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

Summary

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

Location:: 11p15.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (20387716..20509338)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (20508397..20629944)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (20409262..20530884)

Chromosome 11 - NC_000011.10 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?

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.
PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast.
Title: PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast.
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.
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.
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.
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.
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.
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.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH71417 (e-PCR)
- UniSTS:43526

SHGC-152214 (e-PCR)
- UniSTS:177435

D11S4671 (e-PCR)
- UniSTS:70437

D11S4190 (e-PCR), detects polymorphism
- UniSTS:45260

D11S1233 (e-PCR)
- UniSTS:31959

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 methylation	IEA Inferred from Electronic Annotation 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, to asymmetrical-dimethyl arginine	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

EC 2.1.1.319

NP_001138639.1

EC 2.1.1.319

NP_005779.1

EC 2.1.1.319

XP_011518138.1

EC 2.1.1.319

XP_047282183.1

EC 2.1.1.319

XP_047282184.1

EC 2.1.1.319

XP_054223404.1

EC 2.1.1.319

XP_054223405.1

EC 2.1.1.319

XP_054223406.1

EC 2.1.1.319

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)

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). ...
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). ...
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

20387716..20509338

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047426228.1 → XP_047282184.1 protein arginine N-methyltransferase 3 isoform X3
XM_047426227.1 → XP_047282183.1 protein arginine N-methyltransferase 3 isoform X1
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

NC_060935.1 Alternate T2T-CHM13v2.0

Range

20508397..20629944

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054367431.1 → XP_054223406.1 protein arginine N-methyltransferase 3 isoform X3
XM_054367429.1 → XP_054223404.1 protein arginine N-methyltransferase 3 isoform X1
XM_054367430.1 → XP_054223405.1 protein arginine N-methyltransferase 3 isoform X2