PRIM2 DNA primase subunit 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRIM2provided by HGNC
Official Full Name: DNA primase subunit 2provided by HGNC
Primary source: HGNC:HGNC:9370
See related: Ensembl:ENSG00000146143 MIM:176636; AllianceGenome:HGNC:9370
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: p58; PRIM2A
Summary: This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. The encoded protein forms a heterodimer with a 49 kilodalton subunit. This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. Alternative splicing of this gene results in multiple transcript variants. This gene has a related pseudogene, which is also present on chromosome 6. [provided by RefSeq, Apr 2014]
Expression: Broad expression in prostate (RPKM 6.3), lymph node (RPKM 1.3) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p11.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (57221540..57646850)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (57060566..57485715)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (57179603..57513376)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PRIM2: A Marker of MYC-driven Hyper-proliferation, Disease Progression, Tumor Aggressiveness and Poor Survival in Glioma Patients.
Title: PRIM2: A Marker of MYC-driven Hyper-proliferation, Disease Progression, Tumor Aggressiveness and Poor Survival in Glioma Patients.
Genetic variants of CHEK1, PRIM2 and CDK6 in the mitotic phase-related pathway are associated with nonsmall cell lung cancer survival.
Title: Genetic variants of CHEK1, PRIM2 and CDK6 in the mitotic phase-related pathway are associated with nonsmall cell lung cancer survival.
Study results show that although human DNA primase C-terminal domain (p58C) can be stabilized in different conformations in the crystalline state, in solution there is effectively no difference in the structure and functional properties of p58C constructs of different lengths.
Title: Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs.
Data suggest that PRIM1-p58,C-terminal domain stays bound to initiating NTP and 3prime-overhang DNA during whole cycle of RNA primer synthesis; meanwhile, PRIM1-p49 slides along DNA template toward 5prime-end with PRIM1-p58,N-terminal domain attached.
Title: Insight into the Human DNA Primase Interaction with Template-Primer.
Data indicate that the conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis.
Title: Crystal structure of the human primase.
the N-terminal domain of the large subunit of primase (p58N) directly interacts with the C-terminal domain of the catalytic subunit of polalpha (p180C)
Title: The C-terminal domain of the DNA polymerase catalytic subunit regulates the primase and polymerase activities of the human DNA polymerase α-primase complex.
PRIM2 gene is not imprinted in the placenta.
Title: Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells.
The fragment that forms a beta-sheet in the reported structure p58C/3L9Q of the same human primase domain is folded in three alpha-helices in our p58C/3Q36 structure, similarly to yeast primase.
Title: Crystal structure of the C-terminal domain of human DNA primase large subunit: implications for the mechanism of the primase-polymerase α switch.
p58C(C-terminal regulatory domain of the large subunit) structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure.
Title: Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH119346 (e-PCR)
- UniSTS:133908

SHGC-31574 (e-PCR)
- UniSTS:82978

RH65310 (e-PCR)
- UniSTS:87338

RH119380 (e-PCR)
- UniSTS:132920

RH70898 (e-PCR)
- UniSTS:88926

SHGC-58337 (e-PCR)
- UniSTS:94318

RH120995 (e-PCR)
- UniSTS:134047

D6S2137 (e-PCR)
- UniSTS:35774

RH46723 (e-PCR)
- UniSTS:92152

D6S1498 (e-PCR)
- UniSTS:153849

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 4 iron, 4 sulfur cluster binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA/RNA hybrid binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA replication initiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA replication initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA replication, synthesis of primer	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA replication, synthesis of primer	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA replication, synthesis of primer	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA primase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of alpha DNA polymerase:primase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of alpha DNA polymerase:primase complex	IDA Inferred from Direct Assay more info	PubMed
part_of alpha DNA polymerase:primase complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: DNA primase large subunit

Names: DNA primase 58 kDa subunit; primase (DNA) subunit 2; primase, DNA, polypeptide 2 (58kDa)

NP_000938.2

EC 2.7.7.-

NP_001269416.1

EC 2.7.7.-

NP_001269417.1

EC 2.7.7.-

XP_047274943.1

EC 2.7.7.-

XP_047274944.1

EC 2.7.7.-

XP_047274945.1

EC 2.7.7.-

XP_047274946.1

EC 2.7.7.-

XP_047274947.1

EC 2.7.7.-

XP_047274948.1

EC 2.7.7.-

XP_047274949.1

EC 2.7.7.-

XP_054211783.1

EC 2.7.7.-

XP_054211784.1

EC 2.7.7.-

XP_054211785.1

EC 2.7.7.-

XP_054211786.1

EC 2.7.7.-

XP_054211787.1

EC 2.7.7.-

XP_054211788.1

EC 2.7.7.-

XP_054211789.1

EC 2.7.7.-

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_034261.2 RefSeqGene

Range

101092..430312

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000947.5 → NP_000938.2 DNA primase large subunit isoform a

See identical proteins and their annotated locations for NP_000938.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

BC017833, BC064931

Consensus CDS

CCDS75476.1

UniProtKB/Swiss-Prot

P49643, Q53FJ8, Q6P1Q7, Q8WVL2, Q9H413

UniProtKB/TrEMBL

A8K7A0

Related

ENSP00000484105.1, ENST00000615550.5

Conserved Domains (1) summary

cd07322
Location:28 → 451

PriL_PriS_Eukaryotic; Eukaryotic core primase: Large subunit, PriL
NM_001282487.2 → NP_001269416.1 DNA primase large subunit isoform b

See identical proteins and their annotated locations for NP_001269416.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple 3' coding exons and its 3' terminal exon extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).

Source sequence(s)

AL121975, BC017833

Consensus CDS

CCDS75477.1

UniProtKB/TrEMBL

A0A5F9ZHR0

Related

ENSP00000485304.1, ENST00000274891.10

Conserved Domains (1) summary

cl11970
Location:28 → 155

PriL; Archaeal/eukaryotic core primase: Large subunit, PriL
NM_001282488.2 → NP_001269417.1 DNA primase large subunit isoform b

See identical proteins and their annotated locations for NP_001269417.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks multiple 3' coding exons, and its 3' terminal exon extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).

Source sequence(s)

AL121975, BC017833, BI547222

Consensus CDS

CCDS75477.1

UniProtKB/TrEMBL

A0A5F9ZHR0

Related

ENSP00000483201.1, ENST00000370687.6

Conserved Domains (1) summary

cl11970
Location:28 → 155

PriL; Archaeal/eukaryotic core primase: Large subunit, PriL