Gene description for Ybx1
Gene name Y box protein 1
Gene symbol Ybx1
Other names/aliases 1700102N10Rik
C79409
EF1A
MSY1
Nsep1
YB-1
dbpB
mYB-1a
Species Mus musculus
 Database cross references - Ybx1
ExoCarta ExoCarta_22608
Vesiclepedia VP_22608
Entrez Gene 22608
UniProt P62960  
 Ybx1 identified in sEVs derived from the following tissue/cell type
Colon cancer cells 37309723    
Neural stem cells 25242146    
Pancreatic cells 19351151    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Ybx1
Molecular Function
    p53 binding GO:0002039 ISO
    nucleic acid binding GO:0003676 IBA
    chromatin binding GO:0003682 IDA
    single-stranded DNA binding GO:0003697 IDA
    single-stranded DNA binding GO:0003697 ISO
    RNA binding GO:0003723 ISO
    RNA binding GO:0003723 ISS
    mRNA binding GO:0003729 IDA
    mRNA binding GO:0003729 ISO
    protein binding GO:0005515 IPI
    miRNA binding GO:0035198 ISO
    miRNA binding GO:0035198 ISS
    sequence-specific DNA binding GO:0043565 ISO
    GTPase binding GO:0051020 IEA
    GTPase binding GO:0051020 ISO
    C5-methylcytidine-containing RNA reader activity GO:0062153 ISO
    C5-methylcytidine-containing RNA reader activity GO:0062153 ISS
    sequence-specific double-stranded DNA binding GO:1990837 IEA
    sequence-specific double-stranded DNA binding GO:1990837 ISO
Biological Process
    negative regulation of transcription by RNA polymerase II GO:0000122 IDA
    negative regulation of transcription by RNA polymerase II GO:0000122 IGI
    negative regulation of transcription by RNA polymerase II GO:0000122 IMP
    in utero embryonic development GO:0001701 IGI
    in utero embryonic development GO:0001701 IMP
    regulation of DNA-templated transcription GO:0006355 ISO
    regulation of DNA-templated transcription GO:0006355 ISS
    mRNA processing GO:0006397 IEA
    RNA splicing GO:0008380 IEA
    epidermis development GO:0008544 IMP
    regulation of gene expression GO:0010468 IBA
    negative regulation of translation GO:0017148 ISS
    positive regulation of transcription by RNA polymerase II GO:0045944 IEA
    positive regulation of transcription by RNA polymerase II GO:0045944 ISO
    mRNA stabilization GO:0048255 ISO
    mRNA stabilization GO:0048255 ISS
    embryonic morphogenesis GO:0048598 ISS
    RNA transport GO:0050658 ISO
    RNA transport GO:0050658 ISS
    tRNA transport GO:0051031 ISO
    tRNA transport GO:0051031 ISS
    negative regulation of striated muscle cell differentiation GO:0051154 IDA
    positive regulation of cell division GO:0051781 IEA
    CRD-mediated mRNA stabilization GO:0070934 ISO
    CRD-mediated mRNA stabilization GO:0070934 ISS
    cellular response to interleukin-7 GO:0098761 IDA
    negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay GO:1900152 ISO
    protein localization to cytoplasmic stress granule GO:1903608 IEA
    protein localization to cytoplasmic stress granule GO:1903608 ISO
    miRNA transport GO:1990428 ISO
    miRNA transport GO:1990428 ISS
    positive regulation of cytoplasmic translation GO:2000767 ISO
    negative regulation of cellular senescence GO:2000773 IMP
Subcellular Localization
    P-body GO:0000932 IDA
    nucleus GO:0005634 IBA
    nucleus GO:0005634 IDA
    nucleus GO:0005634 IGI
    U12-type spliceosomal complex GO:0005689 IEA
    U12-type spliceosomal complex GO:0005689 ISO
    cytoplasm GO:0005737 IDA
    cytoplasm GO:0005737 ISO
    endoplasmic reticulum GO:0005783 IEA
    endoplasmic reticulum GO:0005783 ISO
    cytosol GO:0005829 ISO
    plasma membrane GO:0005886 IEA
    plasma membrane GO:0005886 ISO
    cytoplasmic stress granule GO:0010494 ISO
    cytoplasmic stress granule GO:0010494 ISS
    dendrite GO:0030425 ISO
    protein-containing complex GO:0032991 ISO
    neuronal cell body GO:0043025 ISO
    intracellular membrane-bounded organelle GO:0043231 ISO
    synapse GO:0045202 EXP
    synapse GO:0045202 IDA
    perinuclear region of cytoplasm GO:0048471 ISO
    extracellular exosome GO:0070062 ISO
    extracellular exosome GO:0070062 ISS
    CRD-mediated mRNA stability complex GO:0070937 ISO
    histone pre-mRNA 3'end processing complex GO:0071204 IDA
    ribonucleoprotein complex GO:1990904 ISO
    ribonucleoprotein complex GO:1990904 ISS
 Experiment description of studies that identified Ybx1 in sEVs
1
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
2
Experiment ID 264
MISEV standards
✘ Biophysical techniques
✔
CD63|CD9
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25242146    
Organism Mus musculus
Experiment description Extracellular Vesicles from Neural Stem Cells Transfer IFN-? via Ifngr1 to Activate Stat1 Signaling in Target Cells
Authors "Chiara Cossetti, Nunzio Iraci, Tim R. Mercer, Tommaso Leonardi, Emanuele Alpi, Denise Drago, Clara Alfaro-Cervello, Harpreet K. Saini, Matthew P. Davis, Julia Schaeffer, Beatriz Vega, Matilde Stefanini, CongJian Zhao, Werner Muller, Jose Manuel Garcia-Verdugo, Suresh Mathivanan, Angela Bachi, Anton J. Enright, John S. Mattick, Stefano Pluchino"
Journal name Molecular Cell
Publication year 2014
Sample Neural stem cells
Sample name NPCs - Th2 treated
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.20 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
3
Experiment ID 188
MISEV standards
✔
EM
Biophysical techniques
✔
GAPDH|UCHL1|HSP90
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 19351151    
Organism Mus musculus
Experiment description Characterization of vesicles secreted from insulinoma NIT-1 cells.
Authors "Lee HS, Jeong J, Lee KJ."
Journal name J Proteome Res
Publication year 2009
Sample Pancreatic cells
Sample name Pancreatic beta cell (NIT-1)
Isolation/purification methods Differential centrifugation
Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
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 Ybx1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 Rps3 27050
Co-fractionation Mus musculus
2 RALY 22913
Affinity Capture-MS Homo sapiens
3 IGF2BP1 10642
Affinity Capture-MS Homo sapiens
4 Nmt1  
Co-fractionation Mus musculus
5 Atxn2 20239
Co-fractionation Mus musculus
6 NOP58 51602
Affinity Capture-MS Homo sapiens
7 Tfe3  
Affinity Capture-MS Mus musculus
8 TRUB2  
Affinity Capture-MS Homo sapiens
9 Fmr1  
Co-fractionation Mus musculus
10 NOP56 10528
Affinity Capture-MS Homo sapiens
11 MRPL24  
Affinity Capture-MS Homo sapiens
12 ZFR 51663
Affinity Capture-MS Homo sapiens
13 SSB 6741
Affinity Capture-MS Homo sapiens
14 Rps6 20104
Co-fractionation Mus musculus
15 Ncl 17975
Co-fractionation Mus musculus
16 Actb 11461
Co-fractionation Mus musculus
17 Snrpd3 67332
Co-fractionation Mus musculus
18 HNRNPUL2 221092
Affinity Capture-MS Homo sapiens
19 IGF2BP3 10643
Affinity Capture-MS Homo sapiens
20 Rps9 76846
Co-fractionation Mus musculus
21 Unk  
Affinity Capture-RNA Mus musculus
22 RRP12 23223
Affinity Capture-MS Homo sapiens
23 Rpl26 19941
Co-fractionation Mus musculus
24 YARS2  
Affinity Capture-MS Homo sapiens
25 MRPL12 6182
Affinity Capture-MS Homo sapiens
26 FBL 2091
Affinity Capture-MS Homo sapiens
27 MRPS26 64949
Affinity Capture-MS Homo sapiens
28 MRPS7 51081
Affinity Capture-MS Homo sapiens
29 MRPL47 57129
Affinity Capture-MS Homo sapiens
30 PABPC4 8761
Affinity Capture-MS Homo sapiens
31 FAM120A 23196
Affinity Capture-MS Homo sapiens
32 Rps4x 20102
Co-fractionation Mus musculus
33 Trove2 20822
Co-fractionation Mus musculus
34 RBMX 27316
Affinity Capture-MS Homo sapiens
35 POP1 10940
Affinity Capture-MS Homo sapiens
36 HNRNPA0 10949
Affinity Capture-MS Homo sapiens
37 DDX21 9188
Affinity Capture-MS Homo sapiens
38 Atg16l1  
Affinity Capture-MS Mus musculus
39 MRPS34 65993
Affinity Capture-MS Homo sapiens
40 Ube2o 217342
Co-fractionation Mus musculus
41 PTCD3 55037
Affinity Capture-MS Homo sapiens
42 Sf3b3 101943
Co-fractionation Mus musculus
43 NOP2 4839
Affinity Capture-MS Homo sapiens
44 Pabpc1 18458
Co-fractionation Mus musculus
45 Fam195b  
Co-fractionation Mus musculus
46 PABPC1 26986
Affinity Capture-MS Homo sapiens
47 Actn4 60595
Co-fractionation Mus musculus
48 DDX5 1655
Affinity Capture-MS Homo sapiens
49 SYNCRIP 10492
Affinity Capture-MS Homo sapiens
50 Rplp0 11837
Co-fractionation Mus musculus
51 DHX9 1660
Affinity Capture-MS Homo sapiens
52 Nlrp3  
Affinity Capture-MS Mus musculus
53 HNRNPA3 220988
Affinity Capture-MS Homo sapiens
54 LARP1 23367
Affinity Capture-MS Homo sapiens
55 RSL1D1 26156
Affinity Capture-MS Homo sapiens
56 ZNF326 284695
Affinity Capture-MS Homo sapiens
57 HNRNPDL 9987
Affinity Capture-MS Homo sapiens
58 Rpl13a 22121
Co-fractionation Mus musculus
59 Grb2 14784
Affinity Capture-MS Mus musculus
60 MRPS35 60488
Affinity Capture-MS Homo sapiens
61 Gapdh 14433
Co-fractionation Mus musculus
62 Rps8 20116
Co-fractionation Mus musculus
63 Snrpd2 107686
Co-fractionation Mus musculus
64 MRPL16  
Affinity Capture-MS Homo sapiens
65 Hnrnpab 15384
Co-fractionation Mus musculus
66 DHX30 22907
Affinity Capture-MS Homo sapiens
67 Ywhae 22627
Affinity Capture-MS Mus musculus
68 Stau1  
Co-fractionation Mus musculus
69 HNRNPR 10236
Affinity Capture-MS Homo sapiens
70 DKC1 1736
Affinity Capture-MS Homo sapiens
71 Dhx9 13211
Co-fractionation Mus musculus
72 Syncrip 56403
Co-fractionation Mus musculus
73 Rps3a1 20091
Co-fractionation Mus musculus
74 HNRNPAB 3182
Affinity Capture-MS Homo sapiens
75 MATR3 9782
Affinity Capture-MS Homo sapiens
76 Eed  
Affinity Capture-MS Mus musculus
77 Rptor  
Co-fractionation Mus musculus
78 MRPL18 29074
Affinity Capture-MS Homo sapiens
79 Fancd2  
Affinity Capture-MS Mus musculus
80 Ncbp1 433702
Co-fractionation Mus musculus
81 MKRN1 23608
Affinity Capture-MS Homo sapiens
82 CLPX 10845
Affinity Capture-MS Homo sapiens
83 ILF3 3609
Affinity Capture-MS Homo sapiens
84 MRPL43 84545
Affinity Capture-MS Homo sapiens
85 Ddx6 13209
Co-fractionation Mus musculus
86 TRA2B 6434
Affinity Capture-MS Homo sapiens
87 HNRNPK 3190
Affinity Capture-MS Homo sapiens
88 Mettl21e  
Affinity Capture-MS Mus musculus
89 Fzr1  
Affinity Capture-MS Mus musculus
90 LARP7 51574
Affinity Capture-MS Homo sapiens
91 MRPS18B 28973
Affinity Capture-MS Homo sapiens
92 MOV10 4343
Affinity Capture-MS Homo sapiens
93 Sf3b1 81898
Co-fractionation Mus musculus
94 Gigyf2  
Co-fractionation Mus musculus
95 HNRNPF 3185
Affinity Capture-MS Homo sapiens
96 HNRNPU 3192
Affinity Capture-MS Homo sapiens
97 MRPS22 56945
Affinity Capture-MS Homo sapiens
98 DDX28  
Affinity Capture-MS Homo sapiens
99 Hnrnpa2b1 53379
Co-fractionation Mus musculus
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