Human Gene PRIM1 (ENST00000338193.11) from GENCODE V44
  Description: Homo sapiens DNA primase subunit 1 (PRIM1), mRNA. (from RefSeq NM_000946)
RefSeq Summary (NM_000946): 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].
Gencode Transcript: ENST00000338193.11
Gencode Gene: ENSG00000198056.16
Transcript (Including UTRs)
   Position: hg38 chr12:56,731,580-56,752,323 Size: 20,744 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg38 chr12:56,731,715-56,752,298 Size: 20,584 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:56,731,580-56,752,323)mRNA (may differ from genome)Protein (420 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=DNA primase small subunit; EC=2.7.7.-; AltName: Full=DNA primase 49 kDa subunit; Short=p49;
FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.
SUBUNIT: 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).
SIMILARITY: Belongs to the eukaryotic-type primase small subunit family.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D010634 Phenobarbital
  • C006780 bisphenol A
  • C006253 pirinixic acid
  • C049325 1,2-dithiol-3-thione
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C023514 2,6-dinitrotoluene
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.62 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 130.89 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.4025-0.216 Picture PostScript Text
3' UTR -19.60135-0.145 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002755 - DNA_primase_S
IPR014052 - DNA_primase_ssu_euk/arc

Pfam Domains:
PF01896 - DNA primase small subunit

ModBase Predicted Comparative 3D Structure on P49642
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein SequenceProtein SequenceProtein Sequence Protein Sequence
AlignmentAlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003697 single-stranded DNA binding
GO:0003896 DNA primase activity
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0000082 G1/S transition of mitotic cell cycle
GO:0006260 DNA replication
GO:0006269 DNA replication, synthesis of RNA primer
GO:0032201 telomere maintenance via semi-conservative replication

Cellular Component:
GO:0005654 nucleoplasm
GO:0005658 alpha DNA polymerase:primase complex
GO:0016020 membrane

-  Descriptions from all associated GenBank mRNAs
  AK223391 - Homo sapiens mRNA for DNA primase small subunit, 49kDa variant, clone: FCC107C02.
X74330 - H.sapiens mRNA for DNA primase (subunit p48).
BC005266 - Homo sapiens primase, DNA, polypeptide 1 (49kDa), mRNA (cDNA clone MGC:12308 IMAGE:3686937), complete cds.
AK314866 - Homo sapiens cDNA, FLJ95767, highly similar to Homo sapiens primase, polypeptide 1, 49kDa (PRIM1), mRNA.
KJ891881 - Synthetic construct Homo sapiens clone ccsbBroadEn_01275 PRIM1 gene, encodes complete protein.
EU176421 - Synthetic construct Homo sapiens clone IMAGE:100006499; FLH193115.01X; RZPDo839D06252D primase, DNA, polypeptide 1 (49kDa) (PRIM1) gene, encodes complete protein.
EU176762 - Synthetic construct Homo sapiens clone IMAGE:100011533; FLH193111.01L; RZPDo839A02256D primase, DNA, polypeptide 1 (49kDa) (PRIM1) gene, encodes complete protein.
AB528338 - Synthetic construct DNA, clone: pF1KB0958, Homo sapiens PRIM1 gene for primase, DNA, polypeptide 1, without stop codon, in Flexi system.
CU675073 - Synthetic construct Homo sapiens gateway clone IMAGE:100017229 5' read PRIM1 mRNA.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa00240 - Pyrimidine metabolism
hsa01100 - Metabolic pathways
hsa03030 - DNA replication

Reactome (by CSHL, EBI, and GO)

Protein P49642 (Reactome details) participates in the following event(s):

R-HSA-68914 DNA polymerase alpha:primase binds at the origin
R-HSA-113504 Detection of damage during initiation of DNA synthesis in S-phase
R-HSA-174452 RFC binding displaces Pol Alpha on the C-strand of the telomere
R-HSA-68950 The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin
R-HSA-68913 The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin
R-HSA-174427 The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere
R-HSA-174425 The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere
R-HSA-69053 RFC binding displaces Pol Alpha
R-HSA-69063 Loading of PCNA - Sliding Clamp Formation
R-HSA-69074 Formation of Processive Complex
R-HSA-69068 RFC dissociates after sliding clamp formation
R-HSA-69116 Formation of Okazaki fragments
R-HSA-69127 Formation of the Flap Intermediate
R-HSA-69152 Removal of remaining Flap
R-HSA-69144 Removal of RNA primer and dissociation of RPA and Dna2
R-HSA-69140 RPA binds to the Flap
R-HSA-69142 Recruitment of Dna2 endonuclease
R-HSA-68962 Activation of the pre-replicative complex
R-HSA-113501 Inhibition of replication initiation of damaged DNA by RB1/E2F1
R-HSA-174411 Polymerase switching on the C-strand of the telomere
R-HSA-68952 DNA replication initiation
R-HSA-174430 Telomere C-strand synthesis initiation
R-HSA-69002 DNA Replication Pre-Initiation
R-HSA-69206 G1/S Transition
R-HSA-113510 E2F mediated regulation of DNA replication
R-HSA-174417 Telomere C-strand (Lagging Strand) Synthesis
R-HSA-69091 Polymerase switching
R-HSA-69239 Synthesis of DNA
R-HSA-68874 M/G1 Transition
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-180786 Extension of Telomeres
R-HSA-69109 Leading Strand Synthesis
R-HSA-69186 Lagging Strand Synthesis
R-HSA-69242 S Phase
R-HSA-69306 DNA Replication
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-157579 Telomere Maintenance
R-HSA-69183 Processive synthesis on the lagging strand
R-HSA-69190 DNA strand elongation
R-HSA-1640170 Cell Cycle
R-HSA-73886 Chromosome Maintenance
R-HSA-69166 Removal of the Flap Intermediate

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000338193.1, ENST00000338193.10, ENST00000338193.2, ENST00000338193.3, ENST00000338193.4, ENST00000338193.5, ENST00000338193.6, ENST00000338193.7, ENST00000338193.8, ENST00000338193.9, NM_000946, P49642, PRI1_HUMAN, uc001smd.1, uc001smd.2, uc001smd.3, uc001smd.4, uc001smd.5
UCSC ID: ENST00000338193.11
RefSeq Accession: NM_000946
Protein: P49642 (aka PRI1_HUMAN)
CCDS: CCDS44926.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.