Human Gene PRMT5 (ENST00000324366.13_9) from GENCODE V47lift37
  Description: protein arginine methyltransferase 5, transcript variant 1 (from RefSeq NM_006109.5)
Gencode Transcript: ENST00000324366.13_9
Gencode Gene: ENSG00000100462.16_14
Transcript (Including UTRs)
   Position: hg19 chr14:23,389,738-23,398,585 Size: 8,848 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr14:23,390,113-23,398,570 Size: 8,458 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:23,389,738-23,398,585)mRNA (may differ from genome)Protein (637 aa)
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-  Comments and Description Text from UniProtKB
  ID: ANM5_HUMAN
DESCRIPTION: RecName: Full=Protein arginine N-methyltransferase 5; EC=2.1.1.-; AltName: Full=72 kDa ICln-binding protein; AltName: Full=Histone-arginine N-methyltransferase PRMT5; EC=2.1.1.125; AltName: Full=Jak-binding protein 1; AltName: Full=Shk1 kinase-binding protein 1 homolog; Short=SKB1 homolog; Short=SKB1Hs; Contains: RecName: Full=Protein arginine N-methyltransferase 5, N-terminally processed;
FUNCTION: Arginine methyltransferase that can both catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA), with a preference for the formation of MMA. Specifically mediates the symmetrical dimethylation of arginine residues in the small nuclear ribonucleoproteins Sm D1 (SNRPD1) and Sm D3 (SNRPD3); such methylation being required for the assembly and biogenesis of snRNP core particles. Methylates SUPT5H. Mono- and dimethylates arginine residues of myelin basic protein (MBP) in vitro. Plays a role in the assembly of snRNP core particles. May play a role in cytokine-activated transduction pathways. Negatively regulates cyclin E1 promoter activity and cellular proliferation. May regulate the SUPT5H transcriptional elongation properties. May be part of a pathway that is connected to a chloride current, possibly through cytoskeletal rearrangement. Methylates histone H2A and H4 'Arg-3' during germ cell development. Methylates histone H3 'Arg-8', which may repress transcription. Methylates the Piwi proteins (PIWIL1, PIWIL2 and PIWIL4), methylation of Piwi proteins being required for the interaction with Tudor domain-containing proteins and subsequent localization to the meiotic nuage. Methylates RPS10. Attenuates EGF signaling through the MAPK1/MAPK3 pathway acting at 2 levels. First, monomethylates EGFR; this enhances EGFR 'Tyr-1197' phosphorylation and PTPN6 recruitment, eventually leading to reduced SOS1 phosphorylation. Second, methylates RAF1 and probably BRAF, hence destabilizing these 2 signaling proteins and reducing their catalytic activity. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation. Methylates HOXA9. Methylates and regulates SRGAP2 which is involved in cell migration and differentiation.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + arginine-[histone] = S-adenosyl-L-homocysteine + N(omega)-methyl-arginine-[histone].
ENZYME REGULATION: Activity is increased by EGF, HGF, FGF1 or FGF2 treatments, and slightly decreased by NGF treatment.
SUBUNIT: Forms, at least, homodimers and homotetramers. Interacts with PRDM1 (By similarity). Component of the methylosome, a 20S complex containing at least pICLn, PRMT1/SKB1 and MEP50. Component of a high molecular weight E2F-pocket protein complex, CERC (cyclin E1 repressor complex). Also interacts with Sm proteins, JAK2, SSTR1 and SUPT5H. Associates with SWI/SNF remodeling complexes containing SMARCA2 and SMARCA4. Interacts with LSM11, PRMT7 and SNRPD3. Interacts with COPR5/C17orf79; promoting its recruitment on histone H4. Interacts with RPS10. Interacts with EGFR; methylates EGFR and stimulates EGFR-mediated ERK activation. Interacts with BRAF and with active RAF1. Interacts with HOXA9. Interacts with SRGAP2.
INTERACTION: P62805:HIST2H4B; NbExp=3; IntAct=EBI-351098, EBI-302023; O75044:SRGAP2; NbExp=4; IntAct=EBI-351098, EBI-1051034;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Disulfide bonds and non-covalent association mediate homooligomers formation.
SIMILARITY: Belongs to the protein arginine N-methyltransferase family.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.73 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 791.05 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -129.50375-0.345 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR025799 - Arg_MeTrfase
IPR007857 - Arg_MeTrfase_PRMT5

Pfam Domains:
PF05185 - PRMT5 arginine-N-methyltransferase
PF17285 - PRMT5 TIM barrel domain
PF17286 - PRMT5 oligomerisation domain

SCOP Domains:
100950 - NagB/RpiA/CoA transferase-like
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on O14744
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001046 core promoter sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008327 methyl-CpG binding
GO:0008469 histone-arginine N-methyltransferase activity
GO:0016274 protein-arginine N-methyltransferase activity
GO:0016740 transferase activity
GO:0035243 protein-arginine omega-N symmetric methyltransferase activity
GO:0042802 identical protein binding
GO:0043021 ribonucleoprotein complex binding
GO:0044020 histone methyltransferase activity (H4-R3 specific)
GO:0044877 macromolecular complex binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006353 DNA-templated transcription, termination
GO:0006355 regulation of transcription, DNA-templated
GO:0006479 protein methylation
GO:0007088 regulation of mitotic nuclear division
GO:0008283 cell proliferation
GO:0018216 peptidyl-arginine methylation
GO:0019918 peptidyl-arginine methylation, to symmetrical-dimethyl arginine
GO:0032259 methylation
GO:0032922 circadian regulation of gene expression
GO:0035246 peptidyl-arginine N-methylation
GO:0042118 endothelial cell activation
GO:0043985 histone H4-R3 methylation
GO:0044030 regulation of DNA methylation
GO:0045596 negative regulation of cell differentiation
GO:0048511 rhythmic process
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0070372 regulation of ERK1 and ERK2 cascade
GO:0090161 Golgi ribbon formation
GO:0097421 liver regeneration
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1903507 negative regulation of nucleic acid-templated transcription
GO:1904992 positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0032991 macromolecular complex
GO:0034709 methylosome
GO:0035097 histone methyltransferase complex


-  Descriptions from all associated GenBank mRNAs
  AK027737 - Homo sapiens cDNA FLJ14831 fis, clone OVARC1001107.
AK075251 - Homo sapiens cDNA FLJ90770 fis, clone THYRO1000866, highly similar to Protein arginine N-methyltransferase 5 (EC 2.1.1.-).
BC005820 - Homo sapiens cDNA clone IMAGE:3937549, containing frame-shift errors.
AL833612 - Homo sapiens mRNA; cDNA DKFZp686A1373 (from clone DKFZp686A1373).
BC025979 - Homo sapiens protein arginine methyltransferase 5, mRNA (cDNA clone MGC:15219 IMAGE:3833019), complete cds.
AK301812 - Homo sapiens cDNA FLJ54566 complete cds, highly similar to Protein arginine N-methyltransferase 5 (EC2.1.1.-).
AF167572 - Homo sapiens protein methyltransferase (JBP1) mRNA, complete cds.
JD455588 - Sequence 436612 from Patent EP1572962.
JD364097 - Sequence 345121 from Patent EP1572962.
JD189278 - Sequence 170302 from Patent EP1572962.
JD183572 - Sequence 164596 from Patent EP1572962.
JD229194 - Sequence 210218 from Patent EP1572962.
JD278559 - Sequence 259583 from Patent EP1572962.
JD345227 - Sequence 326251 from Patent EP1572962.
AF015913 - Homo sapiens SKB1Hs mRNA, complete cds.
JD271768 - Sequence 252792 from Patent EP1572962.
JD400070 - Sequence 381094 from Patent EP1572962.
AK300863 - Homo sapiens cDNA FLJ54039 complete cds, highly similar to Protein arginine N-methyltransferase 5 (EC 2.1.1.-).
JD196439 - Sequence 177463 from Patent EP1572962.
AK302240 - Homo sapiens cDNA FLJ54078 complete cds, highly similar to Protein arginine N-methyltransferase 5 (EC 2.1.1.-).
JD148016 - Sequence 129040 from Patent EP1572962.
DQ893421 - Synthetic construct clone IMAGE:100006051; FLH199507.01X; RZPDo839F0382D protein arginine methyltransferase 5 (PRMT5) gene, encodes complete protein.
AK315500 - Homo sapiens cDNA, FLJ96564, highly similar to Homo sapiens SKB1 homolog (S. pombe) (SKB1), mRNA.
AB451246 - Homo sapiens PRMT5 mRNA for protein arginine methyltransferase 5 isoform a, complete cds, clone: FLJ08052AAAN.
DQ896773 - Synthetic construct Homo sapiens clone IMAGE:100011233; FLH199413.01L; RZPDo839F0381D protein arginine methyltransferase 5 (PRMT5) gene, encodes complete protein.
AB451370 - Homo sapiens PRMT5 mRNA for protein arginine methyltransferase 5 isoform a, partial cds, clone: FLJ08052AAAF.
AB590294 - Synthetic construct DNA, clone: pFN21AE1351, Homo sapiens PRMT5 gene for protein arginine methyltransferase 5, without stop codon, in Flexi system.
CR456741 - Homo sapiens full open reading frame cDNA clone RZPDo834G0114D for gene SKB1, SKB1 homolog (S. pombe); complete cds, incl. stopcodon.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O14744 (Reactome details) participates in the following event(s):

R-HSA-3215391 PRMT5 is tyrosine phosphorylated by JAK2 V617F
R-HSA-3215406 PRMT5 binds WDR77
R-HSA-6804379 PRMT5 binds TTC5
R-HSA-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-HSA-6804383 PRMT5 methylates TP53
R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-3215385 CDK4 in CCND1:CDK4:PRMT5:WDR77 phosphorylates WDR77
R-HSA-3215426 COPRS binds CCND1:CDK4:PRMT5:pT5-WDR77
R-HSA-5205799 CCND1:CDK4:PRMT5:pT5-WDR77 methylates arginine-9 of histone H3 (H3R8)
R-HSA-5661117 CCND1:CDK4:PRMT5:pT5-WDR77 methylates methyl-arginine-9 of histone H3
R-HSA-5218952 PRMT5:WDR77, PRMT7 methylate arginine-3 of histone H3 (H3R2)
R-HSA-5205861 COPRS:CCND1:CDK4:PRMT5:pT5-WDR77 methylates arginine-4 of histone H4 (H4R3)
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-6804760 Regulation of TP53 Activity through Methylation
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-191859 snRNP Assembly
R-HSA-4839726 Chromatin organization
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-212436 Generic Transcription Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8MTP3, A8MZ91, ANM5_HUMAN, B4DX49, B4DY30, B5BU10, D3DS33, E2QRE7, ENST00000324366.1, ENST00000324366.10, ENST00000324366.11, ENST00000324366.12, ENST00000324366.2, ENST00000324366.3, ENST00000324366.4, ENST00000324366.5, ENST00000324366.6, ENST00000324366.7, ENST00000324366.8, ENST00000324366.9, HRMT1L5, IBP72, JBP1, NM_006109, O14744, Q6IBR1, Q9UKH1, SKB1, uc317rqo.1, uc317rqo.2
UCSC ID: ENST00000324366.13_9
RefSeq Accession: NM_006109.5
Protein: O14744 (aka ANM5_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.