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    DNA2 DNA replication helicase/nuclease 2 [ Homo sapiens (human) ]

    Gene ID: 1763, updated on 9-May-2024

    Summary

    Official Symbol
    DNA2provided by HGNC
    Official Full Name
    DNA replication helicase/nuclease 2provided by HGNC
    Primary source
    HGNC:HGNC:2939
    See related
    Ensembl:ENSG00000138346 MIM:601810; AllianceGenome:HGNC:2939
    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
    RTS4; DNA2L; hDNA2
    Summary
    This gene encodes a member of the DNA2/NAM7 helicase family. The encoded protein is a conserved helicase/nuclease involved in the maintenance of mitochondrial and nuclear DNA stability. Mutations in this gene are associated with autosomal dominant progressive external ophthalmoplegia-6 (PEOA6) and Seckel syndrome 8. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
    Expression
    Broad expression in lymph node (RPKM 2.7), testis (RPKM 1.9) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See DNA2 in Genome Data Viewer
    Location:
    10q21.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (68414064..68472521, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (69283292..69341758, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70173821..70231878, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16478 Neighboring gene MPRA-validated peak989 silencer Neighboring gene MPRA-validated peak990 silencer Neighboring gene phenazine biosynthesis like protein domain containing Neighboring gene MPRA-validated peak991 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3460 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70091533-70092347 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70092348-70093161 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16571 Neighboring gene heterogeneous nuclear ribonucleoprotein H3 Neighboring gene MPRA-validated peak992 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16583 Neighboring gene RUN and FYVE domain containing 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16593 Neighboring gene MPRA-validated peak994 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70166191-70166692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70166693-70167192 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16635 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16643 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16656 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_16661/16662 and experimental_16666/16667 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16674 Neighboring gene ribosomal protein L26 pseudogene 29 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16683 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16686/16687 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16694 Neighboring gene RNA, 5S ribosomal pseudogene 319 Neighboring gene MPRA-validated peak997 silencer Neighboring gene solute carrier family 25 member 16 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:70255753-70256326 Neighboring gene ribosomal protein L26 pseudogene 27 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:70285872-70286556 Neighboring gene Sharpr-MPRA regulatory region 5966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70287929-70288614 Neighboring gene transmembrane protein 14D, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10063, KIAA0083, MGC133297

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables 5'-3' DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables 5'-flap endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables 5'-flap endonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables 5'-flap endonuclease activity TAS
    Traceable Author Statement
    more info
     
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT enables DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables helicase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables single-stranded DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables site-specific endodeoxyribonuclease activity, specific for altered base IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA replication checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA replication, Okazaki fragment processing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA replication, removal of RNA primer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in G-quadruplex DNA unwinding TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in base-excision repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mitochondrial DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mitochondrial DNA replication IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mitotic telomere maintenance via semi-conservative replication ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in nucleic acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of DNA replication IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in replication fork reversal IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in t-circle formation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in telomere maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in telomere maintenance via semi-conservative replication TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in chromosome, telomeric region ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of gamma DNA polymerase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA replication ATP-dependent helicase/nuclease DNA2
    Names
    DNA replication ATP-dependent helicase-like homolog
    DNA replication helicase 2 homolog
    DNA2 DNA replication helicase 2-like
    DNA2-like helicase
    NP_001073918.2
    XP_006717743.1
    XP_011537719.1
    XP_016871288.1
    XP_054220919.1
    XP_054220920.1
    XP_054220921.1

    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.

    Genomic

    1. NG_034247.1 RefSeqGene

      Range
      5001..62910
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001080449.3NP_001073918.2  DNA replication ATP-dependent helicase/nuclease DNA2

      See identical proteins and their annotated locations for NP_001073918.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
      Source sequence(s)
      BC073945, D42046, DC404138
      Consensus CDS
      CCDS44415.2
      UniProtKB/Swiss-Prot
      P51530, Q2NKM1, Q5TC49, Q5TC50, Q6P455, Q6PI80, Q7Z6H9, Q8N346
      Related
      ENSP00000351185.3, ENST00000358410.8
      Conserved Domains (5) summary
      TIGR00376
      Location:4711032
      TIGR00376; DNA helicase, putative
      pfam08696
      Location:71282
      Dna2; DNA replication factor Dna2
      pfam13087
      Location:8051017
      AAA_12; AAA domain
      cl00641
      Location:261397
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4
      cl21455
      Location:625875
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    RNA

    1. NR_102264.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs at the 5' end and uses an alternate internal splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC063664, BC111740
      Related
      ENST00000551118.6

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      68414064..68472521 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717680.3XP_006717743.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X1

      Conserved Domains (5) summary
      TIGR00376
      Location:5011062
      TIGR00376; DNA helicase, putative
      pfam08696
      Location:101312
      Dna2; DNA replication factor Dna2
      pfam13087
      Location:8351047
      AAA_12; AAA domain
      cl00641
      Location:291427
      Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4
      cl21455
      Location:655905
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    2. XM_017015799.1XP_016871288.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X2

    3. XM_011539417.1XP_011537719.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X3

      Conserved Domains (3) summary
      TIGR00376
      Location:111672
      TIGR00376; DNA helicase, putative
      pfam13087
      Location:445657
      AAA_12; AAA domain
      cl21455
      Location:265515
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      69283292..69341758 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364944.1XP_054220919.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X1

    2. XM_054364945.1XP_054220920.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X2

    3. XM_054364946.1XP_054220921.1  DNA replication ATP-dependent helicase/nuclease DNA2 isoform X3