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    PRIMPOL primase and DNA directed polymerase [ Homo sapiens (human) ]

    Gene ID: 201973, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PRIMPOLprovided by HGNC
    Official Full Name
    primase and DNA directed polymeraseprovided by HGNC
    Primary source
    HGNC:HGNC:26575
    See related
    Ensembl:ENSG00000164306 MIM:615421; AllianceGenome:HGNC:26575
    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
    MYP22; CCDC111; Primpol1
    Summary
    This gene encodes a DNA primase-polymerase that belongs to a superfamily of archaeao-eukaryotic primases. Members of this family have primase activity, catalyzing the synthesis of short RNA primers that serve as starting points for DNA synthesis, as well as DNA polymerase activity. The encoded protein facilitates DNA damage tolerance by mediating uninterrupted fork progression after UV irradiation and reinitiating DNA synthesis. An allelic variant in this gene is associated with myopia 22. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
    Expression
    Ubiquitous expression in ovary (RPKM 5.3), endometrium (RPKM 5.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRIMPOL in Genome Data Viewer
    Location:
    4q35.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (184649738..184694952)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (187993422..188038703)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (185570892..185616106)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22231 Neighboring gene Sharpr-MPRA regulatory region 13226 Neighboring gene long intergenic non-protein coding RNA 2365 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:185537732-185538289 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:185539175-185539674 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:185546799-185547380 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:185564061-185564639 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:185564640-185565217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:185565519-185566150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15841 Neighboring gene caspase 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:185609328-185610527 Neighboring gene centromere protein U Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15842 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:185654690-185655556 Neighboring gene NANOG hESC enhancer GRCh37_chr4:185657064-185657583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185668497-185668998 Neighboring gene acyl-CoA synthetase long chain family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22233 Neighboring gene NANOG hESC enhancer GRCh37_chr4:185729525-185730070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22239 Neighboring gene proteoglycan 3, pro eosinophil major basic protein 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15844 Neighboring gene uncharacterized LOC105377587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185747691-185748194 Neighboring gene MIR3945 host gene

    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. The DNA ligands Arg47 and Arg76 are crucial for catalysis by human PrimPol. Boldinova EO, et al. DNA Repair (Amst), 2021 Apr. PMID 33571927
    2. Mitochondrial DNA replication: a PrimPol perspective. Bailey LJ, et al. Biochem Soc Trans, 2017 Apr 15. PMID 28408491, Free PMC Article
    3. Significant impact of divalent metal ions on the fidelity, sugar selectivity, and drug incorporation efficiency of human PrimPol. Tokarsky EJ, et al. DNA Repair (Amst), 2017 Jan. PMID 27989484, Free PMC Article
    4. DNA Damage Tolerance by Eukaryotic DNA Polymerase and Primase PrimPol. Boldinova EO, et al. Int J Mol Sci, 2017 Jul 21. PMID 28754021, Free PMC Article
    5. Optimization of the expression, purification and polymerase activity reaction conditions of recombinant human PrimPol. Boldinova EO, et al. PLoS One, 2017. PMID 28902865, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DNA synthesis across DNA hairpins by human PrimPol.
      Title: DNA synthesis across DNA hairpins by human PrimPol.
    2. PrimPol Variant V102A with Altered Primase and Polymerase Activities.
      Title: PrimPol Variant V102A with Altered Primase and Polymerase Activities.
    3. USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress.
      Title: USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress.
    4. PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass.
      Title: PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass.
    5. 3'dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol.
      Title: 3'dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol.
    6. Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress.
      Title: Response of PRIMPOL-Knockout Human Lung Adenocarcinoma A549 Cells to Genotoxic Stress.
    7. Regulation of Human DNA Primase-Polymerase PrimPol.
      Title: Regulation of Human DNA Primase-Polymerase PrimPol.
    8. The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis.
      Title: The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis.
    9. PRIMPOL competes with RAD51 to resolve G-quadruplex-induced replication stress via its interaction with RPA.
      Title: PRIMPOL competes with RAD51 to resolve G-quadruplex-induced replication stress via its interaction with RPA.
    10. Human PrimPol Discrimination against Dideoxynucleotides during Primer Synthesis.
      Title: Human PrimPol Discrimination against Dideoxynucleotides during Primer Synthesis.
    Submit: New GeneRIF Correction See all GeneRIFs (49)

    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

    Associated conditions

    Description Tests
    Myopia 22, autosomal dominant
    MedGen: C3809464 OMIM: 615420 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ33167

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA primase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA primase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-directed DNA polymerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-directed DNA polymerase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA replication, synthesis of primer IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in R-loop processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in error-prone translesion synthesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial DNA repair ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mitochondrial DNA replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial DNA replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in replication fork processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in replication fork processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in replication fork processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to UV IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to UV IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in translesion synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in translesion synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of DNA-directed RNA polymerase complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in replication fork IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA-directed primase/polymerase protein
    Names
    coiled-coil domain-containing protein 111
    hPrimpol1
    NP_001287696.1
    NP_001287697.1
    NP_001332820.1
    NP_001332821.1
    NP_001332822.1
    NP_001332823.1
    NP_001332824.1
    NP_001332825.1
    NP_001332826.1
    NP_001332827.1
    NP_001332828.1
    NP_001332829.1
    NP_001332830.1
    NP_689896.1
    XP_011530022.1
    XP_011530025.1
    XP_011530028.1
    XP_016863356.1
    XP_016863361.1
    XP_047305707.1
    XP_047305708.1
    XP_047305709.1
    XP_054205144.1
    XP_054205145.1
    XP_054205146.1
    XP_054205147.1
    XP_054205148.1
    XP_054205149.1

    NCBI Reference Sequences (RefSeq)

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    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_051582.1 RefSeqGene

      Range
      5126..50340
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001300767.2 → NP_001287696.1  DNA-directed primase/polymerase protein isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK057729, BC047467, BP245596
      Consensus CDS
      CCDS75212.1
      UniProtKB/TrEMBL
      A0A5S6SZ32
      Related
      ENSP00000421913.1, ENST00000515774.5
      Conserved Domains (1) summary
      pfam03121
      Location:273 → 337
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    2. NM_001300768.2 → NP_001287697.1  DNA-directed primase/polymerase protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK057729, BX647575
      Consensus CDS
      CCDS75211.1
      UniProtKB/Swiss-Prot
      Q96LW4
      UniProtKB/TrEMBL
      A0A0A0MTC0
      Related
      ENSP00000425316.1, ENST00000512834.5
      Conserved Domains (1) summary
      pfam03121
      Location:401 → 465
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    3. NM_001345891.2 → NP_001332820.1  DNA-directed primase/polymerase protein isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:402 → 479
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    4. NM_001345892.2 → NP_001332821.1  DNA-directed primase/polymerase protein isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:401 → 478
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    5. NM_001345893.2 → NP_001332822.1  DNA-directed primase/polymerase protein isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:401 → 478
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    6. NM_001345894.2 → NP_001332823.1  DNA-directed primase/polymerase protein isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:170 → 247
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    7. NM_001345895.2 → NP_001332824.1  DNA-directed primase/polymerase protein isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Consensus CDS
      CCDS3837.1
      UniProtKB/Swiss-Prot
      A0A0A0MTC0, D3DP55, D6RDM1, Q5HYJ9, Q96LW4
      Related
      ENSP00000420860.1, ENST00000503752.5
      Conserved Domains (1) summary
      pfam03121
      Location:402 → 466
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    8. NM_001345896.2 → NP_001332825.1  DNA-directed primase/polymerase protein isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Consensus CDS
      CCDS75211.1
      UniProtKB/TrEMBL
      A0A0A0MTC0

    9. NM_001345897.2 → NP_001332826.1  DNA-directed primase/polymerase protein isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:170 → 234
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    10. NM_001345898.2 → NP_001332827.1  DNA-directed primase/polymerase protein isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:169 → 233
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    11. NM_001345899.2 → NP_001332828.1  DNA-directed primase/polymerase protein isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591

    12. NM_001345900.2 → NP_001332829.1  DNA-directed primase/polymerase protein isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC079257
      Conserved Domains (1) summary
      pfam03121
      Location:227 → 291
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    13. NM_001345901.2 → NP_001332830.1  DNA-directed primase/polymerase protein isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Conserved Domains (1) summary
      pfam03121
      Location:170 → 234
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    14. NM_152683.4 → NP_689896.1  DNA-directed primase/polymerase protein isoform 1

      Status: REVIEWED

      Source sequence(s)
      BC064600, BP245596
      Consensus CDS
      CCDS3837.1
      UniProtKB/Swiss-Prot
      A0A0A0MTC0, D3DP55, D6RDM1, Q5HYJ9, Q96LW4
      Related
      ENSP00000313816.6, ENST00000314970.11
      Conserved Domains (1) summary
      pfam03121
      Location:402 → 466
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    RNA

    1. NR_144312.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591

    2. NR_144313.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591

    3. NR_144314.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC079257, KF459591
      Related
      ENST00000509002.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      184649738..184694952
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007867.3 → XP_016863356.1  DNA-directed primase/polymerase protein isoform X2

    2. XM_011531720.2 → XP_011530022.1  DNA-directed primase/polymerase protein isoform X1

      Conserved Domains (1) summary
      pfam03121
      Location:402 → 479
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    3. XM_011531723.2 → XP_011530025.1  DNA-directed primase/polymerase protein isoform X3

      Conserved Domains (1) summary
      pfam03121
      Location:273 → 350
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    4. XM_017007872.2 → XP_016863361.1  DNA-directed primase/polymerase protein isoform X5

      Conserved Domains (1) summary
      pfam03121
      Location:170 → 247
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    5. XM_011531726.4 → XP_011530028.1  DNA-directed primase/polymerase protein isoform X4

      Conserved Domains (1) summary
      pfam03121
      Location:227 → 304
      Herpes_UL52; Herpesviridae UL52/UL70 DNA primase

    6. XM_047449752.1 → XP_047305708.1  DNA-directed primase/polymerase protein isoform X6

    7. XM_047449753.1 → XP_047305709.1  DNA-directed primase/polymerase protein isoform X7

    8. XM_047449751.1 → XP_047305707.1  DNA-directed primase/polymerase protein isoform X4

    RNA

    1. XR_938701.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      187993422..188038703
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054349170.1 → XP_054205145.1  DNA-directed primase/polymerase protein isoform X2

    2. XM_054349169.1 → XP_054205144.1  DNA-directed primase/polymerase protein isoform X1

    3. XM_054349171.1 → XP_054205146.1  DNA-directed primase/polymerase protein isoform X3

    4. XM_054349174.1 → XP_054205149.1  DNA-directed primase/polymerase protein isoform X5

    5. XM_054349173.1 → XP_054205148.1  DNA-directed primase/polymerase protein isoform X4

    6. XM_054349172.1 → XP_054205147.1  DNA-directed primase/polymerase protein isoform X4

    RNA

    1. XR_008486947.1 RNA Sequence

    2. XR_008486948.1 RNA Sequence

    3. XR_008486949.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96LW4.3 GenPept UniProtKB/Swiss-Prot:Q96LW4

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