Gene description for PHF5A
Gene name PHD finger protein 5A
Gene symbol PHF5A
Other names/aliases INI
Rds3
SAP14b
SF3B7
SF3b14b
bK223H9.2
Species Homo sapiens
 Database cross references - PHF5A
ExoCarta ExoCarta_84844
Vesiclepedia VP_84844
Entrez Gene 84844
HGNC 18000
UniProt Q7RTV0  
 PHF5A identified in exosomes 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    
Breast cancer cells 34108659    
Breast cancer cells 34108659    
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Embryonic kidney cells 34108659    
Embryonic kidney cells 34108659    
Pancreatic cancer cells 34108659    
Pancreatic cancer cells 34108659    
 Gene ontology annotations for PHF5A
Molecular Function
    DNA binding GO:0003677 IEA
    poly(A) RNA binding GO:0044822 IDA
    sequence-specific DNA binding transcription factor activity GO:0003700 ISS
Biological Process
    RNA splicing GO:0008380 TAS
    mRNA splicing, via spliceosome GO:0000398 TAS
    transcription, DNA-templated GO:0006351 IEA
    positive regulation of transcription, DNA-templated GO:0045893 ISS
    gene expression GO:0010467 TAS
Subcellular Localization
    U12-type spliceosomal complex GO:0005689 IDA
    nucleoplasm GO:0005654 TAS
    U2 snRNP GO:0005686 IDA
    nuclear matrix GO:0016363 IEA
    nuclear speck GO:0016607 ISS
 Experiment description of studies that identified PHF5A in exosomes
1
Experiment ID 489
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV 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
2
Experiment ID 490
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV 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
3
Experiment ID 491
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV 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
4
Experiment ID 492
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV 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
5
Experiment ID 426
MISEV standards
✘ EV Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MDA-MB-231 - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
6
Experiment ID 427
MISEV standards
✘ EV Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MDA-MB-231 - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
7
Experiment ID 207
MISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|HSP70|FLOT1
EV Enriched markers
✔
VDAC
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DKO-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
8
Experiment ID 208
MISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|HSP70|FLOT1
EV Enriched markers
✔
VDAC
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name Dks-8
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
9
Experiment ID 209
MISEV standards
✘ EV Biophysical techniques
✔
TSG101|HSP70|FLOT1
EV Enriched markers
✔
VDAC
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DLD-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
10
Experiment ID 419
MISEV standards
✘ EV Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
11
Experiment ID 419
MISEV standards
✘ EV Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
12
Experiment ID 420
MISEV standards
✘ EV Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
13
Experiment ID 420
MISEV standards
✘ EV Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
14
Experiment ID 434
MISEV standards
✘ EV Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name PANC-1 - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
15
Experiment ID 435
MISEV standards
✘ EV Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
EV Enriched markers
✔
CANX
EV Negative markers
✘ EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R.
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name PANC-1 - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for PHF5A
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 SF3B5 83443
Invivo Homo sapiens
2 DDX42 11325
Invivo Homo sapiens
3 RNU11 26824
Affinity Capture-MS Homo sapiens
4 SF3B6 51639
Invivo Homo sapiens
5 SF3B3 23450
Invivo Homo sapiens
6 RNU12  
Affinity Capture-MS Homo sapiens
7 SF3B2 10992
Invivo Homo sapiens
8 SF3B4 10262
Invivo Homo sapiens
9 SF3B1 23451
Invivo Homo sapiens
View the network image/svg+xml
 Pathways in which PHF5A is involved
PathwayEvidenceSource
mRNA Splicing - Major Pathway TAS Reactome





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