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

Gene ID: 5558, updated on 5-Nov-2017
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; Vega:OTTHUMG00000016190
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]
Orthologs
Location:
6p11.2
Exon count:
19
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (57314805..57646852)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RAB23, member RAS oncogene family Neighboring gene uncharacterized LOC100506188 Neighboring gene microRNA 548u Neighboring gene uncharacterized LOC105375103 Neighboring gene transfer RNA-Ile (AAT) 1-1

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI 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.
NHGRI GWA Catalog
  • Activation of the pre-replicative complex, organism-specific biosystem (from REACTOME)
    Activation of the pre-replicative complex, organism-specific biosystemIn S. cerevisiae, two ORC subunits, Orc1 and Orc5, both bind ATP, and Orc1 in addition has ATPase activity. Both ATP binding and ATP hydrolysis appear to be essential functions in vivo. ATP binding b...
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Chromosome Maintenance, organism-specific biosystem (from REACTOME)
    Chromosome Maintenance, organism-specific biosystemChromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
  • DNA Replication, organism-specific biosystem (from REACTOME)
    DNA Replication, organism-specific biosystemStudies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyce...
  • DNA Replication, organism-specific biosystem (from WikiPathways)
    DNA Replication, organism-specific biosystemStudies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyce...
  • DNA Replication Pre-Initiation, organism-specific biosystem (from REACTOME)
    DNA Replication Pre-Initiation, organism-specific biosystemAlthough, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase.
  • DNA polymerase alpha / primase complex, organism-specific biosystem (from KEGG)
    DNA polymerase alpha / primase complex, organism-specific biosystemStructural complex; Genetic information processing; DNA polymerase
  • DNA polymerase alpha / primase complex, conserved biosystem (from KEGG)
    DNA polymerase alpha / primase complex, conserved biosystemStructural complex; Genetic information processing; DNA polymerase
  • DNA replication, organism-specific biosystem (from KEGG)
    DNA replication, organism-specific biosystemA complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (D...
  • DNA replication, conserved biosystem (from KEGG)
    DNA replication, conserved biosystemA complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (D...
  • DNA replication initiation, organism-specific biosystem (from REACTOME)
    DNA replication initiation, organism-specific biosystemDNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer...
  • DNA strand elongation, organism-specific biosystem (from REACTOME)
    DNA strand elongation, organism-specific biosystemAccurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replicat...
  • E2F mediated regulation of DNA replication, organism-specific biosystem (from REACTOME)
    E2F mediated regulation of DNA replication, organism-specific biosystemProgression through G1 and G1 to S-phase transition that initiates DNA synthesis involve many complexes that are regulated by RB1:E2F pathway. RB1:E2F pathway plays a key role in gene expression regu...
  • Extension of Telomeres, organism-specific biosystem (from REACTOME)
    Extension of Telomeres, organism-specific biosystemTelomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
  • G1 to S cell cycle control, organism-specific biosystem (from WikiPathways)
    G1 to S cell cycle control, organism-specific biosystemIn the G1 phase there are two types of DNA damage responses, the p53-dependent and the p53-independent pathways. The p53-dependent responses inhibit CDKs through the up-regulation of genes encoding C...
  • G1/S Transition, organism-specific biosystem (from REACTOME)
    G1/S Transition, organism-specific biosystemCyclin E - Cdk2 complexes control the transition from G1 into S-phase. In this case, the binding of p21Cip1/Waf1 or p27kip1 is inhibitory. Important substrates for Cyclin E - Cdk2 complexes include p...
  • Inhibition of replication initiation of damaged DNA by RB1/E2F1, organism-specific biosystem (from REACTOME)
    Inhibition of replication initiation of damaged DNA by RB1/E2F1, organism-specific biosystem
    Inhibition of replication initiation of damaged DNA by RB1/E2F1
  • Lagging Strand Synthesis, organism-specific biosystem (from REACTOME)
    Lagging Strand Synthesis, organism-specific biosystemDue to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching...
  • Leading Strand Synthesis, organism-specific biosystem (from REACTOME)
    Leading Strand Synthesis, organism-specific biosystemThe processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate....
  • M/G1 Transition, organism-specific biosystem (from REACTOME)
    M/G1 Transition, organism-specific biosystemFinally, progression out of mitosis and division of the cell into two daughters (cytokinesis) requires the inactivation of Cyclin B - Cdc2 by ubiquitin-dependent proteolysis of Cyclin A and B, which ...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Mitotic G1-G1/S phases, organism-specific biosystem (from REACTOME)
    Mitotic G1-G1/S phases, organism-specific biosystem
    Mitotic G1-G1/S phases
  • Polymerase switching, organism-specific biosystem (from REACTOME)
    Polymerase switching, organism-specific biosystemAfter the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tig...
  • Polymerase switching on the C-strand of the telomere, organism-specific biosystem (from REACTOME)
    Polymerase switching on the C-strand of the telomere, organism-specific biosystemAfter the primers are synthesized on the G-Rich strand, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic...
  • Processive synthesis on the lagging strand, organism-specific biosystem (from REACTOME)
    Processive synthesis on the lagging strand, organism-specific biosystemThe key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the laggi...
  • Purine metabolism, organism-specific biosystem (from KEGG)
    Purine metabolism, organism-specific biosystem
    Purine metabolism
  • Purine metabolism, conserved biosystem (from KEGG)
    Purine metabolism, conserved biosystem
    Purine metabolism
  • Pyrimidine metabolism, organism-specific biosystem (from KEGG)
    Pyrimidine metabolism, organism-specific biosystem
    Pyrimidine metabolism
  • Pyrimidine metabolism, conserved biosystem (from KEGG)
    Pyrimidine metabolism, conserved biosystem
    Pyrimidine metabolism
  • Removal of the Flap Intermediate, organism-specific biosystem (from REACTOME)
    Removal of the Flap Intermediate, organism-specific biosystemTwo endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer o...
  • S Phase, organism-specific biosystem (from REACTOME)
    S Phase, organism-specific biosystemDNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues,...
  • Synthesis of DNA, organism-specific biosystem (from REACTOME)
    Synthesis of DNA, organism-specific biosystemThe actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of ...
  • Telomere C-strand (Lagging Strand) Synthesis, organism-specific biosystem (from REACTOME)
    Telomere C-strand (Lagging Strand) Synthesis, organism-specific biosystemDue to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching...
  • Telomere C-strand synthesis initiation, organism-specific biosystem (from REACTOME)
    Telomere C-strand synthesis initiation, organism-specific biosystemDNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer...
  • Telomere Maintenance, organism-specific biosystem (from REACTOME)
    Telomere Maintenance, organism-specific biosystemTelomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (B...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC75142

Gene Ontology Provided by GOA

Function Evidence Code Pubs
4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to DNA primase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
DNA-directed DNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
DNA replication initiation TAS
Traceable Author Statement
more info
 
DNA replication, synthesis of RNA primer IEA
Inferred from Electronic Annotation
more info
 
G1/S transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 
telomere maintenance via semi-conservative replication TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
alpha DNA polymerase:primase complex IBA
Inferred from Biological aspect of Ancestor
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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_011513033.1
XP_016866493.1
XP_016866494.1
XP_016866495.1
XP_016866496.1

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_034261.1 RefSeqGene

    Range
    7813..337046
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000947.4NP_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
    Related
    ENSP00000484105.1, OTTHUMP00000277901, ENST00000615550.4, OTTHUMT00000043468
    Conserved Domains (2) summary
    cd07322
    Location:28451
    PriL_PriS_Eukaryotic; Eukaryotic core primase: Large subunit, PriL
    COG2219
    Location:26413
    PRI2; Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]
  2. NM_001282487.1NP_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)
    BC017833
    Consensus CDS
    CCDS75477.1
    UniProtKB/Swiss-Prot
    P49643
    UniProtKB/TrEMBL
    A0A024RD43
    Related
    ENSP00000485304.1, OTTHUMP00000277900, ENST00000274891.10, OTTHUMT00000043472
    Conserved Domains (1) summary
    cl11970
    Location:28155
    PriL; Archaeal/eukaryotic core primase: Large subunit, PriL
  3. NM_001282488.1NP_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)
    BC017833, BI547222
    Consensus CDS
    CCDS75477.1
    UniProtKB/Swiss-Prot
    P49643
    UniProtKB/TrEMBL
    A0A024RD43
    Related
    ENSP00000483201.1, OTTHUMP00000277899, ENST00000370687.6, OTTHUMT00000043471
    Conserved Domains (1) summary
    cl11970
    Location:28155
    PriL; Archaeal/eukaryotic core primase: Large subunit, PriL

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

    Range
    57314805..57646852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011004.1XP_016866493.1  DNA primase large subunit isoform X1

  2. XM_017011005.1XP_016866494.1  DNA primase large subunit isoform X2

  3. XM_017011006.1XP_016866495.1  DNA primase large subunit isoform X3

  4. XM_017011007.1XP_016866496.1  DNA primase large subunit isoform X5

  5. XM_011514731.2XP_011513033.1  DNA primase large subunit isoform X4

    Conserved Domains (1) summary
    cd07322
    Location:17236
    PriL_PriS_Eukaryotic; Eukaryotic core primase: Large subunit, PriL

Alternate CHM1_1.1

Genomic

  1. NC_018917.2 Alternate CHM1_1.1

    Range
    57179974..57645053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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