Human Gene PRIM1 (ENST00000672280.1) from GENCODE V44
  Description: DNA primase subunit 1 (from HGNC PRIM1)
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: ENST00000672280.1
Gencode Gene: ENSG00000198056.16
Transcript (Including UTRs)
   Position: hg38 chr12:56,731,296-56,752,374 Size: 21,079 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr12:56,731,715-56,752,298 Size: 20,584 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureOther SpeciesmRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 09:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:56,731,296-56,752,374)mRNA (may differ from genome)Protein (459 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold

-  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 -29.0076-0.382 Picture PostScript Text
3' UTR -127.30419-0.304 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.

-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  JD112109 - Sequence 93133 from Patent EP1572962.
JD112108 - Sequence 93132 from Patent EP1572962.
JD512583 - Sequence 493607 from Patent EP1572962.
JD412655 - Sequence 393679 from Patent EP1572962.
JD197732 - Sequence 178756 from Patent EP1572962.
JD212328 - Sequence 193352 from Patent EP1572962.
JD212327 - Sequence 193351 from Patent EP1572962.
JD512581 - Sequence 493605 from Patent EP1572962.
JD412654 - Sequence 393678 from Patent EP1572962.
JD140086 - Sequence 121110 from Patent EP1572962.
JD542521 - Sequence 523545 from Patent EP1572962.
JD409681 - Sequence 390705 from Patent EP1572962.
JD497644 - Sequence 478668 from Patent EP1572962.
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.
JD265858 - Sequence 246882 from Patent EP1572962.
JD063862 - Sequence 44886 from Patent EP1572962.
JD265857 - Sequence 246881 from Patent EP1572962.
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

-  Other Names for This Gene
  Alternate Gene Symbols: A0A5F9ZHB6, BC005266, uc288lla.1
UCSC ID: ENST00000672280.1
RefSeq Accession: NM_000946

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