DegronMD - P67809(YBX1)

FUNCTION: DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs (PubMed:29712925). Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection (PubMed:12604611). Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7' (PubMed:18809583). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (PubMed:8188694, PubMed:18809583). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (PubMed:14718551). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (PubMed:14718551). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (PubMed:19483673). {ECO:0000250|UniProtKB:Q28618, ECO:0000269|PubMed:10817758, ECO:0000269|PubMed:11698476, ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:19483673, ECO:0000269|PubMed:19561594, ECO:0000269|PubMed:27559612, ECO:0000269|PubMed:28341602, ECO:0000269|PubMed:29073095, ECO:0000269|PubMed:29712925, ECO:0000269|PubMed:31358969, ECO:0000269|PubMed:8188694}. View more >>

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GO - Cellular component (CC): View more >>

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Mutation	Sample	Cancer	Dataset	Degron hit	Class	Location	Type	Impact score
p.R101C	TCGA-22-5477	LUSC	TCGA	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.719
p.R101C	TCGA-EY-A549	UCEC	TCGA	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.719
p.R101C	DO26894	LUSC	ICGC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.719
p.R101C	DO48174	UCEC	ICGC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.719
p.N266S	TCGA-A2-A1G4	BRCA	TCGA	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation altering degron motif	0.7069
p.N266S	DO1259	BRCA	ICGC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation altering degron motif	0.7069
p.R204C	TCGA-A5-A0G2	UCEC	TCGA	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.R204C	TCGA-A5-A1OF	UCEC	TCGA	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.R204C	DO42568	UCEC	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.R204C	DO41235	UCEC	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.R253T	TCGA-A5-A0VP	UCEC	TCGA	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.0556
p.R253T	DO42600	UCEC	ICGC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.0556
p.A90V	TCGA-A8-A09Z	BRCA	TCGA	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.1667
p.A90V	DO5521	BRCA	ICGC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.1667
p.R199W	TCGA-AX-A2HD	UCEC	TCGA	PPYY	ITCH	194:197	Mutation rewiring degron network	0.2778
p.R199W	DO233935	GACA	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.2778
p.R199W	DO42608	UCEC	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.2778
p.R156H	TCGA-B5-A11E	UCEC	TCGA	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1111
p.R156H	DO41644	UCEC	ICGC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1111
p.R156H	SIDM00217	Colorectal Carcinoma	GDSC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1111
p.R156H	ACH-000999	Colon/Colorectal Cancer	CCLE	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1111
p.R156H	SNU-1040	large intestine	COSMIC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1111
p.R185C	TCGA-B5-A3FC	UCEC	TCGA	PPYY	ITCH	194:197	Mutation rewiring degron network	0.0833
p.R185C	DO41871	UCEC	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.0833
p.Q274P	TCGA-BR-8081	STAD	TCGA	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1389
p.Q274P	DO38795	STAD	ICGC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1389
p.R256T	TCGA-D1-A1NZ	UCEC	TCGA	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1389
p.R256T	DO41536	UCEC	ICGC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1389
p.R97M	TCGA-DF-A2KN	UCEC	TCGA	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.8632
p.R97M	DO223282	UCEC	ICGC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.8632
p.R204H	TCGA-EA-A3HS	CESC	TCGA	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.R204H	DO6260	CESC	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1389
p.E257K	TCGA-EO-A22U	UCEC	TCGA	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1667
p.E257K	DO43755	UCEC	ICGC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.1667
p.R205Q	DO8898	COAD	ICGC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1111
p.P195S	DO228202	LICA	ICGC	PPYY	ITCH	194:197	Mutation altering degron motif	0.6752
p.G168E	DO50970	LICA	ICGC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation altering degron motif	0.7199
p.D105G	DO23504	LINC	ICGC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.3056
p.P178T	DO229275	THCA	ICGC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.0833
p.Q159L	DO229224	THCA	ICGC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1944
p.Q159L	Daudi	haematopoietic and lymphoid tissue	COSMIC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation rewiring degron network	0.1944
p.S102I	SIDM00373	Endometrial Carcinoma	GDSC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.7341
p.S102I	ACH-000974	Endometrial/Uterine Cancer	CCLE	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation altering degron motif	0.7341
p.Q267H	SIDM00789	Colorectal Carcinoma	GDSC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation altering degron motif	0.647
p.Q267H	HCT-15	large intestine	COSMIC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation altering degron motif	0.647
p.I91V	SIDM00567	Other Solid Cancers	GDSC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.1944
p.I91V	ACH-000776	Brain Cancer	CCLE	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.1944
p.I91V	ONS-76	central nervous system	COSMIC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.1944
p.G268R	SIDM00946	T-Lymphoblastic Leukemia	GDSC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.3056
p.G268R	Daudi	haematopoietic and lymphoid tissue	COSMIC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.3056
p.G259D	SIDM00217	Colorectal Carcinoma	GDSC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.2222
p.G259D	ACH-000999	Colon/Colorectal Cancer	CCLE	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.2222
p.G259D	SNU-1040	large intestine	COSMIC	DKENQ	DEG_APCC_KENBOX_2	263:267	Mutation rewiring degron network	0.2222
p.N95I	SIDM00628	Breast Carcinoma	GDSC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.3056
p.N95I	ACH-000849	Breast Cancer	CCLE	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.3056
p.N95I	MDA-MB-468	breast	COSMIC	PRKYLRSVG	DEG_APCC_DBOX_1	96:104	Mutation rewiring degron network	0.3056
p.G203A	SIDM01519	Head and Neck Carcinoma	GDSC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1667
p.G203A	Daudi	haematopoietic and lymphoid tissue	COSMIC	PPYY	ITCH	194:197	Mutation rewiring degron network	0.1667
p.E169A	Daudi	haematopoietic and lymphoid tissue	COSMIC	NSESGE	DEG_Kelch_Keap1_1	164:169	Mutation altering degron motif	0.7701

Kaplan plot for YBX1 in

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*NOTE: the Kaplan plots were collected from OncoLnc

DegronMD: protein-targeted degradation, mutation and drug response to degrons

YBX1

UniProt ID: P67809

Entrez ID: 4904

Protein name: Y-box-binding protein 1 (YB-1) (CCAAT-binding transcription factor I subunit A) (CBF-A) (DNA-binding protein B) (DBPB) (Enhancer factor I subunit A) (EFI-A) (Nuclease-sensitive element-binding protein 1) (Y-box transcription factor)

External links: UniprotKB HGNC RefSeq COSMIC

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Kaplan plot for YBX1 in