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

Gene ID: 201973, updated on 2-Nov-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
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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 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
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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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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

    See identical proteins and their annotated locations for NP_001287696.1

    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

    See identical proteins and their annotated locations for NP_001287697.1

    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

    See identical proteins and their annotated locations for NP_689896.1

    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

    See identical proteins and their annotated locations for XP_011530022.1

    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

    See identical proteins and their annotated locations for XP_011530028.1

    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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