DUSP11

gene
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Also known as PIR1

Summary

DUSP11 (dual specificity phosphatase 11, HGNC:3066) is a protein-coding gene on chromosome 2p13.1, encoding RNA/RNP complex-1-interacting phosphatase (O75319). Possesses RNA 5’-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity.

The protein encoded by this gene is a member of the dual specificity protein phosphatase subfamily. These phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the mitogen-activated protein (MAP) kinase superfamily (MAPK/ERK, SAPK/JNK, p38), which is associated with cellular proliferation and differentiation. Different members of the family of dual specificity phosphatases show distinct substrate specificities for various MAP kinases, different tissue distribution and subcellular localization, and different modes of inducibility of their expression by extracellular stimuli. This gene product is localized to the nucleus and binds directly to RNA and splicing factors, and thus it is suggested to participate in nuclear mRNA metabolism.

Source: NCBI Gene 8446 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 63 total
  • MANE Select transcript: NM_003584

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3066
Approved symbolDUSP11
Namedual specificity phosphatase 11
Location2p13.1
Locus typegene with protein product
StatusApproved
AliasesPIR1
Ensembl geneENSG00000144048
Ensembl biotypeprotein_coding
OMIM603092
Entrez8446

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 13 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000272444, ENST00000443070, ENST00000452812, ENST00000477458, ENST00000480948, ENST00000696050, ENST00000696051, ENST00000696052, ENST00000696053, ENST00000696054, ENST00000696055, ENST00000696056, ENST00000696057, ENST00000717658, ENST00000909492, ENST00000909493, ENST00000972157

RefSeq mRNA: 2 — MANE Select: NM_003584 NM_001424649, NM_003584

CCDS: CCDS1928

Canonical transcript exons

ENST00000272444 — 9 exons

ExonStartEnd
ENSE000017928987377987473780103
ENSE000034837687377491373775044
ENSE000034938817377830173778376
ENSE000035059987376926573769325
ENSE000035376517377380073773923
ENSE000035795627376716173767207
ENSE000040330687376641873766594
ENSE000040330697376682873766903
ENSE000040331817376221373762859

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 95.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.4608 / max 271.5399, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
2914941.38331821
291482.07751193

Top tissues by expression

298 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
esophagus squamous epitheliumUBERON:000692095.11gold quality
epithelium of esophagusUBERON:000197693.29gold quality
penisUBERON:000098992.86gold quality
secondary oocyteCL:000065592.61gold quality
calcaneal tendonUBERON:000370191.48gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.13gold quality
upper leg skinUBERON:000426291.02gold quality
esophagus mucosaUBERON:000246990.96gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.95gold quality
mammalian vulvaUBERON:000099790.84gold quality
oral cavityUBERON:000016790.73gold quality
gingivaUBERON:000182890.72gold quality
endometrium epitheliumUBERON:000481190.62gold quality
gingival epitheliumUBERON:000194990.52gold quality
caput epididymisUBERON:000435890.48gold quality
epithelium of nasopharynxUBERON:000195190.40gold quality
lower esophagus mucosaUBERON:003583490.39gold quality
nasopharynxUBERON:000172890.38gold quality
right uterine tubeUBERON:000130290.26gold quality
oocyteCL:000002389.83gold quality
squamous epitheliumUBERON:000691489.08gold quality
bone marrowUBERON:000237188.96gold quality
pharyngeal mucosaUBERON:000035588.76gold quality
skin of abdomenUBERON:000141688.76gold quality
skin of hipUBERON:000155488.64gold quality
tonsilUBERON:000237288.49gold quality
zone of skinUBERON:000001488.46gold quality
vaginaUBERON:000099688.32gold quality
palpebral conjunctivaUBERON:000181288.28gold quality
lymph nodeUBERON:000002988.14gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.40

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

Literature-anchored findings (GeneRIF, showing 8)

  • results suggest that DUSP11 contributes to p53-dependent inhibition of cell proliferation and that it might be involved in regulating RNA splicing through SAM68 (PMID:19120688)
  • the atomic structure of a catalytically inactive mutant (C152S) of the human PIR1 phosphatase core (PIR1-core, residues 29-205), refined at 1.20 A resolution. (PMID:24447265)
  • DUSP11 converts the 5’ triphosphate of miRNA precursors to a 5’ monophosphate, promoting loading of derivative 5p miRNAs into Argonaute proteins via a Dicer-coupled 5’ monophosphate-dependent strand selection mechanism. (PMID:27798849)
  • DUSP11 regulates host and viral non-coding RNAs in mammalian cells. (PMID:28296624)
  • PIR gene expression is highly dependent on the expression of HR-HPV E6 and E7 oncoproteins HPV-positive cell lines. (PMID:29118270)
  • DUSP11 limits both miR-122-dependent and miR-122-independent Hepatitis C RNA accumulation. (PMID:29672716)
  • Results implicate DUSP11 as an important component of XRN-mediated restriction of hepatitis C virus replication. (PMID:30038017)
  • Atypical phosphatase DUSP11 inhibition promotes nc886 expression and potentiates gemcitabine-mediated cell death through NF-kB modulation. (PMID:39048662)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriodusp11ENSDARG00000038156
mus_musculusDusp11ENSMUSG00000030002
rattus_norvegicusDusp11ENSRNOG00000045539

Paralogs (1): RNGTT (ENSG00000111880)

Protein

Protein identifiers

RNA/RNP complex-1-interacting phosphataseO75319 (reviewed: O75319)

Alternative names: Dual specificity protein phosphatase 11, Phosphatase that interacts with RNA/RNP complex 1

All UniProt accessions (9): O75319, A0A8Q3SI82, A0A8Q3SI85, A0A8Q3SIB0, A0A8Q3SIC9, A0A8Q3SIE6, A0A8Q3SIF8, A0A8Q3WM77, H7C0E6

UniProt curated annotations — full annotation on UniProt →

Function. Possesses RNA 5’-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity. In addition, has phosphatase activity with ATP, ADP and O-methylfluorescein phosphate (in vitro). Binds to RNA. May participate in nuclear mRNA metabolism.

Subunit / interactions. Monomer. May interact with SFRS7 and SFRS9/SRP30C.

Subcellular location. Nucleus. Nucleus speckle.

Miscellaneous. Produced by alternative initiation. Based on proteomic data. Major isoform.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class dual specificity subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
O75319-33yes
O75319-11
O75319-22

RefSeq proteins (2): NP_001411578, NP_003575* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000340Dual-sp_phosphatase_cat-domDomain
IPR000387Tyr_Pase_domDomain
IPR016130Tyr_Pase_ASActive_site
IPR020422TYR_PHOSPHATASE_DUAL_domDomain
IPR029021Prot-tyrosine_phosphatase-likeHomologous_superfamily
IPR051029

Pfam: PF00782

UniProt features (33 total): helix 9, strand 6, mutagenesis site 5, sequence conflict 3, splice variant 3, active site 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, binding site 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
4NYHX-RAY DIFFRACTION1.2
4MBBX-RAY DIFFRACTION1.85
4JMJX-RAY DIFFRACTION2.38

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O75319-F169.340.52

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 152 (phosphocysteine intermediate); 158 (proton donor/acceptor)

Ligand- & substrate-binding residues (1): 153–158

Mutagenesis-validated functional residues (5):

PositionPhenotype
119no effect on phosphatase activity with atp and adp.
152loss of activity. no effect in rna-binding.
154strongly decreases phosphatase activity with atp and adp.
157strongly decreases phosphatase activity with atp and adp.
192slightly decreases phosphatase activity with atp. strongly decreases phosphatase activity with adp.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): RNGTGGGC_UNKNOWN, MORF_RAB5A, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MORF_PSMC2, PUJANA_CHEK2_PCC_NETWORK, ZIC1_01, GENTILE_UV_HIGH_DOSE_DN, GENTILE_UV_RESPONSE_CLUSTER_D5, SCHLOSSER_SERUM_RESPONSE_DN, GOBP_DEPHOSPHORYLATION, GOBP_PROTEIN_DEPHOSPHORYLATION, ZHANG_BREAST_CANCER_PROGENITORS_UP, GOCC_NUCLEAR_SPECK

GO Biological Process (3): RNA processing (GO:0006396), protein dephosphorylation (GO:0006470), dephosphorylation (GO:0016311)

GO Molecular Function (7): RNA binding (GO:0003723), polynucleotide 5’-phosphatase activity (GO:0004651), protein tyrosine phosphatase activity (GO:0004725), phosphatase activity (GO:0016791), catalytic activity (GO:0003824), phosphoprotein phosphatase activity (GO:0004721), hydrolase activity (GO:0016787)

GO Cellular Component (6): fibrillar center (GO:0001650), nucleus (GO:0005634), nucleoplasm (GO:0005654), mitochondrion (GO:0005739), nuclear speck (GO:0016607), intercellular bridge (GO:0045171)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
phosphatase activity2
intracellular membrane-bounded organelle2
gene expression1
RNA biosynthetic process1
primary metabolic process1
dephosphorylation1
protein modification process1
phosphate-containing compound metabolic process1
nucleic acid binding1
phosphoprotein phosphatase activity1
phosphoric ester hydrolase activity1
molecular_function1
catalytic activity, acting on a protein1
catalytic activity1
nucleolus1
nuclear lumen1
cytoplasm1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

1084 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DUSP11DUSP5Q16690894
DUSP11RNF144BQ7Z419729
DUSP11DXOO77932692
DUSP11PIWIL1Q96J94612
DUSP11XRN1Q8IZH2590
DUSP11XRN2Q9H0D6589
DUSP11ERI1Q8IV48501
DUSP11DICER1Q9UPY3501
DUSP11ADARB1P78555496
DUSP11DUSP21Q9H596487
DUSP11DCP2Q8IU60474
DUSP11DUSP3P51452460
DUSP11SACK1HQ6ZRV2460
DUSP11DUSP12Q9UNI6442
DUSP11DUSP22Q9NRW4438

IntAct

69 interactions, top by confidence:

ABTypeScore
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
FGF3GTPBP10psi-mi:“MI:0914”(association)0.530
APBA3DUSP11psi-mi:“MI:0914”(association)0.530
KLHL40CBX4psi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
PRKCADUSP11psi-mi:“MI:0914”(association)0.530
NNOP56psi-mi:“MI:0914”(association)0.530
HNRNPA1PTCD1psi-mi:“MI:0914”(association)0.530
ZNRD2MYO9Apsi-mi:“MI:0914”(association)0.530
ZNRD2CCDC85Cpsi-mi:“MI:0914”(association)0.530
THOC1TARS3psi-mi:“MI:0914”(association)0.350
HNRNPA1MATR3psi-mi:“MI:0914”(association)0.350
Csde1TXNDC9psi-mi:“MI:0914”(association)0.350
KIF11MAP4psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
PLOD1COL25A1psi-mi:“MI:0914”(association)0.350
APOBEC3DIGF2BP3psi-mi:“MI:0914”(association)0.350
SYNCRIPHNRNPRpsi-mi:“MI:0914”(association)0.350
HNRNPA1HNRNPRpsi-mi:“MI:0914”(association)0.350
AHCYL2AHCYL1psi-mi:“MI:0914”(association)0.350
CIAO1SOX1psi-mi:“MI:0914”(association)0.350
FBLN5ZNF320psi-mi:“MI:0914”(association)0.350
NOTCH2ZNF320psi-mi:“MI:0914”(association)0.350

BioGRID (100): DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), NIPAL4 (Affinity Capture-MS), DUSP11 (Affinity Capture-MS), RPS15 (Affinity Capture-MS), MRPS35 (Affinity Capture-MS)

ESM2 similar proteins: A2AD83, A3KMI0, A4Q9F0, A8WRV1, D4A280, O18017, O75319, O95835, P23293, P34442, P81299, Q04859, Q0IJ08, Q2M1K5, Q3MK94, Q4CQJ5, Q4DTX9, Q4KM79, Q5E999, Q5HYM0, Q5HZJ0, Q5U243, Q62726, Q6DJS0, Q6DTM3, Q6NXK5, Q6P158, Q6P5D3, Q6ZT98, Q6ZUT3, Q7PNM6, Q7ZXG4, Q8BGX1, Q8BMD7, Q8BY02, Q8BYR2, Q8C015, Q8K3Y6, Q8R151, Q8TE76

Diamond homologs: O10274, O55236, O60942, O75319, P24656, P34442, Q17607, Q22707, Q4KM79, Q5E999, Q6NXK5, Q6NY98, Q6NT99, Q9BVJ7, Q9P7H1, Q6PFY9, Q6CWR0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 83 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Peptide chain elongation717.8×8e-06
Viral mRNA Translation717.8×8e-06
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA717.6×8e-06
Selenocysteine synthesis716.8×8e-06
Eukaryotic Translation Termination716.8×8e-06
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)716.5×8e-06
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA716.5×8e-06
Formation of a pool of free 40S subunits715.7×9e-06

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis618.2×2e-04
cytoplasmic translation717.3×7e-05
negative regulation of translation513.1×3e-03
translation79.6×1e-03
mRNA splicing, via spliceosome78.6×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

63 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance43
Likely benign6
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

885 predictions. Top by Δscore:

VariantEffectΔscore
2:73762856:TTTT:Tacceptor_gain1.0000
2:73762860:C:CCacceptor_gain1.0000
2:73762861:T:Cacceptor_gain1.0000
2:73762861:T:TCacceptor_gain1.0000
2:73762867:C:CTacceptor_gain1.0000
2:73766821:GACTT:Gdonor_loss1.0000
2:73766822:ACTT:Adonor_loss1.0000
2:73766823:CTTAC:Cdonor_loss1.0000
2:73766824:TTA:Tdonor_loss1.0000
2:73766825:TACT:Tdonor_loss1.0000
2:73766826:A:ACdonor_gain1.0000
2:73766826:A:Cdonor_loss1.0000
2:73766826:ACTTT:Adonor_gain1.0000
2:73766827:C:CTdonor_gain1.0000
2:73766827:CT:Cdonor_gain1.0000
2:73766827:CTT:Cdonor_gain1.0000
2:73766827:CTTT:Cdonor_gain1.0000
2:73766827:CTTTC:Cdonor_gain1.0000
2:73766899:GAATA:Gacceptor_gain1.0000
2:73766900:AATA:Aacceptor_gain1.0000
2:73766901:ATA:Aacceptor_gain1.0000
2:73766902:TA:Tacceptor_gain1.0000
2:73766904:C:CCacceptor_gain1.0000
2:73767159:A:ACdonor_gain1.0000
2:73767160:C:CCdonor_gain1.0000
2:73767160:CA:Cdonor_gain1.0000
2:73767160:CATT:Cdonor_gain1.0000
2:73769260:CTTA:Cdonor_loss1.0000
2:73769261:TTACC:Tdonor_loss1.0000
2:73769262:TAC:Tdonor_loss1.0000

AlphaMissense

2479 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:73769274:A:GL209P0.996
2:73769285:C:AR205S0.996
2:73769285:C:GR205S0.996
2:73769286:C:AR205M0.996
2:73773832:A:TV181D0.996
2:73778329:A:GF97S0.996
2:73769267:G:CC211W0.995
2:73769286:C:GR205T0.995
2:73769295:C:TG202D0.995
2:73769310:A:TV197D0.995
2:73773844:A:GF177S0.995
2:73778316:T:AK101N0.995
2:73778316:T:GK101N0.995
2:73769280:C:TG207D0.994
2:73769288:G:CN204K0.994
2:73769288:G:TN204K0.994
2:73769295:C:AG202V0.994
2:73778373:C:AW82C0.994
2:73778373:C:GW82C0.994
2:73778375:A:GW82R0.994
2:73778375:A:TW82R0.994
2:73766899:G:CF229L0.993
2:73766899:G:TF229L0.993
2:73766901:A:GF229L0.993
2:73769268:C:TC211Y0.993
2:73769278:A:CY208D0.993
2:73773843:G:CF177L0.993
2:73773843:G:TF177L0.993
2:73773845:A:GF177L0.993
2:73769269:A:GC211R0.992

dbSNP variants (sampled 300 via entrez): RS1000366231 (2:73767723 T>C), RS1000529318 (2:73779275 T>C), RS1000530558 (2:73778545 C>T), RS1000782872 (2:73765849 T>C,G), RS1000801749 (2:73772605 G>A), RS1000957102 (2:73766081 G>A), RS1001081248 (2:73778884 C>A,T), RS1001136964 (2:73772898 C>G,T), RS1001353406 (2:73765768 T>C), RS1001382929 (2:73772717 A>G), RS1001475640 (2:73777408 C>G,T), RS1001505350 (2:73778087 T>C), RS1001528143 (2:73777822 A>C,T), RS1001838875 (2:73779473 A>G), RS1001867502 (2:73772786 A>G)

Disease associations

OMIM: gene MIM:603092 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000651_1Creatinine levels1.000000e-15
GCST001220_3Metabolite levels1.000000e-11
GCST006249_13Serum metabolite levels1.000000e-77
GCST006249_37Serum metabolite levels9.000000e-13
GCST006249_52Serum metabolite levels5.000000e-11
GCST006249_62Serum metabolite levels7.000000e-24
GCST006249_77Serum metabolite levels7.000000e-33
GCST008153_48Lean body mass9.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004725metabolite measurement
EFO:0004995lean body mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1affects expression, increases expression3
sodium arseniteaffects expression, decreases expression2
Air Pollutantsaffects expression, increases abundance, decreases expression2
Benzo(a)pyreneincreases mutagenesis, increases expression2
Cisplatinincreases expression2
TAK-243increases sumoylation1
dicrotophosdecreases expression1
4-oxoretinoic aciddecreases expression1
triphenyl phosphateaffects expression1
cobaltous chloridedecreases expression1
tanshinoneincreases expression1
zinc chromateincreases abundance, increases expression1
beta-methylcholineaffects expression1
chromium hexavalent ionincreases abundance, increases expression1
azoxystrobinincreases expression1
K 7174increases expression1
abrineincreases expression1
picoxystrobinincreases expression1
Alitretinoindecreases expression1
Glyphosateincreases expression1
Atrazinedecreases expression1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Golddecreases expression1
Methyl Methanesulfonateincreases expression1
Ozoneaffects expression, increases abundance1
Ribonucleotidesaffects binding1
Rotenoneincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.