Protein: UBP39
Ubiquitin carboxyl-terminal hydrolase 39 (EC 3.4.19.12) (SAD1 homolog) (U4/U6.U5 tri-snRNP-associated 65 kDa protein)

Gene: UBP39, USP39
Organism: Homo sapiens
Interactions: 173
UniProt ID: Q53GS9

Gene Ontology (top 5):
GO:0000245 - spliceosomal complex assembly
GO:0000398 - mRNA splicing, via spliceosome
GO:0005634 - nucleus
GO:0005654 - nucleoplasm
GO:0005681 - spliceosomal complex

Download interactions: TXT   MITAB-2.5

Interaction Interactor Experiments Homologs Category Interaction
Score
Confidence

1199421

PRP8
Pre-mRNA-processing-splicing factor 8

5

2

High-throughput

0.922

High

1199446

SNR40
U5 small nuclear ribonucleoprotein 40 kDa protein

4

13

High-throughput

0.903

High

1138284

U5S1
116 kDa U5 small nuclear ribonucleoprotein component

4

8

Small-scale

0.895

High

321562

PRP6
Pre-mRNA-processing factor 6

3

4

Small-scale

0.847

High

209282

PRP4
U4/U6 small nuclear ribonucleoprotein Prp4

2

15

High-throughput

0.811

High

1199439

PRP31
U4/U6 small nuclear ribonucleoprotein Prp31

2

5

Small-scale

0.789

High

241878

PRKN
E3 ubiquitin-protein ligase parkin

2

17

High-throughput

0.754

High

683470

IKBA
NF-kappa-B inhibitor alpha

1

5

Small-scale

0.724

High

275896

UBP12
Ubiquitin carboxyl-terminal hydrolase 12

1

17

High-throughput

0.691

High

1149080

SF3A1
Splicing factor 3A subunit 1

1

11

High-throughput

0.691

High

335856

CD2B2
CD2 antigen cytoplasmic tail-binding protein 2

5

0

High-throughput

0.690

High

1109138

PRP4K
Serine/threonine-protein kinase PRP4 homolog

3

13

High-throughput

0.675

High

1199450

SRPK1
SRSF protein kinase 1

3

20

Small-scale

0.670

High

1199455

DDX23
Probable ATP-dependent RNA helicase DDX23

3

18

Small-scale

0.656

High

464977

SP1
Transcription factor Sp1

2

5

Small-scale

0.624

High

1006443

SRPK2
SRSF protein kinase 2

2

18

High-throughput

0.619

High

1131044

UBP10
Ubiquitin carboxyl-terminal hydrolase 10

1

18

Small-scale

0.618

High

1199456

FACD2
Fanconi anemia group D2 protein

1

5

High-throughput

0.618

High

212258

SNUT1
U4/U6.U5 tri-snRNP-associated protein 1

2

2

Small-scale

0.611

High

215119

PRPF3
U4/U6 small nuclear ribonucleoprotein Prp3

2

1

Small-scale

0.611

High

1126935

RBM39
RNA-binding protein 39

2

4

High-throughput

0.611

High

1199419

LRRK2
Leucine-rich repeat serine/threonine-protein kinase 2

2

9

High-throughput

0.602

High

1089211

TRI26
Tripartite motif-containing protein 26

2

20

Small-scale

0.586

High

260046

BRD4
Bromodomain-containing protein 4

2

20

High-throughput

0.584

High

998392

H31
Histone H3.1

2

8

High-throughput

0.584

High

354994

CHK2
Serine/threonine-protein kinase Chk2

1

6

Small-scale

0.578

High

573838

CCNB1
G2/mitotic-specific cyclin-B1

1

3

Small-scale

0.578

High

1199470

SIR7
NAD-dependent protein deacetylase sirtuin-7

1

11

Small-scale

0.578

High

764811

CTNB1
Catenin beta-1

1

18

Small-scale

0.561

High

1061585

FOXM1
Forkhead box protein M1

1

10

Small-scale

0.561

High

208273

RRP8
Ribosomal RNA-processing protein 8

1

1

High-throughput

0.536

High

285948

SF3B1
Splicing factor 3B subunit 1

1

6

High-throughput

0.536

High

289569

U520
U5 small nuclear ribonucleoprotein 200 kDa helicase

1

20

High-throughput

0.536

High

344546

LSM8
U6 snRNA-associated Sm-like protein LSm8

1

5

High-throughput

0.536

High

413958

P53
Cellular tumor antigen p53

1

9

High-throughput

0.536

High

471855

RU2B
U2 small nuclear ribonucleoprotein B''

1

9

High-throughput

0.536

High

478074

SNRPA
U1 small nuclear ribonucleoprotein A

1

6

High-throughput

0.536

High

542056

TOP1
DNA topoisomerase 1

1

1

High-throughput

0.536

High

574307

RSMB
Small nuclear ribonucleoprotein-associated proteins B and B'

1

1

High-throughput

0.536

High

775134

FUS
RNA-binding protein FUS

1

7

High-throughput

0.536

High

854097

KI67
Proliferation marker protein Ki-67

1

12

High-throughput

0.536

High

973939

RUXF
Small nuclear ribonucleoprotein F

1

4

High-throughput

0.536

High

1065228

SSRP1
FACT complex subunit SSRP1

1

11

High-throughput

0.536

High

1148594

SF3A2
Splicing factor 3A subunit 2

1

4

High-throughput

0.536

High

1160151

CPSF6
Cleavage and polyadenylation specificity factor subunit 6

1

8

High-throughput

0.536

High

1199429

CAND1
Cullin-associated NEDD8-dissociated protein 1

1

6

High-throughput

0.536

High

1199437

NOC3L
Nucleolar complex protein 3 homolog

1

3

High-throughput

0.536

High

1199442

PRP16
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

1

13

High-throughput

0.536

High

1199452

CDC5L
Cell division cycle 5-like protein

1

3

High-throughput

0.536

High

1199454

RBM42
RNA-binding protein 42

1

7

High-throughput

0.536

High

1199466

COPRS
Coordinator of PRMT5 and differentiation stimulator

1

1

High-throughput

0.536

High

1199469

DDX21
Nucleolar RNA helicase 2

1

19

High-throughput

0.536

High

1199472

GAR1
H/ACA ribonucleoprotein complex subunit 1

1

2

High-throughput

0.536

High

1199473

TLS1
Splicing factor C9orf78

1

1

High-throughput

0.536

High

1199479

LSM7
U6 snRNA-associated Sm-like protein LSm7

1

5

High-throughput

0.536

High

1199481

SRPK3
SRSF protein kinase 3

1

17

High-throughput

0.536

High

1199482

PA2G4
Proliferation-associated protein 2G4

1

2

High-throughput

0.536

High

1199423

RHG36
Rho GTPase-activating protein 36

2

9

High-throughput

0.521

High

1199444

H2B1H
Histone H2B type 1-H

1

20

High-throughput

0.515

High

329756

ZRAB2
Zinc finger Ran-binding domain-containing protein 2

1

0

High-throughput

0.513

High

480173

RU1C
U1 small nuclear ribonucleoprotein C

1

0

High-throughput

0.513

High

973737

RUXE
Small nuclear ribonucleoprotein E

1

0

High-throughput

0.513

High

974574

SMD2
Small nuclear ribonucleoprotein Sm D2

1

0

High-throughput

0.513

High

1013948

TXN4A
Thioredoxin-like protein 4A

1

0

High-throughput

0.513

High

1199425

TM10C
tRNA methyltransferase 10 homolog C

1

0

High-throughput

0.513

High

1199438

SNR27
U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein

1

0

High-throughput

0.513

High

1199445

TSR2
Pre-rRNA-processing protein TSR2 homolog

1

0

High-throughput

0.513

High

608887

PFKAL
ATP-dependent 6-phosphofructokinase, liver type

1

4

Small-scale

0.512

High

1199475

SAE1
SUMO-activating enzyme subunit 1

1

3

Small-scale

0.501

High

389413

FINC
Fibronectin

1

4

High-throughput

0.489

High

540028

BCR
Breakpoint cluster region protein

1

10

High-throughput

0.489

High

902272

RB27A
Ras-related protein Rab-27A

1

3

High-throughput

0.489

High

1013301

HTRA4
Serine protease HTRA4

1

3

High-throughput

0.489

High

1199422

RL22L
Ribosomal protein eL22-like

1

1

High-throughput

0.489

High

1199459

DDX24
ATP-dependent RNA helicase DDX24

1

20

High-throughput

0.489

High

1199463

MRM3
rRNA methyltransferase 3, mitochondrial

1

1

High-throughput

0.489

High

1199483

MAST1
Microtubule-associated serine/threonine-protein kinase 1

1

13

High-throughput

0.489

High

900358

FXR2
RNA-binding protein FXR2

1

7

High-throughput

0.481

High

1125124

TRI25
E3 ubiquitin/ISG15 ligase TRIM25

1

20

High-throughput

0.481

High

1199457

TRIM8
E3 ubiquitin-protein ligase TRIM8

1

20

High-throughput

0.481

High

1199458

TRIM5
Tripartite motif-containing protein 5

1

20

High-throughput

0.481

High

1199464

TRI39
E3 ubiquitin-protein ligase TRIM39

1

20

High-throughput

0.481

High

1199484

TRAF6
TNF receptor-associated factor 6

1

20

High-throughput

0.481

High

134764

SAP18
Histone deacetylase complex subunit SAP18

1

1

High-throughput

0.479

High

143030

NFIB
Nuclear factor 1 B-type

1

2

High-throughput

0.479

High

157455

CTRO
Citron Rho-interacting kinase

1

5

High-throughput

0.479

High

178025

LSM1
U6 snRNA-associated Sm-like protein LSm1

1

5

High-throughput

0.479

High

223099

PRC1
Protein regulator of cytokinesis 1

1

4

High-throughput

0.479

High

247948

NUPR1
Nuclear protein 1

1

1

High-throughput

0.479

High

350028

SNAI1
Zinc finger protein SNAI1

1

15

Small-scale

0.479

High

372204

MYC
Myc proto-oncogene protein

1

18

High-throughput

0.479

High

404108

GCR
Glucocorticoid receptor

1

16

High-throughput

0.479

High

406247

MYCN
N-myc proto-oncogene protein

1

17

High-throughput

0.479

High

472792

RU17
U1 small nuclear ribonucleoprotein 70 kDa

1

10

High-throughput

0.479

High

474033

NFIC
Nuclear factor 1 C-type

1

4

High-throughput

0.479

High

588850

RFA2
Replication protein A 32 kDa subunit

1

5

High-throughput

0.479

High

620402

NUCL
Nucleolin

1

5

High-throughput

0.479

High

674192

BRD2
Bromodomain-containing protein 2

1

20

High-throughput

0.479

High

695625

RFA1
Replication protein A 70 kDa DNA-binding subunit

1

7

High-throughput

0.479

High

731360

STIP1
Stress-induced-phosphoprotein 1

1

5

High-throughput

0.479

High

766611

PHB1
Prohibitin 1

1

1

High-throughput

0.479

High

768351

RFA3
Replication protein A 14 kDa subunit

1

6

High-throughput

0.479

High

822699

VHL
von Hippel-Lindau disease tumor suppressor

1

3

Small-scale

0.479

High

832313

ID1
DNA-binding protein inhibitor ID-1

1

2

Small-scale

0.479

High

838113

STAT1
Signal transducer and activator of transcription 1-alpha/beta

1

7

Small-scale

0.479

High

885003

DGKG
Diacylglycerol kinase gamma

1

1

Small-scale

0.479

High

904802

MECP2
Methyl-CpG-binding protein 2

1

8

High-throughput

0.479

High

951703

PTEN
Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN

1

9

Small-scale

0.479

High

970611

UBE2H
Ubiquitin-conjugating enzyme E2 H

1

8

High-throughput

0.479

High

979771

H4
Histone H4

1

5

High-throughput

0.479

High

980816

H2B1C
Histone H2B type 1-C/E/F/G/I

1

20

High-throughput

0.479

High

1016911

H33
Histone H3.3

1

8

High-throughput

0.479

High

1027503

HNRPU
Heterogeneous nuclear ribonucleoprotein U

1

14

Small-scale

0.479

High

1045360

TF65
Transcription factor p65

1

7

High-throughput

0.479

High

1061010

SRSF1
Serine/arginine-rich splicing factor 1

1

9

Small-scale

0.479

High

1088383

CHD3
Chromodomain-helicase-DNA-binding protein 3

1

10

High-throughput

0.479

High

1092145

NFX1
Transcriptional repressor NF-X1

1

10

High-throughput

0.479

High

1132740

CHD4
Chromodomain-helicase-DNA-binding protein 4

1

10

High-throughput

0.479

High

1135698

HAPR1
HUWE1-associated protein modifying stress responses 1

1

2

High-throughput

0.479

High

1137057

SART3
Spliceosome associated factor 3, U4/U6 recycling protein

1

13

High-throughput

0.479

High

1141157

BRD3
Bromodomain-containing protein 3

1

20

High-throughput

0.479

High

1155434

EZH2
Histone-lysine N-methyltransferase EZH2

1

8

Small-scale

0.479

High

1161475

IF16
Gamma-interferon-inducible protein 16

1

6

High-throughput

0.479

High

1199420

RN123
E3 ubiquitin-protein ligase RNF123

1

13

High-throughput

0.479

High

1199424

TRI67
Tripartite motif-containing protein 67

1

20

High-throughput

0.479

High

1199426

MEPCE
7SK snRNA methylphosphate capping enzyme

1

1

High-throughput

0.479

High

1199428

ZCH18
Zinc finger CCCH domain-containing protein 18

1

12

High-throughput

0.479

High

1199433

ZGPAT
Zinc finger CCCH-type with G patch domain-containing protein

1

3

Small-scale

0.479

High

1199435

FBX22
F-box only protein 22

1

1

High-throughput

0.479

High

1199441

BAP1
Ubiquitin carboxyl-terminal hydrolase BAP1

1

11

High-throughput

0.479

High

1199443

ESR2
Estrogen receptor beta

1

15

High-throughput

0.479

High

1199447

AURKB
Aurora kinase B

1

16

High-throughput

0.479

High

1199453

EPAS1
Endothelial PAS domain-containing protein 1

1

13

Small-scale

0.479

High

1199460

CCDC8
Coiled-coil domain-containing protein 8

1

5

High-throughput

0.479

High

1199461

BACD3
BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 3

1

8

Small-scale

0.479

High

1199462

KAT8
Histone acetyltransferase KAT8

1

3

Small-scale

0.479

High

1199465

BRD7
Bromodomain-containing protein 7

1

20

High-throughput

0.479

High

1199467

PRDM9
Histone-lysine N-methyltransferase PRDM9

1

5

High-throughput

0.479

High

1199468

ANLN
Anillin

1

2

High-throughput

0.479

High

1199471

RAD18
E3 ubiquitin-protein ligase RAD18

1

3

High-throughput

0.479

High

1199476

ZRAN1
Ubiquitin thioesterase ZRANB1

1

10

High-throughput

0.479

High

1199480

FZR1
Fizzy-related protein homolog

1

12

High-throughput

0.479

High

1199485

ARI1
E3 ubiquitin-protein ligase ARIH1

1

12

High-throughput

0.479

High

1199486

LSM4
U6 snRNA-associated Sm-like protein LSm4

1

3

High-throughput

0.479

High

129146

MEN1
Menin

1

0

High-throughput

0.458

High

1029856

RUNX1
Runt-related transcription factor 1

1

0

High-throughput

0.458

High

1199418

EAPP
E2F-associated phosphoprotein

1

0

High-throughput

0.458

High

1199427

SLN11
Schlafen family member 11

1

0

High-throughput

0.458

High

1199431

CMTR1
Cap-specific mRNA

1

0

High-throughput

0.458

High

1199436

DOT1L
Histone-lysine N-methyltransferase, H3 lysine-79 specific

1

0

High-throughput

0.458

High

1199440

SMG7
Nonsense-mediated mRNA decay factor SMG7

1

0

High-throughput

0.458

High

1199451

MMS19
MMS19 nucleotide excision repair protein homolog

1

0

High-throughput

0.458

High

1199474

WWOX
WW domain-containing oxidoreductase

1

0

High-throughput

0.458

High

1199477

ZNHI2
Zinc finger HIT domain-containing protein 2

1

0

High-throughput

0.458

High

422245

A4
Amyloid-beta precursor protein

1

6

High-throughput

0.457

High

429996

JUN
Transcription factor Jun

1

11

High-throughput

0.445

High

756229

MCM7
DNA replication licensing factor MCM7

1

11

Small-scale

0.445

High

765586

BMI1
Polycomb complex protein BMI-1

1

20

High-throughput

0.445

High

1199478

DDX41
Probable ATP-dependent RNA helicase DDX41

1

15

High-throughput

0.445

High

1199487

Q9Y654
Heterochromatin-specific nonhistone protein

1

14

High-throughput

0.445

High

272237

OBSL1
Obscurin-like protein 1

1

5

High-throughput

0.437

High

293788

CD123
Translation initiation factor eIF2 assembly protein

1

3

High-throughput

0.437

High

345907

STAU1
Double-stranded RNA-binding protein Staufen homolog 1

1

12

High-throughput

0.437

High

412041

NTRK1
High affinity nerve growth factor receptor

1

15

High-throughput

0.437

High

761084

GBRA3
Gamma-aminobutyric acid receptor subunit alpha-3

1

1

High-throughput

0.437

High

1134935

CUL7
Cullin-7

1

4

High-throughput

0.437

High

1199432

RHG24
Rho GTPase-activating protein 24

1

4

High-throughput

0.437

High

1199449

DDRGK
DDRGK domain-containing protein 1

1

1

High-throughput

0.437

High

1111030

SNW1
SNW domain-containing protein 1

1

0

High-throughput

0.426

High

886925

CEBPA
CCAAT/enhancer-binding protein alpha

1

5

High-throughput

0.408

High

1199430

DAAF5
Dynein axonemal assembly factor 5

1

0

Small-scale

0.261

Low

1199434

POC5
Centrosomal protein POC5

1

0

Small-scale

0.232

Low

1199448

S41A3
Solute carrier family 41 member 3

1

0

High-throughput

0.232

Low


Service provided by Combinatics, Japan

Last updated: 11Aug2025