ExoCarta: Gene summary

Credits | Contact

Gene description for PDCD11
Gene name	programmed cell death 11
Gene symbol	PDCD11
Other names/aliases	ALG-4 ALG4 NFBP RRP5
Species	Homo sapiens
Database cross references - PDCD11
ExoCarta	ExoCarta_22984
Vesiclepedia	VP_22984
Entrez Gene	22984
HGNC	13408
MIM	612333
UniProt	Q14690
PDCD11 identified in sEVs derived from the following tissue/cell type
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942

Gene ontology annotations for PDCD11

Molecular Function
	RNA binding	GO:0003723	HDA
	RNA binding	GO:0003723	IBA
	protein binding	GO:0005515	IPI
	NF-kappaB binding	GO:0051059	IPI
Biological Process
	rRNA processing	GO:0006364	IEA
Subcellular Localization
	nucleus	GO:0005634	IDA
	nucleoplasm	GO:0005654	TAS
	nucleolus	GO:0005730	IBA
	cytosol	GO:0005829	IEA
	small-subunit processome	GO:0032040	IBA

Experiment description of studies that identified PDCD11 in sEVs

Experiment ID

489

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

Experiment description

Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells

Authors

"Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."

Journal name

Proteomics

Publication year

2023

Sample

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 6

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

490

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

Experiment description

Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells

Authors

"Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."

Journal name

Proteomics

Publication year

2023

Sample

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 7

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

491

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

Experiment description

Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells

Authors

"Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."

Journal name

Proteomics

Publication year

2023

Sample

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 8

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

492

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

Experiment description

Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells

Authors

"Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."

Journal name

Proteomics

Publication year

2023

Sample

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 9

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Protein-protein interactions for PDCD11

Protein Interactor

ExoCarta ID

Identification method

PubMed

Species

HNRNPH1

3187

Affinity Capture-RNA

Homo sapiens

FANCC

2176

Affinity Capture-MS

Homo sapiens

RIT1

6016

Negative Genetic

Homo sapiens

SSBP4

Affinity Capture-MS

Homo sapiens

SLIRP

81892

Proximity Label-MS

Homo sapiens

SENP3

26168

Affinity Capture-MS

Homo sapiens

RPL26L1

51121

Affinity Capture-MS

Homo sapiens

LGR4

55366

Affinity Capture-MS

Homo sapiens

COIL

Proximity Label-MS

Homo sapiens

PAXIP1

Affinity Capture-MS

Homo sapiens

KPNA1

3836

Affinity Capture-MS

Homo sapiens

KLF9

687

Proximity Label-MS

Homo sapiens

SRPK2

6733

Affinity Capture-MS

Homo sapiens

LHX2

Proximity Label-MS

Homo sapiens

RPL13A

23521

Affinity Capture-MS		Homo sapiens
Cross-Linking-MS (XL-MS)		Homo sapiens

NOP56

10528

Proximity Label-MS

Homo sapiens

CHCHD1

Proximity Label-MS

Homo sapiens

RPL14

9045

Cross-Linking-MS (XL-MS)

Homo sapiens

PNMAL1

Affinity Capture-MS

Homo sapiens

CAND1

55832

Affinity Capture-MS

Homo sapiens

RSBN1

Affinity Capture-MS

Homo sapiens

AEN

Affinity Capture-MS

Homo sapiens

SNX6

58533

Cross-Linking-MS (XL-MS)

Homo sapiens

SOX2

Proximity Label-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

CENPA

Proximity Label-MS

Homo sapiens

DNAJB6

10049

Proximity Label-MS

Homo sapiens

APEX1

328

Proximity Label-MS

Homo sapiens

HIST2H3A

333932

Cross-Linking-MS (XL-MS)

Homo sapiens

DDX23

9416

Proximity Label-MS

Homo sapiens

RPL4

6124

Affinity Capture-MS

Homo sapiens

LLPH

Affinity Capture-MS

Homo sapiens

KIF23

9493

Affinity Capture-MS

Homo sapiens

CCDC137

Affinity Capture-MS

Homo sapiens

E2F6

1876

Affinity Capture-MS

Homo sapiens

PRC1

9055

Affinity Capture-MS

Homo sapiens

NPM1

4869

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

ANOS1

3730

Affinity Capture-MS

Homo sapiens

FBL

2091

Affinity Capture-MS		Homo sapiens
Proximity Label-MS		Homo sapiens

POLR1E

Proximity Label-MS

Homo sapiens

OBSL1

23363

Affinity Capture-MS

Homo sapiens

ZSCAN31

Affinity Capture-MS

Homo sapiens

MRPS26

64949

Proximity Label-MS

Homo sapiens

ADARB1

104

Affinity Capture-MS

Homo sapiens

PRKRA

8575

Affinity Capture-MS

Homo sapiens

EXOSC4

54512

Affinity Capture-MS

Homo sapiens

EED

Affinity Capture-MS

Homo sapiens

SRP68

6730

Affinity Capture-MS

Homo sapiens

KLF4

Affinity Capture-MS

Homo sapiens

RRP8

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

AKAP14

Affinity Capture-MS

Homo sapiens

MECP2

4204

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

H2AFY2

55506

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

PKN2

5586

Affinity Capture-MS

Homo sapiens

MYCN

Affinity Capture-MS

Homo sapiens

MAK16

Affinity Capture-MS

Homo sapiens

RRP7A

27341

Affinity Capture-MS

Homo sapiens

CLK3

Affinity Capture-MS

Homo sapiens

KIF14

9928

Affinity Capture-MS

Homo sapiens

APOBEC3C

27350

Affinity Capture-MS

Homo sapiens

MAPK8IP2

Affinity Capture-MS

Homo sapiens

LIN28A

Affinity Capture-MS

Homo sapiens

RPP40

10799

Affinity Capture-MS

Homo sapiens

CHMP4C

92421

Affinity Capture-MS

Homo sapiens

TOLLIP

54472

Affinity Capture-MS

Homo sapiens

DDX31

Affinity Capture-MS

Homo sapiens

CDKN2AIP

Affinity Capture-MS

Homo sapiens

MRPL52

Affinity Capture-MS

Homo sapiens

HIST1H4A

8359

Affinity Capture-MS

Homo sapiens

DDX21

9188

Affinity Capture-MS

Homo sapiens

NOP9

161424

Affinity Capture-MS

Homo sapiens

PLEKHO1

51177

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

RBM28

55131

Affinity Capture-MS

Homo sapiens

NOL6

65083

Affinity Capture-MS

Homo sapiens

RBM19

9904

Affinity Capture-MS

Homo sapiens

RBM4B

Affinity Capture-MS

Homo sapiens

RPF2

84154

Affinity Capture-MS

Homo sapiens

BAG6

7917

Affinity Capture-MS

Homo sapiens

SRSF6

6431

Affinity Capture-MS

Homo sapiens

PURG

Affinity Capture-MS

Homo sapiens

NOP2

4839

Affinity Capture-MS

Homo sapiens

CEP19

Affinity Capture-MS

Homo sapiens

RPL5

6125

Affinity Capture-MS

Homo sapiens

AKR7L

246181

Affinity Capture-MS

Homo sapiens

RPL18A

6142

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

LHX1

Proximity Label-MS

Homo sapiens

NTRK1

4914

Affinity Capture-MS

Homo sapiens

FGF8

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

IFI16

3428

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

HIST1H1E

3008

Affinity Capture-MS

Homo sapiens

S100A8

6279

Two-hybrid

Homo sapiens

RPL36

25873

Affinity Capture-MS

Homo sapiens

HIST1H1C

3006

Affinity Capture-MS

Homo sapiens

DDX54

79039

Affinity Capture-MS

Homo sapiens

ZSCAN32

Affinity Capture-MS

Homo sapiens

HECTD1

25831

Affinity Capture-MS

Homo sapiens

ARL13B

200894

Affinity Capture-MS

Homo sapiens

C3orf17

Affinity Capture-MS

Homo sapiens

SRPK3

Affinity Capture-MS

Homo sapiens

MAGEB2

4113

Affinity Capture-MS

Homo sapiens

100

SPTY2D1

Affinity Capture-MS

Homo sapiens

101

KLF12

Proximity Label-MS

Homo sapiens

102

FGF13

Affinity Capture-MS

Homo sapiens

103

CD3EAP

Proximity Label-MS

Homo sapiens

104

SCARNA22

Affinity Capture-RNA

Homo sapiens

105

ANLN

54443

Affinity Capture-MS

Homo sapiens

106

FGFBP1

9982

Affinity Capture-MS

Homo sapiens

107

PAIP2B

Affinity Capture-MS

Homo sapiens

108

TLX2

Proximity Label-MS

Homo sapiens

109

ISG20L2

81875

Affinity Capture-MS

Homo sapiens

110

ZBTB2

57621

Affinity Capture-MS

Homo sapiens

111

BMS1

Affinity Capture-MS

Homo sapiens

112

RPL31

6160

Proximity Label-MS

Homo sapiens

113

UBE2H

7328

Affinity Capture-MS

Homo sapiens

114

ABT1

29777

Affinity Capture-MS

Homo sapiens

115

RPL13

6137

Affinity Capture-MS

Homo sapiens

116

RPL15

6138

Affinity Capture-MS

Homo sapiens

117

EIF6

3692

Proximity Label-MS

Homo sapiens

118

RC3H2

Affinity Capture-MS

Homo sapiens

119

SIRT7

Affinity Capture-MS

Homo sapiens

120

CD6

923

Affinity Capture-MS

Homo sapiens

121

ERCC4

Affinity Capture-MS

Homo sapiens

122

CUL3

8452

Affinity Capture-MS

Homo sapiens

123

RPL3

6122

Affinity Capture-MS

Homo sapiens

124

HNRNPA1

3178

Affinity Capture-MS

Homo sapiens

125

SUZ12

Affinity Capture-MS

Homo sapiens

126

GTF3C4

9329

Affinity Capture-MS

Homo sapiens

127

HNRNPCL2

440563

Affinity Capture-MS

Homo sapiens

128

ZC3H10

Affinity Capture-MS

Homo sapiens

129

POP7

Affinity Capture-MS

Homo sapiens

130

SOX15

Proximity Label-MS

Homo sapiens

131

ZNF512

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

132

FKBP5

2289

Affinity Capture-MS

Homo sapiens

133

FGF3

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

134

DGKZ

Affinity Capture-MS

Homo sapiens

135

RPP25

Affinity Capture-MS

Homo sapiens

136

MYC

Affinity Capture-MS

Homo sapiens

137

RPA3

6119

Proximity Label-MS

Homo sapiens

138

CEBPZ

Affinity Capture-MS

Homo sapiens

139

FOSL1

Affinity Capture-MS

Homo sapiens

140

DNAJC9

23234

Proximity Label-MS

Homo sapiens

141

RPS14

6208

Affinity Capture-MS

Homo sapiens

142

NDC80

10403

Affinity Capture-MS

Homo sapiens

143

ETV3

Proximity Label-MS

Homo sapiens

144

RPL23A

6147

Affinity Capture-MS

Homo sapiens

145

RPL18

6141

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

146

DDRGK1

65992

Affinity Capture-MS

Homo sapiens

147

RNF2

Affinity Capture-MS

Homo sapiens

148

BMI1

Affinity Capture-MS

Homo sapiens

149

ZC3HAV1

56829

Affinity Capture-MS

Homo sapiens

150

H2AFB2

Affinity Capture-MS

Homo sapiens

151

NOG

9241

Affinity Capture-MS

Homo sapiens

152

LMNA

4000

Proximity Label-MS

Homo sapiens

153

ZC3H3

Affinity Capture-MS

Homo sapiens

154

FTSJ3

117246

Affinity Capture-MS

Homo sapiens

155

TAF1A

Affinity Capture-MS

Homo sapiens

156

CCDC8

Affinity Capture-MS

Homo sapiens

157

RPS16

6217

Affinity Capture-MS

Homo sapiens

158

Cbx1

Affinity Capture-MS

Mus musculus

159

SURF6

Affinity Capture-MS

Homo sapiens

160

PLEKHA4

57664

Affinity Capture-MS

Homo sapiens

161

USE1

55850

Affinity Capture-MS

Homo sapiens

162

AUH

549

Proximity Label-MS

Homo sapiens

163

PARP1

142

Proximity Label-MS

Homo sapiens

164

RPS3

6188

Affinity Capture-MS

Homo sapiens

165

ILF3

3609

Affinity Capture-MS

Homo sapiens

166

RPLP0

6175

Affinity Capture-MS

Homo sapiens

167

IFNA14

Affinity Capture-MS

Homo sapiens

168

TP53

7157

Affinity Capture-MS

Homo sapiens

169

RRS1

23212

Affinity Capture-MS

Homo sapiens

170

BRIX1

55299

Affinity Capture-MS

Homo sapiens

171

KIAA0020

9933

Affinity Capture-MS

Homo sapiens

172

BUD13

Affinity Capture-MS

Homo sapiens

173

MNDA

4332

Affinity Capture-MS

Homo sapiens

174

GRSF1

2926

Proximity Label-MS

Homo sapiens

175

USP36

Affinity Capture-MS

Homo sapiens

176

RPP25L

Affinity Capture-MS

Homo sapiens

177

POP4

10775

Affinity Capture-MS

Homo sapiens

178

ZNF48

Affinity Capture-MS

Homo sapiens

179

COX8A

Proximity Label-MS

Homo sapiens

180

E2F4

Affinity Capture-MS

Homo sapiens

181

MAGEA9

Affinity Capture-MS

Homo sapiens

182

NIFK

84365

Proximity Label-MS

Homo sapiens

183

HNRNPK

3190

Cross-Linking-MS (XL-MS)

Homo sapiens

184

WIF1

11197

Affinity Capture-MS

Homo sapiens

185

NOC3L

64318

Affinity Capture-MS

Homo sapiens

186

DDX27

55661

Affinity Capture-MS

Homo sapiens

187

DHX40

Proximity Label-MS

Homo sapiens

188

RBM4

5936

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

189

NEIL1

Affinity Capture-MS

Homo sapiens

190

NOC2L

26155

Affinity Capture-MS

Homo sapiens

191

RPS24

6229

Proximity Label-MS

Homo sapiens

192

PDIK1L

Affinity Capture-MS

Homo sapiens

193

SUPT6H

6830

Co-fractionation

Homo sapiens

194

RPL23AP32

56969

Affinity Capture-MS

Homo sapiens

195

RPS6

6194

Proximity Label-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

196

RPL8

6132

Affinity Capture-MS

Homo sapiens

197

TRMT10B

Affinity Capture-MS

Homo sapiens

198

RPL28

6158

Affinity Capture-MS

Homo sapiens

199

PTGES3

10728

Affinity Capture-MS

Homo sapiens

200

CUL7

9820

Affinity Capture-MS

Homo sapiens

201

KRAS

3845

Negative Genetic

Homo sapiens

202

HNRNPU

3192

Affinity Capture-MS

Homo sapiens

203

GATAD1

Affinity Capture-MS

Homo sapiens

204

RPL36AL

6166

Affinity Capture-MS

Homo sapiens

205

RC3H1

149041

Affinity Capture-MS

Homo sapiens

206

ZNF467

Affinity Capture-MS

Homo sapiens

207

RPL17

6139

Affinity Capture-MS

Homo sapiens

208

HERC5

51191

Affinity Capture-MS

Homo sapiens

View the network

Pathways in which PDCD11 is involved

Pathway	Evidence	Source
Major pathway of rRNA processing in the nucleolus and cytosol	TAS	Reactome
Metabolism of RNA	IEA	Reactome
Metabolism of RNA	TAS	Reactome
rRNA modification in the nucleus and cytosol	IEA	Reactome
rRNA processing	IEA	Reactome
rRNA processing	TAS	Reactome
rRNA processing in the nucleus and cytosol	IEA	Reactome
rRNA processing in the nucleus and cytosol	TAS	Reactome

Perform bioinformatics analysis of your extracellular vesicle data set using FunRich, a open access standalone tool. NEW UPDATED VERSION OF FunRich available for download (12/09/2016) from here