ExoCarta: Gene summary

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Gene description for ATXN3
Gene name	ataxin 3
Gene symbol	ATXN3
Other names/aliases	AT3 ATX3 JOS MJD MJD1 SCA3
Species	Homo sapiens
Database cross references - ATXN3
ExoCarta	ExoCarta_4287
Vesiclepedia	VP_4287
Entrez Gene	4287
HGNC	7106
MIM	607047
UniProt	P54252
ATXN3 identified in exosomes derived from the following tissue/cell type
Gastric cancer cells	33991177
Gastric cancer cells	33991177
Gastric cancer cells	33991177

Gene ontology annotations for ATXN3

Molecular Function
	cysteine-type deubiquitinase activity	GO:0004843	IBA
	cysteine-type deubiquitinase activity	GO:0004843	IDA
	cysteine-type deubiquitinase activity	GO:0004843	ISS
	cysteine-type deubiquitinase activity	GO:0004843	TAS
	protein binding	GO:0005515	IPI
	ubiquitin protein ligase binding	GO:0031625	IPI
	ubiquitin protein ligase binding	GO:0031625	ISS
	identical protein binding	GO:0042802	IPI
	ATPase binding	GO:0051117	IPI
	K63-linked deubiquitinase activity	GO:0061578	IDA
	K48-linked deubiquitinase activity	GO:1990380	IDA
Biological Process
	microtubule cytoskeleton organization	GO:0000226	IMP
	nucleotide-excision repair	GO:0006289	TAS
	ubiquitin-dependent protein catabolic process	GO:0006511	ISS
	protein quality control for misfolded or incompletely synthesized proteins	GO:0006515	IBA
	protein quality control for misfolded or incompletely synthesized proteins	GO:0006515	ISS
	chemical synaptic transmission	GO:0007268	TAS
	nervous system development	GO:0007399	TAS
	regulation of cell-substrate adhesion	GO:0010810	IMP
	protein deubiquitination	GO:0016579	TAS
	actin cytoskeleton organization	GO:0030036	IMP
	cellular response to amino acid starvation	GO:0034198	IDA
	cellular response to heat	GO:0034605	ISS
	monoubiquitinated protein deubiquitination	GO:0035520	ISS
	proteasome-mediated ubiquitin-dependent protein catabolic process	GO:0043161	IBA
	proteasome-mediated ubiquitin-dependent protein catabolic process	GO:0043161	ISS
	intermediate filament cytoskeleton organization	GO:0045104	IMP
	protein K63-linked deubiquitination	GO:0070536	IDA
	protein K48-linked deubiquitination	GO:0071108	IDA
	cellular response to misfolded protein	GO:0071218	ISS
	negative regulation of TORC1 signaling	GO:1904262	IBA
	negative regulation of TORC1 signaling	GO:1904262	IDA
	positive regulation of ERAD pathway	GO:1904294	IBA
	positive regulation of ERAD pathway	GO:1904294	IMP
	protein localization to cytosolic proteasome complex	GO:1904327	IMP
	positive regulation of ubiquitin-dependent protein catabolic process	GO:2000060	IDA
Subcellular Localization
	nucleus	GO:0005634	IBA
	nucleus	GO:0005634	IDA
	nucleoplasm	GO:0005654	IDA
	nucleoplasm	GO:0005654	TAS
	nucleolus	GO:0005730	IDA
	cytoplasm	GO:0005737	TAS
	mitochondrial matrix	GO:0005759	ISS
	lysosomal membrane	GO:0005765	IDA
	endoplasmic reticulum membrane	GO:0005789	IDA
	cytosol	GO:0005829	IDA
	cytosol	GO:0005829	TAS
	plasma membrane	GO:0005886	IDA
	nuclear matrix	GO:0016363	IEA
	mitochondrial membrane	GO:0031966	ISS
	nuclear inclusion body	GO:0042405	ISS
	synapse	GO:0045202	IEA

Experiment description of studies that identified ATXN3 in exosomes

Experiment ID

363

MISEV standards
✘	Biophysical techniques
✔ TSG101\|GAPDH\|AQP1\|CD151\|CD81\|CD82\|CD9\|EPCAM\|FLOT1\|FLOT2\|ICAM1\|ITGA2B\|LAMP2\|RAB35\|RAB5A\|RAB5B\|SDCBP\|TFRC\|UCHL1	Enriched markers
✔ DCLK1	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

33991177

Organism

Homo sapiens

Experiment description

Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells

Authors

"Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."

Journal name

Proteomics

Publication year

2021

Sample

Gastric cancer cells

Sample name

MKN1 - 100K pellet

Isolation/purification methods

Differential centrifugation
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectrometry

Experiment ID

364

MISEV standards
✘	Biophysical techniques
✔ TSG101\|GAPDH\|AQP1\|CD151\|CD81\|CD82\|CD9\|EPCAM\|FLOT1\|FLOT2\|ICAM1\|ITGA2B\|LAMP2\|RAB35\|RAB5A\|RAB5B\|SDCBP\|TFRC\|UCHL1	Enriched markers
✔ DCLK1	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

33991177

Organism

Homo sapiens

Experiment description

Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells

Authors

"Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."

Journal name

Proteomics

Publication year

2021

Sample

Gastric cancer cells

Sample name

MKN1 - 100K pellet

Isolation/purification methods

Differential centrifugation
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectrometry

Experiment ID

365

MISEV standards
✘	Biophysical techniques
✔ TSG101\|GAPDH\|AQP1\|CD151\|CD81\|CD82\|CD9\|EPCAM\|FLOT1\|FLOT2\|ICAM1\|ITGA2B\|LAMP2\|RAB35\|RAB5A\|RAB5B\|SDCBP\|TFRC\|UCHL1	Enriched markers
✔ DCLK1	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

33991177

Organism

Homo sapiens

Experiment description

Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells

Authors

"Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."

Journal name

Proteomics

Publication year

2021

Sample

Gastric cancer cells

Sample name

MKN1 - 100K pellet

Isolation/purification methods

Differential centrifugation
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectrometry

Protein-protein interactions for ATXN3

Protein Interactor

ExoCarta ID

Identification method

PubMed

Species

EIF3A

8661

Affinity Capture-MS

Homo sapiens

UBL4A

8266

Affinity Capture-MS

Homo sapiens

TK1

7083

Two-hybrid

Homo sapiens

LDHB

3945

Affinity Capture-MS

Homo sapiens

PKM

5315

Affinity Capture-MS

Homo sapiens

ACOT9

23597

Affinity Capture-MS

Homo sapiens

DNAJB2

3300

Affinity Capture-Western

Homo sapiens

TEX11

Two-hybrid

Homo sapiens

UBA1

7317

Affinity Capture-MS

Homo sapiens

TUBB8

347688

Affinity Capture-MS

Homo sapiens

GPALPP1

Affinity Capture-MS

Homo sapiens

UBC

7316

Affinity Capture-MS		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens
Biochemical Activity		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens
Reconstituted Complex		Homo sapiens
Co-crystal Structure		Homo sapiens
Affinity Capture-MS		Homo sapiens
Biochemical Activity		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens
Biochemical Activity		Homo sapiens
Co-crystal Structure		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens
Co-crystal Structure		Homo sapiens

CSE1L

1434

Affinity Capture-MS

Homo sapiens

USP21

Biochemical Activity

Homo sapiens

PRPF40A

55660

Affinity Capture-MS

Homo sapiens

GCN1L1

10985

Affinity Capture-MS

Homo sapiens

SOX2

Affinity Capture-MS

Homo sapiens

KDELR1

10945

Affinity Capture-MS

Homo sapiens

APEX1

328

Affinity Capture-RNA

Homo sapiens

HDAC3

8841

Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens

DPM1

8813

Affinity Capture-MS

Homo sapiens

DARS

1615

Affinity Capture-MS

Homo sapiens

SF3B1

23451

Affinity Capture-MS

Homo sapiens

TIMM23

100287932

Affinity Capture-MS

Homo sapiens

PSMD12

5718

Affinity Capture-MS

Homo sapiens

HSPH1

10808

Affinity Capture-MS

Homo sapiens

PSMB6

5694

Affinity Capture-MS

Homo sapiens

RPS9

6203

Affinity Capture-MS

Homo sapiens

IGF2

3481

Affinity Capture-MS

Homo sapiens

ARHGAP19

Two-hybrid

Homo sapiens

SNRPD3

6634

Affinity Capture-MS

Homo sapiens

UBE2W

Biochemical Activity

Homo sapiens

PSMC1

5700

Affinity Capture-MS

Homo sapiens

RNF126

Affinity Capture-MS

Homo sapiens

RAD23A

5886

Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens
Two-hybrid		Homo sapiens
Two-hybrid		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens

BAG5

9529

Affinity Capture-MS

Homo sapiens

ANXA7

310

Two-hybrid

Homo sapiens

TCP1

6950

Affinity Capture-MS

Homo sapiens

UBE4B

10277

Reconstituted Complex

Homo sapiens

PSMA4

5685

Affinity Capture-MS

Homo sapiens

PGAM5

192111

Affinity Capture-MS

Homo sapiens

PSMD2

5708

Affinity Capture-MS

Homo sapiens

MYH9

4627

Affinity Capture-MS

Homo sapiens

ACTN4

Affinity Capture-MS

Homo sapiens

CYC1

1537

Affinity Capture-MS

Homo sapiens

ENO1

2023

Affinity Capture-MS

Homo sapiens

DBT

1629

Affinity Capture-MS

Homo sapiens

CAPN1

823

Biochemical Activity		Homo sapiens
Protein-peptide		Homo sapiens

TOMM20L

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

TRIM63

Biochemical Activity

Homo sapiens

SLC25A5

292

Affinity Capture-MS

Homo sapiens

UBR2

23304

Affinity Capture-MS

Homo sapiens

SSR4

6748

Affinity Capture-MS

Homo sapiens

BIRC2

Affinity Capture-MS

Homo sapiens

HSPA5

3309

Affinity Capture-MS

Homo sapiens

Tuba1a

64158

Affinity Capture-MS

Rattus norvegicus

SDHA

6389

Affinity Capture-MS

Homo sapiens

HSPE1

3336

Affinity Capture-MS

Homo sapiens

BCAP31

10134

Affinity Capture-MS

Homo sapiens

EEF1B2

1933

Affinity Capture-MS

Homo sapiens

RBBP4

5928

Affinity Capture-MS

Homo sapiens

SDC2

6383

Affinity Capture-MS

Homo sapiens

TUBA4A

7277

Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens

PCBP1

5093

Affinity Capture-MS

Homo sapiens

DND1

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

RPA3

6119

Affinity Capture-MS

Homo sapiens

NME1

4830

Affinity Capture-MS

Homo sapiens

TMCO1

54499

Affinity Capture-MS

Homo sapiens

DLST

1743

Affinity Capture-MS

Homo sapiens

HSPA4

3308

Affinity Capture-MS

Homo sapiens

PSMC5

5705

Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens

LAMA4

3910

Affinity Capture-MS

Homo sapiens

PML

5371

Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens

LIG3

3980

Affinity Capture-Western

Homo sapiens

PRKDC

5591

Affinity Capture-MS

Homo sapiens

RPS16

6217

Affinity Capture-MS

Homo sapiens

STUB1

10273

Biochemical Activity		Homo sapiens
Biochemical Activity		Homo sapiens
Biochemical Activity		Homo sapiens
Biochemical Activity		Homo sapiens
Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens
Biochemical Activity		Homo sapiens

PSMB2

5690

Affinity Capture-MS

Homo sapiens

RELA

5970

Affinity Capture-MS

Homo sapiens

FASN

2194

Affinity Capture-MS

Homo sapiens

PSAT1

29968

Affinity Capture-MS

Homo sapiens

RBM25

58517

Affinity Capture-MS

Homo sapiens

PCMT1

5110

Affinity Capture-MS

Homo sapiens

CKB

1152

Affinity Capture-MS

Homo sapiens

DCTN2

10540

Affinity Capture-MS

Homo sapiens

TKT

7086

Affinity Capture-MS

Homo sapiens

HSP90AA1

3320

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

SSBP1

6742

Affinity Capture-MS

Homo sapiens

PSMA1

5682

Affinity Capture-MS

Homo sapiens

DYNC1H1

1778

Affinity Capture-MS

Homo sapiens

WWP2

11060

Biochemical Activity

Homo sapiens

GAPDH

2597

Affinity Capture-MS

Homo sapiens

PSMA5

5686

Affinity Capture-MS

Homo sapiens

PSMC4

5704

Affinity Capture-MS

Homo sapiens

PTCH1

Affinity Capture-Western

Homo sapiens

SEC61A1

29927

Affinity Capture-MS

Homo sapiens

PSMA6

5687

Affinity Capture-MS

Homo sapiens

HSP90AB2P

391634

Affinity Capture-MS

Homo sapiens

SPRTN

Affinity Capture-MS

Homo sapiens

100

GART

2618

Affinity Capture-MS

Homo sapiens

101

HSPA6

3310

Affinity Capture-MS

Homo sapiens

102

USP13

Affinity Capture-MS

Homo sapiens

103

KCTD10

83892

Affinity Capture-MS

Homo sapiens

104

RPA2

6118

Affinity Capture-MS

Homo sapiens

105

HSP90AB1

3326

Affinity Capture-MS

Homo sapiens

106

HSPB1

3315

Affinity Capture-MS

Homo sapiens

107

NDUFA4

4697

Affinity Capture-MS

Homo sapiens

108

SYVN1

84447

Affinity Capture-Western

Homo sapiens

109

COPA

1314

Affinity Capture-MS

Homo sapiens

110

RPS3

6188

Affinity Capture-MS

Homo sapiens

111

NCOR1

Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens

112

PGK1

5230

Affinity Capture-MS

Homo sapiens

113

OGDH

4967

Affinity Capture-MS

Homo sapiens

114

ASIC1

Two-hybrid

Homo sapiens

115

NPM1

4869

Affinity Capture-MS

Homo sapiens

116

ACTR1A

10121

Affinity Capture-MS

Homo sapiens

117

PRDX2

7001

Affinity Capture-MS

Homo sapiens

118

STIP1

10963

Affinity Capture-MS

Homo sapiens

119

Ubr2

224826

Affinity Capture-Western

Mus musculus

120

DNAJC7

7266

Affinity Capture-MS

Homo sapiens

121

HAP1

Affinity Capture-Western		Homo sapiens
Affinity Capture-Western		Homo sapiens

122

DDX6

1656

Affinity Capture-MS

Homo sapiens

123

TIMM50

92609

Affinity Capture-MS

Homo sapiens

124

TMEM136

Affinity Capture-MS

Homo sapiens

125

USP7

7874

Affinity Capture-MS

Homo sapiens

126

MAD2L1

4085

Affinity Capture-MS

Homo sapiens

127

GSK3B

2932

Two-hybrid		Homo sapiens
Affinity Capture-Western		Homo sapiens
Biochemical Activity		Homo sapiens
Reconstituted Complex		Homo sapiens

128

CCT2

10576

Affinity Capture-MS

Homo sapiens

129

GTF2I

2969

Affinity Capture-MS

Homo sapiens

130

PFN1

5216

Affinity Capture-MS

Homo sapiens

131

SLC1A5

6510

Affinity Capture-MS

Homo sapiens

132

DSG1

1828

Affinity Capture-MS

Homo sapiens

133

PRPF8

10594

Affinity Capture-MS

Homo sapiens

134

CDKN1A

Two-hybrid

Homo sapiens

135

AMFR

267

Affinity Capture-Western		Homo sapiens
Co-localization		Homo sapiens

136

PSMD14

10213

Affinity Capture-MS

Homo sapiens

137

BAG6

7917

Affinity Capture-MS

Homo sapiens

138

SNRNP200

23020

Affinity Capture-MS

Homo sapiens

139

CCT6A

908

Affinity Capture-MS

Homo sapiens

140

TUBA1C

84790

Affinity Capture-MS

Homo sapiens

141

BCL7C

Affinity Capture-MS

Homo sapiens

142

S100A8

6279

Affinity Capture-MS

Homo sapiens

143

HNRNPL

3191

Affinity Capture-MS

Homo sapiens

144

IARS

3376

Affinity Capture-MS

Homo sapiens

145

GET4

51608

Affinity Capture-MS

Homo sapiens

146

LANCL1

10314

Affinity Capture-MS

Homo sapiens

147

AIMP2

7965

Affinity Capture-MS

Homo sapiens

148

TUBB

203068

Reconstituted Complex		Homo sapiens
Affinity Capture-MS		Homo sapiens

149

ACLY

Affinity Capture-MS

Homo sapiens

150

AIFM1

9131

Affinity Capture-MS

Homo sapiens

151

CANX

821

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

152

RPS2

6187

Affinity Capture-MS

Homo sapiens

153

XPO1

7514

Affinity Capture-MS

Homo sapiens

154

UBE2L3

7332

Reconstituted Complex

Homo sapiens

155

SLC25A22

Affinity Capture-MS

Homo sapiens

156

ATP5F1

515

Affinity Capture-MS

Homo sapiens

157

TUBB4B

10383

Affinity Capture-MS

Homo sapiens

158

LARS

51520

Affinity Capture-MS

Homo sapiens

159

Cep152

Affinity Capture-MS

Mus musculus

160

EFTUD2

9343

Affinity Capture-MS

Homo sapiens

161

RPS27

6232

Affinity Capture-MS

Homo sapiens

162

ATP5J2

9551

Affinity Capture-MS

Homo sapiens

163

SLC3A2

6520

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

164

DDB1

1642

Affinity Capture-MS

Homo sapiens

165

Cntfr

Affinity Capture-MS

Rattus norvegicus

166

PSMB1

5689

Affinity Capture-MS

Homo sapiens

167

TAF4

6874

Affinity Capture-Western

Homo sapiens

168

HUWE1

10075

Affinity Capture-MS

Homo sapiens

169

PHGDH

26227

Affinity Capture-MS

Homo sapiens

170

DSP

1832

Affinity Capture-MS

Homo sapiens

171

SLC25A3

5250

Affinity Capture-MS

Homo sapiens

172

TFG

10342

Affinity Capture-MS

Homo sapiens

173

TRAF2

7186

Affinity Capture-MS

Homo sapiens

174

PARP1

142

Affinity Capture-MS

Homo sapiens

175

TP53

7157

Reconstituted Complex		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens
Biochemical Activity		Homo sapiens

176

MKNK1

Two-hybrid

Homo sapiens

177

HDAC6

10013

Reconstituted Complex

Homo sapiens

178

RPS12

6206

Affinity Capture-MS

Homo sapiens

179

RPS4X

6191

Affinity Capture-MS

Homo sapiens

180

SQSTM1

8878

Affinity Capture-Western		Homo sapiens
Reconstituted Complex		Homo sapiens

181

HNRNPK

3190

Affinity Capture-MS

Homo sapiens

182

EEF1D

1936

Affinity Capture-MS

Homo sapiens

183

ATP1A1

476

Affinity Capture-MS

Homo sapiens

184

PRDX1

5052

Affinity Capture-MS

Homo sapiens

185

C1QBP

708

Affinity Capture-MS

Homo sapiens

186

HSPA4L

22824

Affinity Capture-MS

Homo sapiens

187

AEBP2

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

188

PSMD1

5707

Affinity Capture-MS

Homo sapiens

189

PSMD3

5709

Affinity Capture-MS

Homo sapiens

190

RAD23B

5887

Reconstituted Complex		Homo sapiens
Affinity Capture-Western		Homo sapiens
Two-hybrid		Homo sapiens
Affinity Capture-Western		Homo sapiens
Two-hybrid		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens