Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RNASEH2A Gene

Aliases for RNASEH2A Gene

  • Ribonuclease H2 Subunit A 2 3 3 5
  • Aicardi-Goutieres Syndrome 4 Protein 3 4
  • Ribonuclease H2, Large Subunit 2 3
  • Ribonuclease HI Large Subunit 3 4
  • Ribonuclease HI Subunit A 3 4
  • RNase HI Large Subunit 3 4
  • RNase H2 Subunit A 3 4
  • RNase H(35) 3 4
  • RNASEHI 3 4
  • RNHIA 3 4
  • AGS4 3 4
  • Aicardi-Goutieres Syndrome 4 2
  • Ribonuclease H2, Subunit A 2
  • EC 4
  • JUNB 3
  • RNHL 3

External Ids for RNASEH2A Gene

Previous GeneCards Identifiers for RNASEH2A Gene

  • GC19P013048
  • GC19P013140
  • GC19P012762
  • GC19P012778
  • GC19P012918
  • GC19P012489

Summaries for RNASEH2A Gene

Entrez Gene Summary for RNASEH2A Gene

  • The protein encoded by this gene is a component of the heterotrimeric type II ribonuclease H enzyme (RNAseH2). RNAseH2 is the major source of ribonuclease H activity in mammalian cells and endonucleolytically cleaves ribonucleotides. It is predicted to remove Okazaki fragment RNA primers during lagging strand DNA synthesis and to excise single ribonucleotides from DNA-DNA duplexes. Mutations in this gene cause Aicardi-Goutieres Syndrome (AGS), a an autosomal recessive neurological disorder characterized by progressive microcephaly and psychomotor retardation, intracranial calcifications, elevated levels of interferon-alpha and white blood cells in the cerebrospinal fluid.[provided by RefSeq, Aug 2009]

GeneCards Summary for RNASEH2A Gene

RNASEH2A (Ribonuclease H2 Subunit A) is a Protein Coding gene. Diseases associated with RNASEH2A include Aicardi-Goutieres Syndrome 4 and Aicardi-Goutieres Syndrome. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ribonuclease activity.

UniProtKB/Swiss-Prot for RNASEH2A Gene

  • Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.

Gene Wiki entry for RNASEH2A Gene

Additional gene information for RNASEH2A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNASEH2A Gene

Genomics for RNASEH2A Gene

GeneHancer (GH) Regulatory Elements for RNASEH2A Gene

Promoters and enhancers for RNASEH2A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J012800 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 659.2 -0.6 -553 2.8 HDGF PKNOX1 SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RNASEH2A PRDX2 THSD8 ZNF136 CCDC130 TRMT1 ZNF791 ZNF442 WDR83OS ZNF564
GH19J012805 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 669.5 +4.7 4701 1.6 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 RNASEH2A ZNF136 ZNF20 ZNF763 CCDC130 TRMT1 ZNF700 ZNF44 ZNF442 ZNF625
GH19J012813 Promoter 0.5 EPDnew 650.4 +11.1 11094 0.1 RNASEH2A MAST1 RTBDN BEST2 DNASE2 THSD8 LOC105372281 HOOK2
GH19J013148 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26.2 +351.6 351641 10.2 MLX DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 STX10 IER2 ENSG00000267598 CCDC130 ZNF136 TRMT1 ZNF44 ZNF564 WDR83OS ZNF791
GH19J013089 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 26.2 +295.7 295677 17.3 IRF4 E2F8 ZNF143 MEF2D GLIS1 NBN NR2C1 KDM1A WT1 SP7 LYL1 PIR62376 ZNF136 CCDC130 TRMT1 ZNF564 ZNF799 ZNF442 ZNF44 ZNF791
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNASEH2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNASEH2A gene promoter:
  • ATF-2
  • c-Jun
  • STAT1
  • SRF (504 AA)

Genomic Locations for RNASEH2A Gene

Genomic Locations for RNASEH2A Gene
13,148 bases
Plus strand
7,069 bases
Plus strand

Genomic View for RNASEH2A Gene

Genes around RNASEH2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNASEH2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNASEH2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNASEH2A Gene

Proteins for RNASEH2A Gene

  • Protein details for RNASEH2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ribonuclease H2 subunit A
    Protein Accession:
    Secondary Accessions:
    • B2RCY1
    • Q96F11

    Protein attributes for RNASEH2A Gene

    299 amino acids
    Molecular mass:
    33395 Da
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • The RNase H2 complex is a heterotrimer composed of the catalytic subunit RNASEH2A and the non-catalytic subunits RNASEH2B and RNASEH2C.

    Three dimensional structures from OCA and Proteopedia for RNASEH2A Gene

neXtProt entry for RNASEH2A Gene

Post-translational modifications for RNASEH2A Gene

  • Ubiquitination at posLast=267267, posLast=221221, posLast=215215, Lys198, Lys192, Lys167, Lys165, posLast=6464, and Lys26
  • Modification sites at PhosphoSitePlus

Other Protein References for RNASEH2A Gene

Antibody Products

No data available for DME Specific Peptides for RNASEH2A Gene

Domains & Families for RNASEH2A Gene

Gene Families for RNASEH2A Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for RNASEH2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the RNase HII family. Eukaryotic subfamily.
  • Belongs to the RNase HII family. Eukaryotic subfamily.
genes like me logo Genes that share domains with RNASEH2A: view

Function for RNASEH2A Gene

Molecular function for RNASEH2A Gene

UniProtKB/Swiss-Prot Function:
Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.
UniProtKB/Swiss-Prot CatalyticActivity:
Endonucleolytic cleavage to 5-phosphomonoester.

Enzyme Numbers (IUBMB) for RNASEH2A Gene

Phenotypes From GWAS Catalog for RNASEH2A Gene

Gene Ontology (GO) - Molecular Function for RNASEH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0004523 RNA-DNA hybrid ribonuclease activity IEA,IDA 21177858
GO:0004540 ribonuclease activity TAS 9789007
genes like me logo Genes that share ontologies with RNASEH2A: view
genes like me logo Genes that share phenotypes with RNASEH2A: view

Human Phenotype Ontology for RNASEH2A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for RNASEH2A

miRNA for RNASEH2A Gene

miRTarBase miRNAs that target RNASEH2A

Transcription Factor Targets for RNASEH2A Gene

Selected GeneGlobe predicted Target genes for RNASEH2A

Clone Products

No data available for Animal Models and HOMER Transcription for RNASEH2A Gene

Localization for RNASEH2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNASEH2A Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNASEH2A gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleus (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RNASEH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
GO:0032299 ribonuclease H2 complex IDA 21177858
genes like me logo Genes that share ontologies with RNASEH2A: view

Pathways & Interactions for RNASEH2A Gene

SuperPathways for RNASEH2A Gene

SuperPathway Contained pathways
1 Telomere C-strand (Lagging Strand) Synthesis
genes like me logo Genes that share pathways with RNASEH2A: view

Pathways by source for RNASEH2A Gene

1 KEGG pathway for RNASEH2A Gene

Gene Ontology (GO) - Biological Process for RNASEH2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006260 DNA replication TAS 21177858
GO:0006298 mismatch repair IDA 23603115
GO:0006401 RNA catabolic process IDA,TAS 21177858
GO:0016070 RNA metabolic process IEA --
GO:0043137 DNA replication, removal of RNA primer IBA --
genes like me logo Genes that share ontologies with RNASEH2A: view

No data available for SIGNOR curated interactions for RNASEH2A Gene

Drugs & Compounds for RNASEH2A Gene

(2) Drugs for RNASEH2A Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0
Manganese Approved Nutra 37
genes like me logo Genes that share compounds with RNASEH2A: view

Transcripts for RNASEH2A Gene


Unigene Clusters for RNASEH2A Gene

Ribonuclease H2, subunit A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNASEH2A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8
SP1: - -
SP2: - -
SP3: -
SP4: -

Relevant External Links for RNASEH2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RNASEH2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNASEH2A Gene

Protein differential expression in normal tissues from HIPED for RNASEH2A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.7), Lymph node (13.4), and Monocytes (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNASEH2A Gene

Protein tissue co-expression partners for RNASEH2A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RNASEH2A Gene:


SOURCE GeneReport for Unigene cluster for RNASEH2A Gene:


Evidence on tissue expression from TISSUES for RNASEH2A Gene

  • Nervous system(4.4)
  • Lung(2.4)
  • Skin(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RNASEH2A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • meninges
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • chest wall
  • abdominal wall
  • liver
  • spleen
  • stomach
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with RNASEH2A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RNASEH2A Gene

Orthologs for RNASEH2A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RNASEH2A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RNASEH2A 34 33
  • 98.77 (n)
(Canis familiaris)
Mammalia RNASEH2A 34 33
  • 86.8 (n)
(Bos Taurus)
Mammalia RNASEH2A 34 33
  • 86.69 (n)
(Rattus norvegicus)
Mammalia Rnaseh2a 33
  • 82.77 (n)
(Mus musculus)
Mammalia Rnaseh2a 16 34 33
  • 81.94 (n)
(Monodelphis domestica)
Mammalia RNASEH2A 34
  • 66 (a)
(Ornithorhynchus anatinus)
Mammalia RNASEH2A 34
  • 62 (a)
(Anolis carolinensis)
Reptilia RNASEH2A 34
  • 64 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rnaseh2a 33
  • 63.48 (n)
MGC76169 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8314 33
(Danio rerio)
Actinopterygii rnaseh2a 34 33
  • 64.66 (n)
wufa92h07 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2178 33
fruit fly
(Drosophila melanogaster)
Insecta CG13690 34 35 33
  • 54.98 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007741 33
  • 53.72 (n)
(Caenorhabditis elegans)
Secernentea rnh-2 34 35 33
  • 49.63 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER363W 33
  • 53.91 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RNH201 36 34 33
  • 51.45 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04774g 33
  • 50 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G25100 33
  • 55.27 (n)
(Oryza sativa)
Liliopsida Os11g0153900 33
  • 54.17 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU09608 33
  • 53.5 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
Cin.1877 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rnh201 33
  • 48.17 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1877 33
Species where no ortholog for RNASEH2A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RNASEH2A Gene

Gene Tree for RNASEH2A (if available)
Gene Tree for RNASEH2A (if available)
Evolutionary constrained regions (ECRs) for RNASEH2A: view image

Paralogs for RNASEH2A Gene

(1) SIMAP similar genes for RNASEH2A Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RNASEH2A: view

No data available for Paralogs for RNASEH2A Gene

Variants for RNASEH2A Gene

Sequence variations from dbSNP and Humsavar for RNASEH2A Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1046220 likely-benign, Aicardi Goutieres syndrome 12,806,658(+) T/C 5_prime_UTR_variant, intron_variant
rs11554400 benign, likely-benign, not specified, Aicardi Goutieres syndrome 12,806,706(+) A/G coding_sequence_variant, intron_variant, synonymous_variant
rs143534021 uncertain-significance, Aicardi Goutieres syndrome 12,813,107(+) A/G coding_sequence_variant, missense_variant
rs145662304 uncertain-significance, Aicardi Goutieres syndrome 12,813,203(+) T/C coding_sequence_variant, missense_variant
rs199696470 uncertain-significance, Aicardi Goutieres syndrome 12,813,482(+) G/A/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for RNASEH2A Gene

Variant ID Type Subtype PubMed ID
dgv138n111 CNV deletion 26073780
nsv1160586 CNV duplication 26073780
nsv513711 OTHER inversion 21212237
nsv513712 OTHER inversion 21212237
nsv953977 CNV deletion 24416366

Variation tolerance for RNASEH2A Gene

Residual Variation Intolerance Score: 54.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.31; 53.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNASEH2A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNASEH2A Gene

Disorders for RNASEH2A Gene

MalaCards: The human disease database

(3) MalaCards diseases for RNASEH2A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
aicardi-goutieres syndrome 4
  • aicardi-goutieres syndrome 1
aicardi-goutieres syndrome
  • cree encephalitis
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards


  • Aicardi-Goutieres syndrome 4 (AGS4) [MIM:610333]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269 PubMed:16845400, ECO:0000269 PubMed:17846997, ECO:0000269 PubMed:20131292}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RNASEH2A

genes like me logo Genes that share disorders with RNASEH2A: view

No data available for Genatlas for RNASEH2A Gene

Publications for RNASEH2A Gene

  1. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection. (PMID: 16845400) Crow YJ … Jackson AP (Nature genetics 2006) 2 3 4 22 58
  2. Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII. (PMID: 9789007) Frank P … Büsen W (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 58
  3. The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects. (PMID: 21177858) Figiel M … Nowotny M (The Journal of biological chemistry 2011) 3 4 58
  4. Expanding the phenotypic spectrum of lupus erythematosus in Aicardi-Goutières syndrome. (PMID: 20131292) Ramantani G … Lee-Kirsch MA (Arthritis and rheumatism 2010) 4 22 58
  5. Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex. (PMID: 19015152) Chon H … Cerritelli SM (Nucleic acids research 2009) 3 22 58

Products for RNASEH2A Gene

Sources for RNASEH2A Gene

Loading form....