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Aliases for PRIM1 Gene

Aliases for PRIM1 Gene

  • DNA Primase Subunit 1 2 3 5
  • Primase, DNA, Polypeptide 1 (49kDa) 2 3
  • DNA Primase 49 KDa Subunit 3 4
  • Primase (DNA) Subunit 1 2 3
  • P49 3 4
  • Primase Polypeptide 1, 49kDa 3
  • DNA Primase Small Subunit 3
  • DNA Primase Subunit 48 3
  • Primase P49 Subunit 3
  • DNA Primase 1 3
  • EC 2.7.7.- 4

External Ids for PRIM1 Gene

Previous GeneCards Identifiers for PRIM1 Gene

  • GC12M057097
  • GC12M057351
  • GC12M056842
  • GC12M055411
  • GC12M054164
  • GC12M057125

Summaries for PRIM1 Gene

Entrez Gene Summary for PRIM1 Gene

  • The replication of DNA in eukaryotic cells is carried out by a complex chromosomal replication apparatus, in which DNA polymerase alpha and primase are two key enzymatic components. Primase, which is a heterodimer of a small subunit and a large subunit, synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. The protein encoded by this gene is the small, 49 kDa primase subunit. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRIM1 Gene

PRIM1 (DNA Primase Subunit 1) 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 DNA primase activity.

UniProtKB/Swiss-Prot for PRIM1 Gene

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

Additional gene information for PRIM1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRIM1 Gene

Genomics for PRIM1 Gene

GeneHancer (GH) Regulatory Elements for PRIM1 Gene

Promoters and enhancers for PRIM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J056748 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 660.1 +1.4 1414 4.1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF213 E2F8 ZNF143 PRIM1 HSD17B6 BAZ2A MBD6 NEMP1 RN7SL809P CDK2 ZC3H10 TMEM198B DNAJC14
GH12J056114 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 44.5 +634.0 634049 6.8 CLOCK MLX ZFP64 DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZC3H10 RPL41 ESYT1 GC12M056121 PIR42205 ENSG00000258345 BAZ2A NEMP1 DNAJC14 RN7SL809P
GH12J057487 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 45.8 -736.3 -736290 2.9 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B ZNF766 ARHGAP9 MARS BAZ2A NEMP1 PRIM1 MBD6 ZBTB39 RN7SL809P DCTN2 EEF1AKMT3
GH12J056220 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 43.6 +529.5 529491 5.7 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 NABP2 RNF41 NEMP1 BAZ2A PAN2 DNAJC14 ZBTB39 RN7SL809P ZC3H10 PHC1P1
GH12J057109 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 33.4 -358.9 -358881 3.8 CLOCK FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF416 ZNF143 ZNF548 MCM3 STAT6 NEMP1 EEF1AKMT3 ENSG00000257740 BAZ2A PAN2 SMARCC2 CDK4 ANKRD52 DTX3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRIM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRIM1 gene promoter:
  • AP-1
  • PPAR-gamma2
  • PPAR-gamma1
  • STAT3
  • ATF-2
  • c-Jun
  • Sp1
  • RSRFC4
  • Brachyury

Genomic Locations for PRIM1 Gene

Genomic Locations for PRIM1 Gene
chr12:56,731,580-56,752,373
(GRCh38/hg38)
Size:
20,794 bases
Orientation:
Minus strand
chr12:57,125,364-57,146,157
(GRCh37/hg19)
Size:
20,794 bases
Orientation:
Minus strand

Genomic View for PRIM1 Gene

Genes around PRIM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRIM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRIM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRIM1 Gene

Proteins for PRIM1 Gene

  • Protein details for PRIM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49642-PRI1_HUMAN
    Recommended name:
    DNA primase small subunit
    Protein Accession:
    P49642

    Protein attributes for PRIM1 Gene

    Size:
    420 amino acids
    Molecular mass:
    49902 Da
    Quaternary structure:
    • Heterodimer of a small subunit and a large subunit.
    Miscellaneous:
    • The bound zinc ion is not a cofactor. It is bound to a zinc knuckle motif that may be involved in sequence recognition and the binding of ssDNA (By similarity).

    Three dimensional structures from OCA and Proteopedia for PRIM1 Gene

neXtProt entry for PRIM1 Gene

Post-translational modifications for PRIM1 Gene

  • Ubiquitination at posLast=377377, posLast=261261, Lys207, posLast=193193, posLast=153153, posLast=147147, posLast=130130, and Lys95
  • Modification sites at PhosphoSitePlus

Other Protein References for PRIM1 Gene

No data available for DME Specific Peptides for PRIM1 Gene

Domains & Families for PRIM1 Gene

Gene Families for PRIM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRIM1 Gene

Suggested Antigen Peptide Sequences for PRIM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P49642

UniProtKB/Swiss-Prot:

PRI1_HUMAN :
  • Belongs to the eukaryotic-type primase small subunit family.
Family:
  • Belongs to the eukaryotic-type primase small subunit family.
genes like me logo Genes that share domains with PRIM1: view

Function for PRIM1 Gene

Molecular function for PRIM1 Gene

UniProtKB/Swiss-Prot Function:
DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.
GENATLAS Biochemistry:
DNA primase 1,49kDa,replication protein catalyzing the synthesis of Okazaki fragments,smallest subunit of the pol alpha (POLA)/primare complex,amplified in osteosarcoma with CDK4,OS9 and SAS

Enzyme Numbers (IUBMB) for PRIM1 Gene

Phenotypes From GWAS Catalog for PRIM1 Gene

Gene Ontology (GO) - Molecular Function for PRIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003697 single-stranded DNA binding IBA --
GO:0003896 DNA primase activity IEA,IBA --
GO:0003899 DNA-directed 5-3 RNA polymerase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016779 nucleotidyltransferase activity IEA --
genes like me logo Genes that share ontologies with PRIM1: view
genes like me logo Genes that share phenotypes with PRIM1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PRIM1

CRISPR Products

miRNA for PRIM1 Gene

miRTarBase miRNAs that target PRIM1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRIM1

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRIM1 Gene

Localization for PRIM1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRIM1 gene
Compartment Confidence
nucleus 5
peroxisome 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRIM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005658 alpha DNA polymerase:primase complex IBA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with PRIM1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PRIM1 Gene

Pathways & Interactions for PRIM1 Gene

genes like me logo Genes that share pathways with PRIM1: view

Gene Ontology (GO) - Biological Process for PRIM1 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,IBA --
GO:0006270 DNA replication initiation TAS --
GO:0032201 telomere maintenance via semi-conservative replication TAS --
genes like me logo Genes that share ontologies with PRIM1: view

No data available for SIGNOR curated interactions for PRIM1 Gene

Drugs & Compounds for PRIM1 Gene

(4) Drugs for PRIM1 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 PRIM1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
14000-31-8
Thymidine 5'-triphosphate
  • 2'-Deoxythymidine triphosphate
  • 5'-TTP
  • Deoxy-TTP
  • Deoxythymidine 5'-triphosphate
  • Deoxythymidine triphosphate
365-08-2

(1) ApexBio Compounds for PRIM1 Gene

Compound Action Cas Number
Fludarabine Phosphate (Fludara) Inhibits STAT1 activation and DNA synthesis 75607-67-9
genes like me logo Genes that share compounds with PRIM1: view

Drug Products

Transcripts for PRIM1 Gene

mRNA/cDNA for PRIM1 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(109) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PRIM1 Gene

Primase, DNA, polypeptide 1 (49kDa):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRIM1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRIM1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - - -
SP2: - -
SP3: - -
SP4: - - - - -
SP5:

Relevant External Links for PRIM1 Gene

GeneLoc Exon Structure for
PRIM1
ECgene alternative splicing isoforms for
PRIM1

Expression for PRIM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRIM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRIM1 Gene

This gene is overexpressed in Fetal ovary (26.0), Testis (13.6), Fetal Liver (11.4), Fetal gut (7.9), and Lymph node (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRIM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of PRIM1 Gene:

PRIM1

SOURCE GeneReport for Unigene cluster for PRIM1 Gene:

Hs.534339

Evidence on tissue expression from TISSUES for PRIM1 Gene

  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with PRIM1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRIM1 Gene

Orthologs for PRIM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRIM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRIM1 34 33
  • 99.84 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PRIM1 34 33
  • 91.79 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PRIM1 34 33
  • 91.23 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Prim1 16 34 33
  • 87.05 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRIM1 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRIM1 33
  • 59.06 (n)
lizard
(Anolis carolinensis)
Reptilia PRIM1 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prim1 33
  • 69.14 (n)
Str.2884 33
African clawed frog
(Xenopus laevis)
Amphibia dnapol-alpha50-prov 33
zebrafish
(Danio rerio)
Actinopterygii prim1 34 33
  • 66.1 (n)
OneToOne
wufa12c04 33
fruit fly
(Drosophila melanogaster)
Insecta DNApol-alpha50 34 35 33
  • 51.58 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006065 33
  • 51.26 (n)
worm
(Caenorhabditis elegans)
Secernentea T24C4.5 34 35 33
  • 47.94 (n)
OneToMany
pri-1 34 35
  • 37 (a)
OneToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B11682g 33
  • 47.4 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR018W 33
  • 47.24 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRI1 36 34 33
  • 47.17 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons POLA3 33
  • 52.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7258 34
  • 50 (a)
OneToOne
Cin.9952 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes spp1 33
  • 48.84 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02232 33
  • 48.32 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9952 33
Species where no ortholog for PRIM1 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • 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 PRIM1 Gene

ENSEMBL:
Gene Tree for PRIM1 (if available)
TreeFam:
Gene Tree for PRIM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRIM1: view image

Paralogs for PRIM1 Gene

Pseudogenes.org Pseudogenes for PRIM1 Gene

genes like me logo Genes that share paralogs with PRIM1: view

No data available for Paralogs for PRIM1 Gene

Variants for PRIM1 Gene

Sequence variations from dbSNP and Humsavar for PRIM1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000114124 -- 56,748,559(-) G/A intron_variant
rs1000194776 -- 56,737,639(-) G/A/C intron_variant
rs1000203005 -- 56,737,967(-) T/C intron_variant
rs1000392825 -- 56,752,393(-) G/A upstream_transcript_variant
rs1000778054 -- 56,754,079(-) G/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PRIM1 Gene

Variant ID Type Subtype PubMed ID
nsv482992 CNV gain+loss 15286789

Variation tolerance for PRIM1 Gene

Residual Variation Intolerance Score: 80.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.23; 81.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRIM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRIM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRIM1 Gene

Disorders for PRIM1 Gene

Additional Disease Information for PRIM1

No disorders were found for PRIM1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRIM1 Gene

Publications for PRIM1 Gene

  1. Mapping of the human DNA primase 1 (PRIM1) to chromosome 12q13. (PMID: 9268648) Cloutier S … Yotov WV (Genomics 1997) 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. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PMID: 22267201) Stolk L … Lunetta KL (Nature genetics 2012) 3 44 58
  4. 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
  5. Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma. (PMID: 10441007) Yotov WV … Levy E (Genes, chromosomes & cancer 1999) 3 22 58

Products for PRIM1 Gene

Sources for PRIM1 Gene