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PRMT3 protein arginine methyltransferase 3 [ Homo sapiens (human) ]

Gene ID: 10196, updated on 2-Nov-2024

Summary

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Official Symbol
PRMT3provided by HGNC
Official Full Name
protein arginine methyltransferase 3provided by HGNC
Primary source
HGNC:HGNC:30163
See related
Ensembl:ENSG00000185238 MIM:603190; AllianceGenome:HGNC:30163
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HRMT1L3
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 7.5), brain (RPKM 3.3) and 25 other tissues See more
Orthologs
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Genomic context

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See PRMT3 in Genome Data Viewer
Location:
11p15.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (20387716..20509338)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (20508397..20629944)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (20409262..20530884)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376583 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:20234917-20235147 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19843 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:20364173-20364700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4525 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:20385467-20385609 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:20388793-20389992 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:20406589-20407090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:20409013-20409620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:20409621-20410227 Neighboring gene HIV-1 Tat interactive protein 2 Neighboring gene uncharacterized LOC124902808 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19926 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3204 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:20566010-20566716 Neighboring gene uncharacterized LOC105376584 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_20020 Neighboring gene high mobility group box 1 pseudogene 40

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Regulation of post-translational protein arginine methylation during HeLa cell cycle. Kim C, et al. Biochim Biophys Acta, 2010 Sep. PMID 20541591
  2. Tyrosine 87 is vital for the activity of human protein arginine methyltransferase 3 (PRMT3). Handrkova H, et al. Biochim Biophys Acta, 2011 Feb. PMID 21059412
  3. Expression of nitric oxide related enzymes in coronary heart disease. Chen X, et al. Basic Res Cardiol, 2006 Jul. PMID 16705470
  4. PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast. Zhi R, et al. Cancer Sci, 2023 May. PMID 36637351, Free PMC Article
  5. Protein arginine methyltransferase 3: A crucial regulator in metabolic reprogramming and gene expression in cancers. Hsu SH, et al. Cancer Lett, 2023 Feb 1. PMID 36400311

See all (96) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PRMT3-Mediated Arginine Methylation of METTL14 Promotes Malignant Progression and Treatment Resistance in Endometrial Carcinoma.
    Title: PRMT3-Mediated Arginine Methylation of METTL14 Promotes Malignant Progression and Treatment Resistance in Endometrial Carcinoma.
  2. PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast.
    Title: PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast.
  3. PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer.
    Title: PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer.
  4. Protein arginine methyltransferase 3: A crucial regulator in metabolic reprogramming and gene expression in cancers.
    Title: Protein arginine methyltransferase 3: A crucial regulator in metabolic reprogramming and gene expression in cancers.
  5. Decreased nitric oxide content mediated by asymmetrical dimethylarginine and protein l-arginine methyltransferase 3 in macrophages induces trophoblast apoptosis: a potential cause of recurrent miscarriage.
    Title: Decreased nitric oxide content mediated by asymmetrical dimethylarginine and protein l-arginine methyltransferase 3 in macrophages induces trophoblast apoptosis: a potential cause of recurrent miscarriage.
  6. PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling.
    Title: PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling.
  7. Arginine methyltransferase PRMT3 promote tumorigenesis through regulating c-MYC stabilization in colorectal cancer.
    Title: Arginine methyltransferase PRMT3 promote tumorigenesis through regulating c-MYC stabilization in colorectal cancer.
  8. PRMT3 is an essential regulator of mesenchymal stem cell-mediated osteogenesis and bone homeostasis.
    Title: Asymmetrical methyltransferase PRMT3 regulates human mesenchymal stem cell osteogenesis via miR-3648.
  9. ZNF277 and PRMT3 compete for uS5 binding, because overexpression of PRMT3 inhibited the formation of the ZNF277-uS5 complex, whereas depletion of cellular ZNF277 resulted in increased levels of uS5-PRMT3.
    Title: The 40S ribosomal protein uS5 (RPS2) assembles into an extraribosomal complex with human ZNF277 that competes with the PRMT3-uS5 interaction.
  10. Findings uncover the existence of an extra-ribosomal complex consisting of PDCD2L, RPS2, and PRMT3 and support a role for PDCD2L in the late maturation of 40S ribosomal subunits.
    Title: Human PDCD2L Is an Export Substrate of CRM1 That Associates with 40S Ribosomal Subunit Precursors.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of protein arginine methyltransferase 3 (PRMT3) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-arginine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-arginine N-methyltransferase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein-arginine N-methyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein-arginine omega-N asymmetric methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein-arginine omega-N monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables ribosome binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of retinoic acid biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in peptidyl-arginine methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein arginine N-methyltransferase 3
Names
HMT1 hnRNP methyltransferase-like 3
heterogeneous nuclear ribonucleoprotein methyltransferase-like protein 3
NP_001138638.1
NP_001138639.1
NP_005779.1
XP_011518138.1
XP_047282183.1
XP_047282184.1
XP_054223404.1
XP_054223405.1
XP_054223406.1

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.

mRNA and Protein(s)

  1. NM_001145166.2 → NP_001138638.1  protein arginine N-methyltransferase 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) is missing two non-consecutive internal coding exons compared to transcript variant 1. It uses the same translation start site as variant 1, however, the first missing exon throws it out of frame, and the second missing exon puts it back in frame, resulting in a shorter isoform (2) with a novel 28 aa segment compared to isoform 1.
    Source sequence(s)
    AC025972, AC108005, KC877396, KF459543
    Consensus CDS
    CCDS44554.1
    UniProtKB/TrEMBL
    B4DP44
    Related
    ENSP00000397766.2, ENST00000437750.2
    Conserved Domains (1) summary
    cd02440
    Location:197 → 297
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. NM_001145167.2 → NP_001138639.1  protein arginine N-methyltransferase 3 isoform 3

    See identical proteins and their annotated locations for NP_001138639.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) is missing a coding exon at the 5' end compared to transcript variant 1. This results in translation initiation from an in-frame downstream AUG by leaky scanning, and a shorter isoform (3) with a truncated N-terminus compared to isoform 1.
    Source sequence(s)
    AC025972, AC108005, KC877396, KF459543
    UniProtKB/TrEMBL
    B4DP44
    Conserved Domains (1) summary
    cd02440
    Location:182 → 282
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  3. NM_005788.4 → NP_005779.1  protein arginine N-methyltransferase 3 isoform 1

    See identical proteins and their annotated locations for NP_005779.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC025972, AC108005, KC877396, KF459543
    Consensus CDS
    CCDS7853.1
    UniProtKB/Swiss-Prot
    A0A0A0MSN7, B4DUC7, O60678
    UniProtKB/TrEMBL
    B4DWB1
    Related
    ENSP00000331879.6, ENST00000331079.11
    Conserved Domains (2) summary
    cd02440
    Location:259 → 359
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
    pfam12756
    Location:50 → 99
    zf-C2H2_2; C2H2 type zinc-finger (2 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    20387716..20509338
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426228.1 → XP_047282184.1  protein arginine N-methyltransferase 3 isoform X3

  2. XM_047426227.1 → XP_047282183.1  protein arginine N-methyltransferase 3 isoform X1

  3. XM_011519836.3 → XP_011518138.1  protein arginine N-methyltransferase 3 isoform X2

    UniProtKB/TrEMBL
    B4DP44
    Conserved Domains (1) summary
    cd02440
    Location:154 → 254
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    20508397..20629944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367431.1 → XP_054223406.1  protein arginine N-methyltransferase 3 isoform X3

  2. XM_054367429.1 → XP_054223404.1  protein arginine N-methyltransferase 3 isoform X1

  3. XM_054367430.1 → XP_054223405.1  protein arginine N-methyltransferase 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60678.4 GenPept UniProtKB/Swiss-Prot:O60678

Gene LinkOut

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