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    PRIM2 DNA primase subunit 2 [ Homo sapiens (human) ]

    Gene ID: 5558, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PRIM2provided by HGNC
    Official Full Name
    DNA primase subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:9370
    See related
    Ensembl:ENSG00000146143 MIM:176636; AllianceGenome:HGNC:9370
    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
    p58; PRIM2A
    Summary
    This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in prostate (RPKM 6.3), lymph node (RPKM 1.3) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PRIM2 in Genome Data Viewer
    Location:
    6p11.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (57221540..57646850)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (57060566..57485715)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (57179603..57513376)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ZNF451 regulatory antisense RNA 1 Neighboring gene zinc finger protein 451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:57037271-57038028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17304 Neighboring gene BAG cochaperone 2 Neighboring gene RAB23, member RAS oncogene family Neighboring gene long intergenic non-protein coding RNA 3001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:57211753-57212253 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:57288076-57288610 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:57288611-57289144 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:57298773-57298947 Neighboring gene microRNA 548u Neighboring gene uncharacterized LOC105375103 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:58146291-58147490 Neighboring gene uncharacterized LOC105375102 Neighboring gene tRNA-Ala (anticodon AGC) 24-1 Neighboring gene tRNA-Ile (anticodon AAT) 1-1

    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. XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase. Lévy N, et al. Nucleic Acids Res, 2009 Jun. PMID 19305001, Free PMC Article
    2. Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs. Holt ME, et al. PLoS One, 2018. PMID 30562384, Free PMC Article
    3. Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells. Chung J, et al. Epigenetics, 2012 May. PMID 22437878, Free PMC Article
    4. Crystal structure of the C-terminal domain of human DNA primase large subunit: implications for the mechanism of the primase-polymerase α switch. Agarkar VB, et al. Cell Cycle, 2011 Mar 15. PMID 21346410, Free PMC Article
    5. The genomic distribution and local context of coincident SNPs in human and chimpanzee. Hodgkinson A, et al. Genome Biol Evol, 2010. PMID 20675616, Free PMC Article

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRIM2: A Marker of MYC-driven Hyper-proliferation, Disease Progression, Tumor Aggressiveness and Poor Survival in Glioma Patients.
      Title: PRIM2: A Marker of MYC-driven Hyper-proliferation, Disease Progression, Tumor Aggressiveness and Poor Survival in Glioma Patients.
    2. Genetic variants of CHEK1, PRIM2 and CDK6 in the mitotic phase-related pathway are associated with nonsmall cell lung cancer survival.
      Title: Genetic variants of CHEK1, PRIM2 and CDK6 in the mitotic phase-related pathway are associated with nonsmall cell lung cancer survival.
    3. Study results show that although human DNA primase C-terminal domain (p58C) can be stabilized in different conformations in the crystalline state, in solution there is effectively no difference in the structure and functional properties of p58C constructs of different lengths.
      Title: Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs.
    4. Data suggest that PRIM1-p58,C-terminal domain stays bound to initiating NTP and 3prime-overhang DNA during whole cycle of RNA primer synthesis; meanwhile, PRIM1-p49 slides along DNA template toward 5prime-end with PRIM1-p58,N-terminal domain attached.
      Title: Insight into the Human DNA Primase Interaction with Template-Primer.
    5. Data indicate that the conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis.
      Title: Crystal structure of the human primase.
    6. the N-terminal domain of the large subunit of primase (p58N) directly interacts with the C-terminal domain of the catalytic subunit of polalpha (p180C)
      Title: The C-terminal domain of the DNA polymerase catalytic subunit regulates the primase and polymerase activities of the human DNA polymerase α-primase complex.
    7. PRIM2 gene is not imprinted in the placenta.
      Title: Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells.
    8. The fragment that forms a beta-sheet in the reported structure p58C/3L9Q of the same human primase domain is folded in three alpha-helices in our p58C/3Q36 structure, similarly to yeast primase.
      Title: Crystal structure of the C-terminal domain of human DNA primase large subunit: implications for the mechanism of the primase-polymerase α switch.
    9. p58C(C-terminal regulatory domain of the large subunit) structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure.
      Title: Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase.
    10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • MGC75142

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 4 iron, 4 sulfur cluster binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA/RNA hybrid binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA replication initiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA replication initiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA replication, synthesis of primer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA replication, synthesis of primer IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA replication, synthesis of primer ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA primase activity 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 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    DNA primase large subunit
    Names
    DNA primase 58 kDa subunit
    primase (DNA) subunit 2
    primase, DNA, polypeptide 2 (58kDa)
    NP_000938.2
    NP_001269416.1
    NP_001269417.1
    XP_047274943.1
    XP_047274944.1
    XP_047274945.1
    XP_047274946.1
    XP_047274947.1
    XP_047274948.1
    XP_047274949.1
    XP_054211783.1
    XP_054211784.1
    XP_054211785.1
    XP_054211786.1
    XP_054211787.1
    XP_054211788.1
    XP_054211789.1

    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_034261.2 RefSeqGene

      Range
      101092..430312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000947.5 → NP_000938.2  DNA primase large subunit isoform a

      See identical proteins and their annotated locations for NP_000938.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      BC017833, BC064931
      Consensus CDS
      CCDS75476.1
      UniProtKB/Swiss-Prot
      P49643, Q53FJ8, Q6P1Q7, Q8WVL2, Q9H413
      UniProtKB/TrEMBL
      A8K7A0
      Related
      ENSP00000484105.1, ENST00000615550.5
      Conserved Domains (1) summary
      cd07322
      Location:28 → 451
      PriL_PriS_Eukaryotic; Eukaryotic core primase: Large subunit, PriL

    2. NM_001282487.2 → NP_001269416.1  DNA primase large subunit isoform b

      See identical proteins and their annotated locations for NP_001269416.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks multiple 3' coding exons and its 3' terminal exon extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AL121975, BC017833
      Consensus CDS
      CCDS75477.1
      UniProtKB/TrEMBL
      A0A5F9ZHR0
      Related
      ENSP00000485304.1, ENST00000274891.10
      Conserved Domains (1) summary
      cl11970
      Location:28 → 155
      PriL; Archaeal/eukaryotic core primase: Large subunit, PriL

    3. NM_001282488.2 → NP_001269417.1  DNA primase large subunit isoform b

      See identical proteins and their annotated locations for NP_001269417.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks multiple 3' coding exons, and its 3' terminal exon extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AL121975, BC017833, BI547222
      Consensus CDS
      CCDS75477.1
      UniProtKB/TrEMBL
      A0A5F9ZHR0
      Related
      ENSP00000483201.1, ENST00000370687.6
      Conserved Domains (1) summary
      cl11970
      Location:28 → 155
      PriL; Archaeal/eukaryotic core primase: Large subunit, PriL

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      57221540..57646850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418987.1 → XP_047274943.1  DNA primase large subunit isoform X1

      UniProtKB/Swiss-Prot
      P49643, Q53FJ8, Q6P1Q7, Q8WVL2, Q9H413
      UniProtKB/TrEMBL
      A8K7A0

    2. XM_047418988.1 → XP_047274944.1  DNA primase large subunit isoform X2

      UniProtKB/TrEMBL
      A8K7A0

    3. XM_047418990.1 → XP_047274946.1  DNA primase large subunit isoform X4

    4. XM_047418989.1 → XP_047274945.1  DNA primase large subunit isoform X3

    5. XM_047418992.1 → XP_047274948.1  DNA primase large subunit isoform X6

    6. XM_047418993.1 → XP_047274949.1  DNA primase large subunit isoform X7

    7. XM_047418991.1 → XP_047274947.1  DNA primase large subunit isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      57060566..57485715
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355808.1 → XP_054211783.1  DNA primase large subunit isoform X1

      UniProtKB/Swiss-Prot
      P49643, Q53FJ8, Q6P1Q7, Q8WVL2, Q9H413
      UniProtKB/TrEMBL
      A8K7A0

    2. XM_054355809.1 → XP_054211784.1  DNA primase large subunit isoform X2

      UniProtKB/TrEMBL
      A8K7A0

    3. XM_054355811.1 → XP_054211786.1  DNA primase large subunit isoform X4

    4. XM_054355810.1 → XP_054211785.1  DNA primase large subunit isoform X3

    5. XM_054355813.1 → XP_054211788.1  DNA primase large subunit isoform X6

    6. XM_054355814.1 → XP_054211789.1  DNA primase large subunit isoform X7

    7. XM_054355812.1 → XP_054211787.1  DNA primase large subunit isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P49643.2 GenPept UniProtKB/Swiss-Prot:P49643

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