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POLA1 DNA polymerase alpha 1, catalytic subunit [ Homo sapiens (human) ]

Gene ID: 5422, updated on 11-Apr-2024

Summary

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Official Symbol
POLA1provided by HGNC
Official Full Name
DNA polymerase alpha 1, catalytic subunitprovided by HGNC
Primary source
HGNC:HGNC:9173
See related
Ensembl:ENSG00000101868 MIM:312040; AllianceGenome:HGNC:9173
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
NSX; PDR; POLA; p180; VEODS
Summary
This gene encodes the catalytic subunit of DNA polymerase, which together with a regulatory and two primase subunits, forms the DNA polymerase alpha complex. The catalytic subunit plays an essential role in the initiation of DNA replication. [provided by RefSeq, Mar 2010]
Expression
Ubiquitous expression in lymph node (RPKM 2.6), bone marrow (RPKM 2.2) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
Xp22.11-p21.3
Exon count:
44
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (24693918..24996986)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (24278197..24581230)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (24712035..25015103)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene phosphate cytidylyltransferase 1B, choline Neighboring gene uncharacterized LOC124905262 Neighboring gene ribosomal protein L23 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24710004-24710504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29507 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:24783273-24783773 Neighboring gene small Cajal body-specific RNA 23 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 3 Neighboring gene VISTA enhancer hs118 Neighboring gene VISTA enhancer hs119 Neighboring gene uncharacterized LOC124905263 Neighboring gene VISTA enhancer hs121 Neighboring gene VISTA enhancer hs122 Neighboring gene VISTA enhancer hs145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:25021017-25021551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:25022180-25022754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:25022755-25023328 Neighboring gene aristaless related homeobox polyalanine expansion region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:25038709-25039287 Neighboring gene PAFAH1B2 pseudogene 1 Neighboring gene aristaless related homeobox

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. Pol α-primase dependent nuclear localization of the mammalian CST complex. Kelich JM, et al. Commun Biol, 2021 Mar 17. PMID 33731801, Free PMC Article
  2. Activity and fidelity of human DNA polymerase α depend on primer structure. Baranovskiy AG, et al. J Biol Chem, 2018 May 4. PMID 29555682, Free PMC Article
  3. Functional monosomy of 6q27-qter and functional disomy of Xpter-p22.11 due to X;6 translocation with an atypical X-inactivation pattern. Podolska A, et al. Am J Med Genet A, 2017 May. PMID 28371302
  4. Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction. Zhang Y, et al. DNA Repair (Amst), 2016 Jul. PMID 27235627, Free PMC Article
  5. Human DNA polymerase α in binary complex with a DNA:DNA template-primer. Coloma J, et al. Sci Rep, 2016 Apr 1. PMID 27032819, Free PMC Article

See all (141) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Small tandem DNA duplications result from CST-guided Pol alpha-primase action at DNA break termini.
    Title: Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini.
  2. Pol alpha-primase dependent nuclear localization of the mammalian CST complex.
    Title: Pol α-primase dependent nuclear localization of the mammalian CST complex.
  3. Defective DNA Polymerase alpha-Primase Leads to X-Linked Intellectual Disability Associated with Severe Growth Retardation, Microcephaly, and Hypogonadism.
    Title: Defective DNA Polymerase α-Primase Leads to X-Linked Intellectual Disability Associated with Severe Growth Retardation, Microcephaly, and Hypogonadism.
  4. detailed structural comparison of Polalpha with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication
    Title: Activity and fidelity of human DNA polymerase α depend on primer structure.
  5. High POLA1 expression is associated with bladder cancer.
    Title: Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy.
  6. Divalent ions attenuate DNA synthesis by human DNA polymerase alpha by changing the structure of the template/primer or by perturbing the polymerase reaction.
    Title: Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction.
  7. We propose that completely skewed XCI favoring the normal X chromosome resulted from death of cells with an active derivative X that was caused by a non-functional POLA1 gene. In summary, we conclude that functional monosomy of 6q27-qter and functional disomy of Xpter-p22.11 are responsible for the clinical phenotype of the patient
    Title: Functional monosomy of 6q27-qter and functional disomy of Xpter-p22.11 due to X;6 translocation with an atypical X-inactivation pattern.
  8. The first crystal structure of human Polalpha polymerase subunit in complex with a DNA:DNA helix shows that portion of the DNA:DNA helix in contact with the polymerase is not in a B-form but in a hybrid A-B form. The free energy cost of distorting DNA from B- to hybrid A-B form may augur the termination of primer synthesis.
    Title: Human DNA polymerase α in binary complex with a DNA:DNA template-primer.
  9. Data indicate that X-linked reticulate pigmentary disorder (XLPDR) is caused by an intronic mutation that disrupts the expression of POLA1, which encodes the catalytic subunit of DNA polymerase-alpha.
    Title: DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis.
  10. Mutation in POLA1 is responsible for XLPDR (MIM: 312040) and demonstrates a role for this gene in interferon regulation
    Title: DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis.
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

Associated conditions

Description Tests
X-linked intellectual disability, van Esch type
MedGen: C4305072 OMIM: 301030 GeneReviews: Not available
Compare labs
X-linked reticulate pigmentary disorder
MedGen: C1845050 OMIM: 301220 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)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr downregulates POLA1 in HeLa cells within 12 hours of exposure PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp686K1672

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA replication origin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 DNA-directed DNA polymerase activity IMP
Inferred from Mutant Phenotype
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 nucleotide binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
NOT involved_in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA replication initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA replication, synthesis of primer IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA strand elongation involved in DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA synthesis involved in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in DNA synthesis involved in UV-damage excision repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in lagging strand elongation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in leading strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in leading strand elongation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mitotic DNA replication initiation IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT involved_in nucleotide-excision repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of type I interferon production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of alpha DNA polymerase:primase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of alpha DNA polymerase:primase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of alpha DNA polymerase:primase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of alpha DNA polymerase:primase complex TAS
Traceable Author Statement
more info
 PubMed 
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear envelope IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA polymerase alpha catalytic subunit
Names
DNA polymerase alpha catalytic subunit p180
polymerase (DNA directed), alpha 1, catalytic subunit
polymerase (DNA) alpha 1, catalytic subunit
polymerase (DNA-directed), alpha (70kD)
NP_001317289.1
NP_001365232.1
NP_058633.2
XP_011543842.1
XP_011543843.1
XP_016885083.1
XP_016885084.1
XP_016885085.1
XP_024308160.1
XP_047298136.1
XP_047298137.1
XP_047298138.1
XP_047298139.1
XP_054183220.1
XP_054183221.1
XP_054183222.1
XP_054183223.1
XP_054183224.1
XP_054183225.1
XP_054183226.1
XP_054183227.1
XP_054183228.1
XP_054183229.1

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_016798.2 RefSeqGene

    Range
    4972..308040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001330360.2 → NP_001317289.1  DNA polymerase alpha catalytic subunit isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC002504, AC004655, AC079375, AC135280, KF459037
    Consensus CDS
    CCDS83462.1
    UniProtKB/TrEMBL
    A6NMQ1
    Related
    ENSP00000368358.3, ENST00000379068.8
    Conserved Domains (5) summary
    cd05776
    Location:541 → 773
    DNA_polB_alpha_exo; inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase
    cd05532
    Location:838 → 1248
    POLBc_alpha; DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively ...
    TIGR00592
    Location:56 → 1231
    pol2; DNA polymerase (pol2)
    pfam08996
    Location:1271 → 1461
    zf-DNA_Pol; DNA Polymerase alpha zinc finger
    pfam12254
    Location:41 → 101
    DNA_pol_alpha_N; DNA polymerase alpha subunit p180 N terminal

  2. NM_001378303.1 → NP_001365232.1  DNA polymerase alpha catalytic subunit isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC002504, AC004655, AC079375, AC135280, KF459037
    Conserved Domains (2) summary
    TIGR00592
    Location:56 → 1206
    pol2; DNA polymerase (pol2)
    pfam08996
    Location:1246 → 1436
    zf-DNA_Pol; DNA Polymerase alpha zinc finger

  3. NM_016937.4 → NP_058633.2  DNA polymerase alpha catalytic subunit isoform 2

    See identical proteins and their annotated locations for NP_058633.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC004655, BM664024, BU508486, BX648513, CN364591, X06745
    Consensus CDS
    CCDS14214.1
    UniProtKB/Swiss-Prot
    P09884, Q86UQ7
    Related
    ENSP00000368349.3, ENST00000379059.7
    Conserved Domains (5) summary
    cd05776
    Location:535 → 767
    DNA_polB_alpha_exo; inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase
    cd05532
    Location:832 → 1242
    POLBc_alpha; DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively ...
    TIGR00592
    Location:50 → 1225
    pol2; DNA polymerase (pol2)
    pfam08996
    Location:1265 → 1455
    zf-DNA_Pol; DNA Polymerase alpha zinc finger
    pfam12254
    Location:35 → 95
    DNA_pol_alpha_N; DNA polymerase alpha subunit p180 N terminal

RNA

  1. NR_165482.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC002504, AC004655, AC079375, AC135280
    Related
    ENST00000672178.1

  2. NR_165483.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC002504, AC004655, AC079375, AC135280, KF459037

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    24693918..24996986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029595.3 → XP_016885084.1  DNA polymerase alpha catalytic subunit isoform X2

  2. XM_017029594.3 → XP_016885083.1  DNA polymerase alpha catalytic subunit isoform X1

  3. XM_017029596.2 → XP_016885085.1  DNA polymerase alpha catalytic subunit isoform X3

  4. XM_011545540.4 → XP_011543842.1  DNA polymerase alpha catalytic subunit isoform X4

    Conserved Domains (5) summary
    cd05776
    Location:541 → 773
    DNA_polB_alpha_exo; inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase
    cd05532
    Location:838 → 1248
    POLBc_alpha; DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively ...
    TIGR00592
    Location:56 → 1231
    pol2; DNA polymerase (pol2)
    pfam08996
    Location:1271 → 1349
    zf-DNA_Pol; DNA Polymerase alpha zinc finger
    pfam12254
    Location:41 → 101
    DNA_pol_alpha_N; DNA polymerase alpha subunit p180 N terminal

  5. XM_047442180.1 → XP_047298136.1  DNA polymerase alpha catalytic subunit isoform X5

  6. XM_024452392.2 → XP_024308160.1  DNA polymerase alpha catalytic subunit isoform X7

    Conserved Domains (1) summary
    TIGR00592
    Location:56 → 1187
    pol2; DNA polymerase (pol2)

  7. XM_011545541.3 → XP_011543843.1  DNA polymerase alpha catalytic subunit isoform X8

    Conserved Domains (5) summary
    cd05776
    Location:541 → 773
    DNA_polB_alpha_exo; inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase
    COG0417
    Location:615 → 856
    PolB; DNA polymerase elongation subunit (family B) [Replication, recombination and repair]
    cl10023
    Location:838 → 856
    POLBc; DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic ...
    pfam03104
    Location:377 → 717
    DNA_pol_B_exo1; DNA polymerase family B, exonuclease domain
    pfam12254
    Location:41 → 101
    DNA_pol_alpha_N; DNA polymerase alpha subunit p180 N terminal

  8. XM_047442183.1 → XP_047298139.1  DNA polymerase alpha catalytic subunit isoform X9

  9. XM_047442181.1 → XP_047298137.1  DNA polymerase alpha catalytic subunit isoform X6

  10. XM_047442182.1 → XP_047298138.1  DNA polymerase alpha catalytic subunit isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    24278197..24581230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327246.1 → XP_054183221.1  DNA polymerase alpha catalytic subunit isoform X2

  2. XM_054327245.1 → XP_054183220.1  DNA polymerase alpha catalytic subunit isoform X1

  3. XM_054327247.1 → XP_054183222.1  DNA polymerase alpha catalytic subunit isoform X3

  4. XM_054327248.1 → XP_054183223.1  DNA polymerase alpha catalytic subunit isoform X4

  5. XM_054327249.1 → XP_054183224.1  DNA polymerase alpha catalytic subunit isoform X5

  6. XM_054327252.1 → XP_054183227.1  DNA polymerase alpha catalytic subunit isoform X7

  7. XM_054327253.1 → XP_054183228.1  DNA polymerase alpha catalytic subunit isoform X8

  8. XM_054327254.1 → XP_054183229.1  DNA polymerase alpha catalytic subunit isoform X9

  9. XM_054327250.1 → XP_054183225.1  DNA polymerase alpha catalytic subunit isoform X6

  10. XM_054327251.1 → XP_054183226.1  DNA polymerase alpha catalytic subunit isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09884.2 GenPept UniProtKB/Swiss-Prot:P09884

Gene LinkOut

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