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PRMT5 protein arginine methyltransferase 5 [ Homo sapiens (human) ]

Gene ID: 10419, updated on 14-Oct-2018

Summary

Official Symbol
PRMT5provided by HGNC
Official Full Name
protein arginine methyltransferase 5provided by HGNC
Primary source
HGNC:HGNC:10894
See related
Ensembl:ENSG00000100462 MIM:604045; Vega:OTTHUMG00000028709
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
JBP1; SKB1; IBP72; SKB1Hs; HRMT1L5
Summary
This gene encodes an enzyme that belongs to the methyltransferase family. The encoded protein catalyzes the transfer of methyl groups to the amino acid arginine, in target proteins that include histones, transcriptional elongation factors and the tumor suppressor p53. This gene plays a role in several cellular processes, including transcriptional regulation, and the assembly of small nuclear ribonucleoproteins. A pseudogene of this gene has been defined on chromosome 4. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]
Expression
Ubiquitous expression in thyroid (RPKM 21.2), ovary (RPKM 18.5) and 25 other tissues See more
Orthologs

Genomic context

See PRMT5 in Genome Data Viewer
Location:
14q11.2
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (22920511..22929585, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (23389733..23398789, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RRAD and GEM like GTPase 2 Neighboring gene RNA binding motif protein 23 Neighboring gene PRMT5 antisense RNA 1 Neighboring gene uncharacterized LOC101926933 Neighboring gene transfer RNA-Arg (ACG) 1-3 Neighboring gene HAUS augmin like complex subunit 4 Neighboring gene microRNA 4707

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • E2F transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    E2F transcription factor network, organism-specific biosystem
    E2F transcription factor network
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Metabolism of non-coding RNA, organism-specific biosystem (from REACTOME)
    Metabolism of non-coding RNA, organism-specific biosystemThe term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence tha...
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
  • Regulation of TP53 Activity through Methylation, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity through Methylation, organism-specific biosystemTP53 (p53) undergoes methylation on several lysine and arginine residues, which modulates its transcriptional activity.PRMT5, recruited to TP53 as part of the ATM-activated complex that includes TTC5...
  • Signaling events mediated by HDAC Class I, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by HDAC Class I, organism-specific biosystem
    Signaling events mediated by HDAC Class I
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...
  • p53 pathway, organism-specific biosystem (from Pathway Interaction Database)
    p53 pathway, organism-specific biosystem
    p53 pathway
  • snRNP Assembly, organism-specific biosystem (from REACTOME)
    snRNP Assembly, organism-specific biosystemSmall nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The U6 snRNA...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
E-box binding ISS
Inferred from Sequence or Structural Similarity
more info
 
histone methyltransferase activity (H4-R3 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone-arginine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone-arginine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
methyl-CpG binding IDA
Inferred from Direct Assay
more info
PubMed 
methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein-arginine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein-arginine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
protein-arginine omega-N symmetric methyltransferase activity EXP
Inferred from Experiment
more info
PubMed 
protein-arginine omega-N symmetric methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ribonucleoprotein complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
DNA-templated transcription, termination IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi ribbon formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell proliferation TAS
Traceable Author Statement
more info
PubMed 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
endothelial cell activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H4-R3 methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H4-R3 methylation NAS
Non-traceable Author Statement
more info
PubMed 
histone arginine methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
liver regeneration IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
peptidyl-arginine N-methylation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-arginine methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-arginine methylation, to symmetrical-dimethyl arginine IEA
Inferred from Electronic Annotation
more info
 
positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of DNA methylation IEA
Inferred from Electronic Annotation
more info
 
regulation of ERK1 and ERK2 cascade IEA
Inferred from Electronic Annotation
more info
 
regulation of mitotic nuclear division TAS
Traceable Author Statement
more info
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
spliceosomal snRNP assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
methylosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
protein arginine N-methyltransferase 5
Names
72 kDa ICln-binding protein
HMT1 hnRNP methyltransferase-like 5
SKB1 homolog
histone-arginine N-methyltransferase PRMT5
jak-binding protein 1
shk1 kinase-binding protein 1 homolog
NP_001034708.1
NP_001269882.1
NP_001269883.1
NP_001269884.1
NP_001269885.1
NP_006100.2

NCBI Reference Sequences (RefSeq)

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_001039619.2NP_001034708.1  protein arginine N-methyltransferase 5 isoform b

    See identical proteins and their annotated locations for NP_001034708.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AA496357, AK027737, AK075251, DC395183
    Consensus CDS
    CCDS41922.1
    UniProtKB/Swiss-Prot
    O14744
    Related
    ENSP00000380583.2, OTTHUMP00000246076, ENST00000397441.6, OTTHUMT00000413505
    Conserved Domains (1) summary
    pfam05185
    Location:166602
    PRMT5; PRMT5 arginine-N-methyltransferase
  2. NM_001282953.1NP_001269882.1  protein arginine N-methyltransferase 5 isoform c

    See identical proteins and their annotated locations for NP_001269882.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains multiple differences in the 5' coding region, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AA496357, AK301812, DC395183
    Consensus CDS
    CCDS61394.1
    UniProtKB/Swiss-Prot
    O14744
    Related
    ENSP00000216350.8, OTTHUMP00000246077, ENST00000216350.12, OTTHUMT00000413506
    Conserved Domains (1) summary
    pfam05185
    Location:122558
    PRMT5; PRMT5 arginine-N-methyltransferase
  3. NM_001282954.1NP_001269883.1  protein arginine N-methyltransferase 5 isoform d

    See identical proteins and their annotated locations for NP_001269883.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the 5' coding region, compared to variant 1, including initiation of translation at a downstream in-frame start codon. The encoded isoform (d) has a shorter N-terminus than isoform a.
    Source sequence(s)
    AA496357, AK300863, AL833612, DC395183
    UniProtKB/TrEMBL
    B4DV00
    Conserved Domains (1) summary
    pfam05185
    Location:77513
    PRMT5; PRMT5 arginine-N-methyltransferase
  4. NM_001282955.1NP_001269884.1  protein arginine N-methyltransferase 5 isoform e

    See identical proteins and their annotated locations for NP_001269884.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon and uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (e) is shorter than isoform a.
    Source sequence(s)
    AA496357, AK302240, AL833612, DC395183
    Consensus CDS
    CCDS61396.1
    UniProtKB/Swiss-Prot
    O14744
    Related
    ENSP00000452555.1, OTTHUMP00000246079, ENST00000553897.5, OTTHUMT00000413508
    Conserved Domains (1) summary
    pfam05185
    Location:139575
    PRMT5; PRMT5 arginine-N-methyltransferase
  5. NM_001282956.1NP_001269885.1  protein arginine N-methyltransferase 5 isoform f

    See identical proteins and their annotated locations for NP_001269885.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains multiple differences in the 5' coding region, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (f) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AA496357, AL833612, BC005820, DC395183
    Consensus CDS
    CCDS61395.1
    UniProtKB/Swiss-Prot
    O14744
    Related
    ENSP00000380582.4, OTTHUMP00000164558, ENST00000397440.8, OTTHUMT00000071676
    Conserved Domains (1) summary
    pfam05185
    Location:95448
    PRMT5; PRMT5 arginine-N-methyltransferase
  6. NM_006109.4NP_006100.2  protein arginine N-methyltransferase 5 isoform a

    See identical proteins and their annotated locations for NP_006100.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AA496357, AL833612, DC395183
    Consensus CDS
    CCDS9579.1
    UniProtKB/Swiss-Prot
    O14744
    Related
    ENSP00000319169.8, OTTHUMP00000027922, ENST00000324366.12, OTTHUMT00000071674
    Conserved Domains (1) summary
    pfam05185
    Location:183619
    PRMT5; PRMT5 arginine-N-methyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    22920511..22929585 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_429287.2 RNA Sequence

  2. XR_001750113.2 RNA Sequence

    Related
    ENST00000553915.5
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