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Aliases for PRMT3 Gene

Aliases for PRMT3 Gene

  • Protein Arginine Methyltransferase 3 2 3 5
  • Heterogeneous Nuclear Ribonucleoprotein Methyltransferase-Like Protein 3 3 4
  • HRMT1L3 3 4
  • HMT1 HnRNP Methyltransferase-Like 3 (S. Cerevisiae) 2
  • Protein Arginine N-Methyltransferase 3 3
  • HMT1 HnRNP Methyltransferase-Like 3 3
  • EC 2.1.1.- 4

External Ids for PRMT3 Gene

Previous HGNC Symbols for PRMT3 Gene

  • HRMT1L3

Previous GeneCards Identifiers for PRMT3 Gene

  • GC11M021595
  • GC11U900019
  • GC11P020448
  • GC11P020373
  • GC11P020092

Summaries for PRMT3 Gene

Entrez Gene Summary for PRMT3 Gene

  • This gene belongs to the protein arginine methyltransferase (PRMT) family. The encoded enzyme catalyzes the methylation of guanidino nitrogens of arginyl residues of proteins. The enzyme acts on 40S ribosomal protein S2 (rpS2), which is its major in-vivo substrate, and is involved in the proper maturation of the 80S ribosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

GeneCards Summary for PRMT3 Gene

PRMT3 (Protein Arginine Methyltransferase 3) is a Protein Coding gene. Diseases associated with PRMT3 include Myopathy Of Extraocular Muscle. Among its related pathways are Metabolism of proteins and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include methyltransferase activity and histone-arginine N-methyltransferase activity. An important paralog of this gene is PRMT1.

UniProtKB/Swiss-Prot for PRMT3 Gene

  • Methylates (mono and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in some proteins.

Tocris Summary for PRMT3 Gene

  • Protein arginine methyltransferases are enyzmes that catalyze the transfer of methyl groups from S-adenosylmethionine (SAM) to the arginine residues on histones and other proteins. The dysregulation of this methylation is critical in the development of certain cancers.

Gene Wiki entry for PRMT3 Gene

Additional gene information for PRMT3 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRMT3 Gene

Genomics for PRMT3 Gene

GeneHancer (GH) Regulatory Elements for PRMT3 Gene

Promoters and enhancers for PRMT3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J020386 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 657.2 +0.5 492 3.3 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF766 CBX5 PRMT3 HTATIP2 LOC105376584
GH11J020362 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 0.3 -23.2 -23234 3.2 HDGF PKNOX1 SMAD1 ARNT SIN3A YY1 SP3 SMARCB1 ZNF592 SMARCA4 HTATIP2 PRMT3
GH11J020366 Enhancer 1.1 Ensembl ENCODE 0.4 -19.5 -19516 3.5 PKNOX1 ATF1 ARNT SIN3A BRCA1 ATF7 FOS JUNB NCOA1 TSHZ1 HTATIP2 SLC6A5 PRMT3
GH11J020458 Enhancer 0.9 ENCODE 0.2 +72.0 72017 1.3 SMAD1 ATF1 ARNT NCOA2 TCF12 ZNF766 GATA2 ATF7 NCOA1 ZNF592 HTATIP2 PRMT3 LOC105376584
GH11J020473 Enhancer 0.7 Ensembl ENCODE 0.2 +87.2 87207 1.5 FOXK2 HDAC2 IKZF1 ZFX ZNF592 NR2C2 HTATIP2 PRMT3 LOC105376584
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRMT3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRMT3 gene promoter:
  • HNF-1A
  • HNF-1
  • POU6F1 (c2)
  • TBP
  • AML1a
  • NF-E2
  • NF-E2 p45
  • N-Myc
  • Lhx3a

Genomic Locations for PRMT3 Gene

Genomic Locations for PRMT3 Gene
121,804 bases
Plus strand
121,804 bases
Plus strand

Genomic View for PRMT3 Gene

Genes around PRMT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRMT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRMT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRMT3 Gene

Proteins for PRMT3 Gene

  • Protein details for PRMT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein arginine N-methyltransferase 3
    Protein Accession:
    Secondary Accessions:
    • A0A0A0MSN7
    • B4DUC7

    Protein attributes for PRMT3 Gene

    531 amino acids
    Molecular mass:
    59903 Da
    Quaternary structure:
    • Monomer or homodimer (By similarity). Interacts with EPB41L3; this inhibits methylation of target proteins. Interacts with the 40S ribosomal protein RPS2.

    Three dimensional structures from OCA and Proteopedia for PRMT3 Gene

    Alternative splice isoforms for PRMT3 Gene


neXtProt entry for PRMT3 Gene

Post-translational modifications for PRMT3 Gene

  • Ubiquitination at posLast=187187
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PRMT3 Gene

Domains & Families for PRMT3 Gene

Gene Families for PRMT3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PRMT3 Gene

Suggested Antigen Peptide Sequences for PRMT3 Gene

Graphical View of Domain Structure for InterPro Entry



  • The zinc-finger is responsible for substrate specificity.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Protein arginine N-methyltransferase family.
  • The zinc-finger is responsible for substrate specificity.
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Protein arginine N-methyltransferase family.
genes like me logo Genes that share domains with PRMT3: view

Function for PRMT3 Gene

Molecular function for PRMT3 Gene

UniProtKB/Swiss-Prot Function:
Methylates (mono and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in some proteins.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by N-ethylmaleimide and high concentrations of zinc chloride.

Enzyme Numbers (IUBMB) for PRMT3 Gene

Phenotypes From GWAS Catalog for PRMT3 Gene

Gene Ontology (GO) - Molecular Function for PRMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0005515 protein binding IPI 18573314
GO:0008168 methyltransferase activity IEA,IDA 18573314
GO:0008469 histone-arginine N-methyltransferase activity IBA --
GO:0016274 protein-arginine N-methyltransferase activity IEA,TAS --
genes like me logo Genes that share ontologies with PRMT3: view
genes like me logo Genes that share phenotypes with PRMT3: view

Animal Models for PRMT3 Gene

MGI Knock Outs for PRMT3:
  • Prmt3 Prmt3<tm1a(EUCOMM)Wtsi>

Animal Model Products

Clone Products

  • Addgene plasmids for PRMT3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRMT3 Gene

Localization for PRMT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRMT3 Gene


Subcellular locations from

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 PRMT3 gene
Compartment Confidence
cytosol 5
nucleus 4

Gene Ontology (GO) - Cellular Components for PRMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm NAS 9642256
GO:0005829 cytosol IEA,TAS --
GO:0005840 ribosome IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PRMT3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRMT3 Gene

Pathways & Interactions for PRMT3 Gene

genes like me logo Genes that share pathways with PRMT3: view

Gene Ontology (GO) - Biological Process for PRMT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IBA --
GO:0006479 protein methylation IEA,TAS --
GO:0019919 peptidyl-arginine methylation, to asymmetrical-dimethyl arginine IEA --
GO:0031397 negative regulation of protein ubiquitination IDA 18573314
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PRMT3: view

No data available for SIGNOR curated interactions for PRMT3 Gene

Drugs & Compounds for PRMT3 Gene

(7) Drugs for PRMT3 Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Histidine Approved Nutra 50
s-adenosylhomocysteine Experimental Pharma Target 0
2-Hydroxyestradiol Experimental Pharma 0
2-Methoxyestradiol Investigational Pharma 9
Serotonin Investigational Nutra 3755

(8) Additional Compounds for PRMT3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid
  • 1-Methylhistidine
  • Pi-methylhistidine
  • (2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate
  • 1 Methylhistidine
  • 5-Hial
  • 5-Hydroxyindole-3-acetaldehyde
  • (5-Hydroxy-1H-indol-3-yl)acetaldehyde
  • (5-Hydroxyindol-3-yl)acetaldehyde
  • 5-Hydroxy-1H-indole-3-acetaldehyde
  • 2-(5-Methoxyindol-3-yl)ethylamine
  • 3-(2-Aminoethyl)-5-methoxyindole
  • 5-MeOT
  • 5-Methoxy-1H-indole-3-ethanamine
  • 5-MT
Chloride ion
  • Chloride(1-)
  • Chlorine anion
  • CL(-)
  • Bertholite
  • Chloor
  • 4-[2-(dimethylamino)Ethyl]phenol
  • N,N-Dimethyl-2-(4-hydroxyphenyl)ethylamine
  • N,N-Dimethyl-4-hydroxy-beta-phenethylamine
  • N,N-Dimethyltyramine
  • P-(2-Dimethylaminoethyl)phenol
genes like me logo Genes that share compounds with PRMT3: view

Transcripts for PRMT3 Gene

Unigene Clusters for PRMT3 Gene

Protein arginine methyltransferase 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for PRMT3

Alternative Splicing Database (ASD) splice patterns (SP) for PRMT3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b
SP2: -

Relevant External Links for PRMT3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRMT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRMT3 Gene

Protein differential expression in normal tissues from HIPED for PRMT3 Gene

This gene is overexpressed in Breast (51.6) and Peripheral blood mononuclear cells (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRMT3 Gene

Protein tissue co-expression partners for PRMT3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRMT3 Gene:


SOURCE GeneReport for Unigene cluster for PRMT3 Gene:


Evidence on tissue expression from TISSUES for PRMT3 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with PRMT3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRMT3 Gene

Orthologs for PRMT3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRMT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRMT3 34 33
  • 99.56 (n)
(Canis familiaris)
Mammalia PRMT3 34 33
  • 92.4 (n)
(Bos Taurus)
Mammalia PRMT3 34 33
  • 91.9 (n)
(Mus musculus)
Mammalia Prmt3 16 34 33
  • 87.1 (n)
(Rattus norvegicus)
Mammalia Prmt3 33
  • 86.46 (n)
(Ornithorhynchus anatinus)
Mammalia PRMT3 34
  • 86 (a)
(Monodelphis domestica)
Mammalia PRMT3 34
  • 84 (a)
(Gallus gallus)
Aves PRMT3 34 33
  • 73.78 (n)
(Anolis carolinensis)
Reptilia PRMT3 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prmt3 33
  • 66.6 (n)
MGC76034 33
(Danio rerio)
Actinopterygii prmt3 34 33
  • 63.73 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003593 33
  • 51.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta Art3 34 33
  • 47.89 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HMT1 34
  • 42 (a)
(Oryza sativa)
Liliopsida Os.12267 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rmt3 33
  • 49.25 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01669 33
  • 45.5 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.11923 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11923 33
Species where no ortholog for PRMT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PRMT3 Gene

Gene Tree for PRMT3 (if available)
Gene Tree for PRMT3 (if available)
Evolutionary constrained regions (ECRs) for PRMT3: view image

Paralogs for PRMT3 Gene

Paralogs for PRMT3 Gene

(5) SIMAP similar genes for PRMT3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with PRMT3: view

Variants for PRMT3 Gene

Sequence variations from dbSNP and Humsavar for PRMT3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000120912 -- 20,440,533(+) T/G intron_variant
rs1000124689 -- 20,456,608(+) T/C intron_variant
rs1000200330 -- 20,397,043(+) C/G intron_variant
rs1000230690 -- 20,493,896(+) A/C/G intron_variant
rs1000232884 -- 20,407,489(+) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRMT3 Gene

Variant ID Type Subtype PubMed ID
nsv832083 CNV gain 17160897
nsv553678 CNV gain 21841781
nsv469939 CNV gain 18288195
nsv467720 CNV gain 19166990
nsv1122587 CNV deletion 24896259
esv3723 CNV loss 18987735
esv3547406 CNV deletion 23714750
esv2744184 CNV deletion 23290073
esv2744183 CNV deletion 23290073
esv2663802 CNV deletion 23128226
esv2616116 CNV deletion 19546169

Variation tolerance for PRMT3 Gene

Residual Variation Intolerance Score: 54.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.27; 70.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRMT3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRMT3 Gene

Disorders for PRMT3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PRMT3 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
myopathy of extraocular muscle
  • myopathy of extraocular muscles
- elite association - COSMIC cancer census association via MalaCards
Search PRMT3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PRMT3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRMT3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRMT3 Gene

Publications for PRMT3 Gene

  1. DAL-1/4.1B tumor suppressor interacts with protein arginine N-methyltransferase 3 (PRMT3) and inhibits its ability to methylate substrates in vitro and in vivo. (PMID: 15334060) Singh V … Newsham IF (Oncogene 2004) 3 4 22 58
  2. PRMT 3, a type I protein arginine N-methyltransferase that differs from PRMT1 in its oligomerization, subcellular localization, substrate specificity, and regulation. (PMID: 9642256) Tang J … Herschman HR (The Journal of biological chemistry 1998) 2 3 4 58
  3. Tyrosine 87 is vital for the activity of human protein arginine methyltransferase 3 (PRMT3). (PMID: 21059412) Handrkova H … Cmejla R (Biochimica et biophysica acta 2011) 3 4 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. PRMT3 inhibits ubiquitination of ribosomal protein S2 and together forms an active enzyme complex. (PMID: 18573314) Choi S … Im DS (Biochimica et biophysica acta 2008) 3 22 58

Products for PRMT3 Gene

  • Addgene plasmids for PRMT3

Sources for PRMT3 Gene

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