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

    Gene ID: 10196, updated on 28-Oct-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
    mouse all
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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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