Human Gene PRIM1 (ENST00000338193.11) from GENCODE V41
  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: ENSG00000198056.15
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 CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2022-05-14 09:57:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:56,731,580-56,752,323)mRNA (may differ from genome)Protein (420 aa)
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-  Comments and Description Text from UniProtKB
  ID: PRI1_HUMAN
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.

-  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
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-  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
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AlignmentAlignmentAlignmentAlignmentAlignmentAlignment

-  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.