ExoCarta: Gene summary

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Gene description for Rps13
Gene name	ribosomal protein S13
Gene symbol	Rps13
Other names/aliases	2700063M04Rik
Species	Mus musculus
Database cross references - Rps13
ExoCarta	ExoCarta_68052
Vesiclepedia	VP_68052
Entrez Gene	68052
UniProt	P62301
Rps13 identified in sEVs derived from the following tissue/cell type
Colon cancer cells	37309723
Mast cells	17486113
T-cell lymphoma cells	37309723

Gene ontology annotations for Rps13

Molecular Function
	mRNA binding	GO:0003729	ISO
	structural constituent of ribosome	GO:0003735	IBA
	structural constituent of ribosome	GO:0003735	IDA
	structural constituent of ribosome	GO:0003735	ISO
	mRNA 5'-UTR binding	GO:0048027	IEA
	mRNA 5'-UTR binding	GO:0048027	ISO
	small ribosomal subunit rRNA binding	GO:0070181	IBA
	5.8S rRNA binding	GO:1990932	ISO
Biological Process
	cytoplasmic translation	GO:0002181	NAS
	negative regulation of RNA splicing	GO:0033119	IEA
	negative regulation of RNA splicing	GO:0033119	ISO
	ribosomal small subunit biogenesis	GO:0042274	ISO
	ribosomal small subunit biogenesis	GO:0042274	ISS
Subcellular Localization
	nucleus	GO:0005634	ISO
	nucleolus	GO:0005730	IBA
	nucleolus	GO:0005730	IEA
	nucleolus	GO:0005730	ISO
	cytoplasm	GO:0005737	NAS
	cytosol	GO:0005829	TAS
	postsynaptic density	GO:0014069	IEA
	postsynaptic density	GO:0014069	ISO
	cytosolic ribosome	GO:0022626	ISO
	cytosolic small ribosomal subunit	GO:0022627	IBA
	cytosolic small ribosomal subunit	GO:0022627	IDA
	cytosolic small ribosomal subunit	GO:0022627	ISO
	cytosolic small ribosomal subunit	GO:0022627	NAS
	small-subunit processome	GO:0032040	ISO
	small-subunit processome	GO:0032040	ISS
	synapse	GO:0045202	ISO

Experiment description of studies that identified Rps13 in sEVs

Experiment ID

907

MISEV standards
✔ EM	Biophysical techniques
✔ Tsg101\|Sdcbp\|Cd151\|Gapdh\|Lamp2\|Cd81\|Cd82\|Cd9\|Cd63\|Cd80\|Flot2\|Tfrc\|Rab35\|Rab5a	Enriched markers
✔ HSPA5	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

37309723

Organism

Mus musculus

Experiment description

Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells

Authors

"Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."

Journal name

Proteomics

Publication year

2023

Sample

Colon cancer cells

Sample name

C26

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

MISEV standards
✔ EM	Biophysical techniques
✔ CD63	Enriched markers
✘	Negative markers
✘	Particle analysis

Identified molecule

protein

Identification method

Mass spectrometry

PubMed ID

17486113

Organism

Mus musculus
Homo sapiens

Experiment description

Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells.

Authors

"Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, Lotvall JO"

Journal name

NCB

Publication year

2007

Sample

Mast cells

Sample name

MC9
Bone marrow-derived mast cells
HMC-1

Isolation/purification methods

Filtration
Ultracentrifugation
Sucrose density gradient

Flotation density

1.11-1.21 g/mL

Molecules identified in the study

Protein
mRNA
miRNA

Methods used in the study

Mass spectrometry [MALDI TOF]
Western blotting
Microarray
miRCURY LNA Array

Experiment ID

908

MISEV standards
✔ EM	Biophysical techniques
✔ Tsg101\|Sdcbp\|Cd151\|Gapdh\|Lamp2\|Cd81\|Cd82\|Cd9\|Cd63\|Cd80\|Flot2\|Tfrc\|Rab35\|Rab5a	Enriched markers
✔ HSPA5	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

37309723

Organism

Mus musculus

Experiment description

Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells

Authors

"Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."

Journal name

Proteomics

Publication year

2023

Sample

T-cell lymphoma cells

Sample name

EL4

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 Rps13

Protein Interactor

ExoCarta ID

Identification method

PubMed

Species

Rps27a

78294

Co-fractionation

Mus musculus

Rps3

27050

Co-fractionation

Mus musculus

Rpl11

67025

Co-fractionation

Mus musculus

Rpl35

66489

Co-fractionation

Mus musculus

Rps18

20084

Co-fractionation

Mus musculus

Hsp90ab1

15516

Co-fractionation

Mus musculus

Rps28

54127

Co-fractionation

Mus musculus

Rps10

67097

Co-fractionation

Mus musculus

Rpl13a

22121

Co-fractionation

Mus musculus

Eif5a

276770

Co-fractionation

Mus musculus

Rpl15

66480

Co-fractionation

Mus musculus

Rplp2

67186

Co-fractionation

Mus musculus

Actg1

11465

Co-fractionation

Mus musculus

Rps4x

20102

Co-fractionation

Mus musculus

Rpl4

67891

Co-fractionation

Mus musculus

Rpl14

67115

Co-fractionation

Mus musculus

Rps2

16898

Co-fractionation

Mus musculus

Rps5

20103

Co-fractionation

Mus musculus

Rps8

20116

Co-fractionation

Mus musculus

Rps23

66475

Co-fractionation

Mus musculus

Rpl7a

27176

Co-fractionation

Mus musculus

Tmem173

Proximity Label-MS

Mus musculus

Rpl32

19951

Co-fractionation

Mus musculus

Rbm39

170791

Co-fractionation

Mus musculus

Rpl6

19988

Co-fractionation

Mus musculus

Kctd13

Affinity Capture-MS

Mus musculus

Rps19

20085

Co-fractionation

Mus musculus

Rps26

27370

Co-fractionation

Mus musculus

Rps3a1

20091

Co-fractionation

Mus musculus

Pkm

18746

Co-fractionation

Mus musculus

Rps11

27207

Co-fractionation

Mus musculus

Eef2

13629

Co-fractionation

Mus musculus

Rpl31

114641

Co-fractionation

Mus musculus

Rps7

20115

Co-fractionation

Mus musculus

Rpl22

19934

Co-fractionation

Mus musculus

Psmc1

19179

Co-fractionation

Mus musculus

Rpl5

100503670

Co-fractionation

Mus musculus

Srp9

Co-fractionation

Mus musculus

Fzr1

Affinity Capture-MS

Mus musculus

Psmd7

17463

Co-fractionation

Mus musculus

Rps24

20088

Co-fractionation

Mus musculus

Rpl7

19989

Co-fractionation

Mus musculus

Eef1a1

13627

Co-fractionation

Mus musculus

Rps9

76846

Co-fractionation

Mus musculus

Rps21

66481

Co-fractionation

Mus musculus

Rpl12

269261

Co-fractionation

Mus musculus

Rps15a

267019

Co-fractionation

Mus musculus

Gnb2l1

14694

Co-fractionation

Mus musculus

Rpl18

19899

Co-fractionation

Mus musculus

Psmd3

22123

Co-fractionation

Mus musculus

Rpl26

19941

Co-fractionation

Mus musculus

Rpl13

270106

Co-fractionation

Mus musculus

Rplp0

11837

Co-fractionation

Mus musculus

Rpl23a

268449

Co-fractionation

Mus musculus

Rps14

20044

Co-fractionation

Mus musculus

Rps6

20104

Co-fractionation

Mus musculus

Rpl30

19946

Co-fractionation

Mus musculus

Eed

Affinity Capture-MS

Mus musculus

Rpsa

16785

Co-fractionation

Mus musculus

Rpl8

26961

Co-fractionation

Mus musculus

Eef1b2

55949

Co-fractionation

Mus musculus

Rpl3

27367

Co-fractionation

Mus musculus

Rps16

20055

Co-fractionation

Mus musculus

Hba

15121

Co-fractionation

Mus musculus

Fancd2

Affinity Capture-MS

Mus musculus

Kcna3

Affinity Capture-MS

Mus musculus

Rps12

20042

Co-fractionation

Mus musculus

Pgam1

18648

Co-fractionation

Mus musculus

View the network

Pathways in which Rps13 is involved

Pathway	Evidence	Source
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	IEA	Reactome
Cap-dependent Translation Initiation	IEA	Reactome
Eukaryotic Translation Initiation	IEA	Reactome
Formation of a pool of free 40S subunits	IEA	Reactome
Formation of the ternary complex, and subsequently, the 43S complex	IEA	Reactome
GTP hydrolysis and joining of the 60S ribosomal subunit	IEA	Reactome
L13a-mediated translational silencing of Ceruloplasmin expression	IEA	Reactome
Major pathway of rRNA processing in the nucleolus and cytosol	IEA	Reactome
Metabolism of proteins	IEA	Reactome
Metabolism of RNA	IEA	Reactome
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	IEA	Reactome
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	IEA	Reactome
Nonsense-Mediated Decay (NMD)	IEA	Reactome
Ribosomal scanning and start codon recognition	IEA	Reactome
rRNA processing	IEA	Reactome
rRNA processing in the nucleus and cytosol	IEA	Reactome
SRP-dependent cotranslational protein targeting to membrane	IEA	Reactome
Translation	IEA	Reactome
Translation initiation complex formation	IEA	Reactome

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