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Aliases for PRIM2 Gene

Aliases for PRIM2 Gene

  • DNA Primase Subunit 2 2 3 5
  • Primase, DNA, Polypeptide 2 (58kDa) 2 3
  • DNA Primase 58 KDa Subunit 3 4
  • Primase (DNA) Subunit 2 2 3
  • PRIM2A 3 4
  • P58 3 4
  • Primase, Polypeptide 2A (58kD) 2
  • Primase, Polypeptide 2A, 58kDa 2
  • DNA Primase Large Subunit 3
  • EC 2.7.7.- 4

External Ids for PRIM2 Gene

Previous HGNC Symbols for PRIM2 Gene

  • PRIM2A

Previous GeneCards Identifiers for PRIM2 Gene

  • GC06P057287
  • GC06P057179
  • GC06P057016

Summaries for PRIM2 Gene

Entrez Gene Summary for PRIM2 Gene

  • 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]

GeneCards Summary for PRIM2 Gene

PRIM2 (DNA Primase Subunit 2) is a Protein Coding gene. Among its related pathways are Telomere C-strand (Lagging Strand) Synthesis and Cell Cycle, Mitotic. Gene Ontology (GO) annotations related to this gene include 4 iron, 4 sulfur cluster binding and DNA primase activity.

UniProtKB/Swiss-Prot for PRIM2 Gene

  • DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.

Gene Wiki entry for PRIM2 Gene

Additional gene information for PRIM2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRIM2 Gene

Genomics for PRIM2 Gene

GeneHancer (GH) Regulatory Elements for PRIM2 Gene

Promoters and enhancers for PRIM2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J057312 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE 686.9 +0.5 549 6.4 PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 ZNF2 IRF4 PRIM2 BEND6 ZNF451-AS1 BAG2 DST RAB23 GC06P057297 GC06M057367
GH06J057045 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.3 -267.8 -267817 2 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 KIAA1586 ZNF451 GC06M057041 PRIM2 BEND6 BAG2 ZNF451-AS1 ENSG00000272316 PIR59769
GH06J056765 Enhancer 1.3 Ensembl ENCODE dbSUPER 36.2 -547.6 -547642 2.8 PKNOX1 ZFP64 BATF RAD21 ZNF213 ATF7 FOS ETV6 BCLAF1 IKZF2 ZNF451 PRIM2 KIAA1586 BEND6 LOC101930010 ZNF451-AS1 DST GC06M056744 GC06P056805
GH06J057220 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 19.4 -93.0 -92984 3 SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZBTB7B YY1 POLR2B ZNF213 ZNF207 RAB23 PRIM2 RBBP4P4 BEND6 POM121L14P GC06M057222 ZNF451-AS1
GH06J057089 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.8 -224.6 -224603 2.4 HDGF PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 GC06M057088 ZNF451 BEND6 KIAA1586 PRIM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRIM2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRIM2 gene promoter:
  • STAT5A
  • Pbx1a
  • IRF-7A
  • ATF-2
  • Spz1
  • COMP1
  • STAT3
  • FOXJ2 (long isoform)
  • FOXJ2
  • E2F

Genomic Locations for PRIM2 Gene

Genomic Locations for PRIM2 Gene
332,046 bases
Plus strand
333,773 bases
Plus strand

Genomic View for PRIM2 Gene

Genes around PRIM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRIM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRIM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRIM2 Gene

Proteins for PRIM2 Gene

  • Protein details for PRIM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    DNA primase large subunit
    Protein Accession:
    Secondary Accessions:
    • Q53FJ8
    • Q6P1Q7
    • Q8WVL2
    • Q9H413

    Protein attributes for PRIM2 Gene

    509 amino acids
    Molecular mass:
    58806 Da
    Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
    Quaternary structure:
    • Heterodimer of a small subunit and a large subunit.

    Three dimensional structures from OCA and Proteopedia for PRIM2 Gene

    Alternative splice isoforms for PRIM2 Gene


neXtProt entry for PRIM2 Gene

Post-translational modifications for PRIM2 Gene

  • Ubiquitination at posLast=416416, posLast=402402, Lys395, Lys139, posLast=6565, and Lys54
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PRIM2 Gene

Domains & Families for PRIM2 Gene

Gene Families for PRIM2 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PRIM2 Gene

Suggested Antigen Peptide Sequences for PRIM2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the eukaryotic-type primase large subunit family.
  • Belongs to the eukaryotic-type primase large subunit family.
genes like me logo Genes that share domains with PRIM2: view

Function for PRIM2 Gene

Molecular function for PRIM2 Gene

UniProtKB/Swiss-Prot Function:
DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.

Enzyme Numbers (IUBMB) for PRIM2 Gene

Phenotypes From GWAS Catalog for PRIM2 Gene

Gene Ontology (GO) - Molecular Function for PRIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding IBA --
GO:0003887 DNA-directed DNA polymerase activity IBA --
GO:0003896 contributes_to DNA primase activity IEA,IBA --
GO:0003899 DNA-directed 5-3 RNA polymerase activity IEA --
genes like me logo Genes that share ontologies with PRIM2: view
genes like me logo Genes that share phenotypes with PRIM2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRIM2

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRIM2 Gene

Localization for PRIM2 Gene

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005658 alpha DNA polymerase:primase complex IBA --
genes like me logo Genes that share ontologies with PRIM2: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from COMPARTMENTS for PRIM2 Gene

Pathways & Interactions for PRIM2 Gene

genes like me logo Genes that share pathways with PRIM2: view

Gene Ontology (GO) - Biological Process for PRIM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle TAS --
GO:0006260 DNA replication IEA --
GO:0006269 DNA replication, synthesis of RNA primer IEA --
GO:0006270 DNA replication initiation TAS --
GO:0032201 telomere maintenance via semi-conservative replication TAS --
genes like me logo Genes that share ontologies with PRIM2: view

No data available for SIGNOR curated interactions for PRIM2 Gene

Drugs & Compounds for PRIM2 Gene

(4) Drugs for PRIM2 Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
dATP Experimental Pharma Full agonist, Agonist 0
dctp Experimental Pharma 0
dgtp Experimental Pharma 0
Fludarabine Phosphate (Fludara) Pharma Inhibits STAT1 activation and DNA synthesis 0

(2) Additional Compounds for PRIM2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
Thymidine 5'-triphosphate
  • 2'-Deoxythymidine triphosphate
  • 5'-TTP
  • Deoxy-TTP
  • Deoxythymidine 5'-triphosphate
  • Deoxythymidine triphosphate
genes like me logo Genes that share compounds with PRIM2: view

Transcripts for PRIM2 Gene

Unigene Clusters for PRIM2 Gene

Primase, DNA, polypeptide 2 (58kDa):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRIM2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRIM2 Gene

No ASD Table

Relevant External Links for PRIM2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRIM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRIM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRIM2 Gene

This gene is overexpressed in Cervix (28.6), CD8 Tcells (23.6), and CD4 Tcells (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRIM2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRIM2 Gene:


SOURCE GeneReport for Unigene cluster for PRIM2 Gene:

genes like me logo Genes that share expression patterns with PRIM2: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRIM2 Gene

Orthologs for PRIM2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRIM2 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia PRIM2 34 33
  • 90.93 (n)
(Bos Taurus)
Mammalia PRIM2 34 33
  • 87.32 (n)
(Rattus norvegicus)
Mammalia Prim2 33
  • 84.44 (n)
(Mus musculus)
Mammalia Prim2 16 34 33
  • 84.36 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 69 (a)
-- 34
  • 60 (a)
-- 34
  • 22 (a)
-- 34
  • 8 (a)
(Monodelphis domestica)
Mammalia PRIM2 34
  • 54 (a)
(Gallus gallus)
Aves PRIM2 34 33
  • 69.43 (n)
(Anolis carolinensis)
Reptilia PRIM2 34
  • 41 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prim2 33
  • 62.8 (n)
Str.15796 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7459 33
(Danio rerio)
Actinopterygii zgc:110727 33
  • 67.16 (n)
PRIM2 34
  • 44 (a)
anxa1c 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2459 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006387 33
  • 47.12 (n)
fruit fly
(Drosophila melanogaster)
Insecta DNApol-alpha60 34 33
  • 47 (n)
(Caenorhabditis elegans)
Secernentea pri-2 34 33
  • 49.15 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRI2 34 33
  • 47.05 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04818g 33
  • 46.67 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR056C 33
  • 41.25 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G67320 33
  • 50.82 (n)
(Oryza sativa)
Liliopsida Os07g0406800 33
  • 50.08 (n)
Os.11383 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes spp2 33
  • 49.52 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU04646 33
  • 45.63 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4944 34
  • 31 (a)
Cin.9000 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9000 33
Species where no ortholog for PRIM2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PRIM2 Gene

Gene Tree for PRIM2 (if available)
Gene Tree for PRIM2 (if available)
Evolutionary constrained regions (ECRs) for PRIM2: view image

Paralogs for PRIM2 Gene Pseudogenes for PRIM2 Gene

genes like me logo Genes that share paralogs with PRIM2: view

No data available for Paralogs for PRIM2 Gene

Variants for PRIM2 Gene

Sequence variations from dbSNP and Humsavar for PRIM2 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000004170 -- 57,383,656(+) G/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000010060 -- 57,334,781(+) A/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000078177 -- 57,335,897(+) G/A genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000109874 -- 57,339,525(+) A/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000146286 -- 57,456,696(+) T/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PRIM2 Gene

Variant ID Type Subtype PubMed ID
dgv10677n54 CNV gain 21841781
dgv109n16 CNV deletion 17901297
dgv1184e214 CNV gain 21293372
dgv1185e214 CNV gain 21293372
dgv1782e212 CNV gain 25503493
dgv32e194 CNV deletion 18987734
dgv3320n106 CNV duplication 24896259
dgv3321n106 CNV deletion 24896259
dgv3322n106 CNV deletion 24896259
dgv3323n106 CNV duplication 24896259
dgv3324n106 CNV deletion 24896259
dgv5967n100 CNV gain 25217958
dgv5968n100 CNV gain 25217958
dgv5969n100 CNV gain 25217958
esv1002659 CNV deletion 20482838
esv1005755 CNV deletion 20482838
esv1007913 CNV deletion 20482838
esv1930914 CNV deletion 18987734
esv22079 CNV gain 19812545
esv2408738 CNV deletion 18987734
esv2453782 CNV gain 19546169
esv2579565 CNV deletion 19546169
esv2591679 CNV deletion 19546169
esv2635100 CNV deletion 19546169
esv2732129 CNV deletion 23290073
esv2732130 CNV deletion 23290073
esv2732131 CNV deletion 23290073
esv2732132 CNV deletion 23290073
esv2759432 CNV gain 17122850
esv3286162 CNV deletion 24192839
esv3286273 CNV deletion 24192839
esv3309145 CNV mobile element insertion 20981092
esv3327194 CNV insertion 20981092
esv3388764 CNV insertion 20981092
esv3391992 CNV insertion 20981092
esv3539788 CNV deletion 23714750
esv3539793 CNV deletion 23714750
esv3539794 CNV deletion 23714750
esv3571096 CNV loss 25503493
esv3609117 CNV gain 21293372
esv3609125 CNV loss 21293372
esv3609126 CNV gain 21293372
esv6364 CNV loss 19470904
esv9696 CNV loss 19470904
esv988239 CNV deletion 20482838
nsv1073981 CNV deletion 25765185
nsv1073982 CNV deletion 25765185
nsv1074934 CNV deletion 25765185
nsv1077472 CNV duplication 25765185
nsv1077473 CNV duplication 25765185
nsv1077474 CNV duplication 25765185
nsv1109779 CNV deletion 24896259
nsv1117624 CNV deletion 24896259
nsv1124065 CNV deletion 24896259
nsv1124066 CNV deletion 24896259
nsv1128237 CNV deletion 24896259
nsv1131967 CNV deletion 24896259
nsv1131968 CNV deletion 24896259
nsv1137083 CNV deletion 24896259
nsv1137085 CNV deletion 24896259
nsv1139861 CNV duplication 24896259
nsv1140634 CNV deletion 24896259
nsv1140635 CNV deletion 24896259
nsv1140636 CNV deletion 24896259
nsv1145967 CNV duplication 26484159
nsv1147971 CNV duplication 26484159
nsv1149095 CNV duplication 26484159
nsv1150365 CNV duplication 26484159
nsv1161384 CNV duplication 26073780
nsv349821 CNV deletion 16902084
nsv435841 CNV deletion 17901297
nsv436502 CNV deletion 17901297
nsv470820 CNV gain 18288195
nsv473987 CNV novel sequence insertion 20440878
nsv476390 CNV novel sequence insertion 20440878
nsv477791 CNV novel sequence insertion 20440878
nsv510916 OTHER complex 20534489
nsv511884 CNV loss 21212237
nsv511885 CNV loss 21212237
nsv515916 CNV gain+loss 19592680
nsv528053 CNV loss 19592680
nsv603193 CNV gain 21841781
nsv818418 CNV gain 17921354
nsv950183 CNV duplication 24416366
nsv950184 CNV duplication 24416366
nsv955793 CNV deletion 24416366
nsv955948 CNV deletion 24416366
nsv956536 CNV deletion 24416366
nsv969404 CNV duplication 23825009
nsv970125 CNV duplication 23825009
nsv981147 CNV duplication 23825009

Variation tolerance for PRIM2 Gene

Gene Damage Index Score: 1.50; 29.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRIM2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRIM2 Gene

Disorders for PRIM2 Gene

Additional Disease Information for PRIM2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PRIM2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRIM2 Gene

Publications for PRIM2 Gene

  1. An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase. (PMID: 17893144) Weiner BE … Chazin WJ (The Journal of biological chemistry 2007) 3 4 22 58
  2. Assignment of the 49-kDa (PRIM1) and 58-kDa (PRIM2A and PRIM2B) subunit genes of the human DNA primase to chromosome bands 1q44 and 6p11.1-p12. (PMID: 8530050) Shiratori A … Miyazawa H (Genomics 1995) 2 3 22 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. The genomic distribution and local context of coincident SNPs in human and chimpanzee. (PMID: 20675616) Hodgkinson A … Eyre-Walker A (Genome biology and evolution 2010) 2 3 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PRIM2 Gene

Sources for PRIM2 Gene

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