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Aliases for PRIM1 Gene

Aliases for PRIM1 Gene

  • DNA Primase Subunit 1 2 3
  • Primase (DNA) Subunit 1 2 3 5
  • Primase, DNA, Polypeptide 1 (49kDa) 2 3
  • DNA Primase 49 KDa Subunit 3 4
  • 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
  • EC 2.7.7 58

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 DNA Damage and E2F mediated regulation of DNA replication. 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

Regulatory Elements for PRIM1 Gene

Enhancers for PRIM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H056220 1.4 ENCODE dbSUPER 34.9 +529.5 529492 5 MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 SP3 ZC3H11A NEMP1 BAZ2A PAN2 DNAJC14 ZBTB39 ANKRD52 PHC1P1 TMEM198B ENSG00000258317 ZC3H10
GH12H056114 1.5 ENCODE dbSUPER 21.6 +634.1 634050 6 MLX ZFP64 DMAP1 YBX1 YY1 ZNF143 SP3 NFYC MEF2D SSRP1 BAZ2A NEMP1 DNAJC14 ZC3H10 RN7SL809P ENSG00000258317 ANKRD52 SMARCC2 RNU6-343P PYM1
GH12H057487 1.4 ENCODE dbSUPER 22.9 -736.3 -736290 2 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF766 ZNF416 ZNF207 NEMP1 BAZ2A MBD6 RN7SL809P PRIM1 EEF1AKMT3 CDK4 ENSG00000224713 NAB2 ZBTB39
GH12H056683 1.8 FANTOM5 ENCODE dbSUPER 17.2 +65.6 65602 7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC BAZ2A NEMP1 ZC3H10 ENSG00000258317 RN7SL809P DNAJC14 PYM1 RNU6-343P MBD6 STAT2
GH12H057109 1.5 ENCODE dbSUPER 19.5 -358.9 -358881 3 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 MCM3 MEF2D SSRP1 NEMP1 BAZ2A EEF1AKMT3 ENSG00000257740 SMARCC2 CDK4 CTDSP2 PAN2 ANKRD52 DTX3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PRIM1 on UCSC Golden Path with GeneCards custom track

Promoters for PRIM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000052547 373 1600 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 SP3 MXD4 REST

Genomic Location for PRIM1 Gene

Chromosome:
12
Start:
56,731,580 bp from pter
End:
56,752,373 bp from pter
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

Selected DME Specific Peptides for PRIM1 Gene

P49642:
  • NHLLKSPF
  • ELVFDID
  • LWVYSGRRG

Post-translational modifications for PRIM1 Gene

  • Ubiquitination at Lys95, isoforms=130, isoforms=147, isoforms=153, isoforms=193, Lys207, Lys261, and isoforms=377
  • Modification sites at PhosphoSitePlus

Other Protein References 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

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
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 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 IBA,IEA --
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

Clone Products

  • Applied Biological Materials Clones for PRIM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 IDA 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
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
Thymidine 5'-triphosphate
  • 2'-Deoxythymidine 5'-triphosphate
  • 2'-Deoxythymidine triphosphate
  • 5'-TTP
  • 5-Methyl-dUTP
  • Deoxy-TTP
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

Unigene Clusters for PRIM1 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PRIM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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, PaxDb, 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

Primer Products

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 33 34
  • 99.84 (n)
dog
(Canis familiaris)
Mammalia PRIM1 33 34
  • 91.79 (n)
cow
(Bos Taurus)
Mammalia PRIM1 33 34
  • 91.23 (n)
mouse
(Mus musculus)
Mammalia Prim1 33 16 34
  • 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 33 34
  • 66.1 (n)
wufa12c04 33
fruit fly
(Drosophila melanogaster)
Insecta DNApol-alpha50 35 33 34
  • 51.58 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006065 33
  • 51.26 (n)
worm
(Caenorhabditis elegans)
Secernentea T24C4.5 35 33 34
  • 47.94 (n)
pri-1 35 34
  • 38 (a)
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 33 34 36
  • 47.17 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons POLA3 33
  • 52.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7258 34
  • 50 (a)
OneToOne
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)

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 Sequence Context AA Info Type
rs1000114124 -- 56,748,559(+) GAGGC(A/G)GAGGC intron-variant
rs1000194776 -- 56,737,639(+) CCATC(A/C/G)CGCCT intron-variant
rs1000203005 -- 56,737,967(+) TGATT(C/T)GCCTG intron-variant
rs1000392825 -- 56,752,393(+) GCCGA(A/G)GTCGG upstream-variant-2KB
rs1000778054 -- 56,754,079(+) CTAGA(C/G)TGGGC intron-variant, upstream-variant-2KB

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)

Relevant External Links for PRIM1 Gene

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

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

Disorders for PRIM1 Gene

Relevant External Links for PRIM1

Genetic Association Database (GAD)
PRIM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 60
  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 45 60
  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 60
  5. Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma. (PMID: 10441007) Yotov WV … Levy E (Genes, chromosomes & cancer 1999) 3 22 60

Products for PRIM1 Gene

Sources for PRIM1 Gene

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