenPept UniProtKB/Swiss-Prot:O60930

Gene LinkOut

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