Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene miRNA Transcription factors Gene ontology Other IDs Protein Pathways
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	4904
Gene name Gene Name - the full gene name approved by the HGNC.	Y-box binding protein 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	YBX1
Synonyms (NCBI Gene) Gene synonyms aliases	BP-8, CBF-A, CSDA2, CSDB, DBPB, EFI-A, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p34.2
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation

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miRTarBase ID	miRNA	Experiments	Reference
MIRT007092	hsa-miR-137	Luciferase reporter assay	23178914
MIRT007092	hsa-miR-137	Luciferase reporter assay	23178914
MIRT022450	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT031527	hsa-miR-16-5p	Proteomics	18668040
MIRT050595	hsa-miR-20a-5p	CLASH	23622248
MIRT050297	hsa-miR-25-3p	CLASH	23622248
MIRT047343	hsa-miR-34a-5p	CLASH	23622248
MIRT045400	hsa-miR-149-5p	CLASH	23622248
MIRT044272	hsa-miR-106b-5p	CLASH	23622248
MIRT041860	hsa-miR-484	CLASH	23622248
MIRT040476	hsa-miR-605-5p	CLASH	23622248
MIRT039737	hsa-miR-615-3p	CLASH	23622248
MIRT037523	hsa-miR-744-5p	CLASH	23622248
MIRT036695	hsa-miR-935	CLASH	23622248
MIRT036078	hsa-miR-1296-5p	CLASH	23622248
MIRT035829	hsa-miR-1292-5p	CLASH	23622248
MIRT035821	hsa-miR-1307-3p	CLASH	23622248
MIRT007092	hsa-miR-137	Luciferase reporter assay, qRT-PCR, Western blot	23151846
MIRT007092	hsa-miR-137	Luciferase reporter assay, qRT-PCR, Western blot	23151846
MIRT007092	hsa-miR-137	Luciferase reporter assay, qRT-PCR, Western blot	24465609
MIRT463791	hsa-miR-379-5p	PAR-CLIP	20371350
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	20371350
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	20371350
MIRT463787	hsa-miR-8069	PAR-CLIP	20371350
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	20371350
MIRT341355	hsa-miR-4451	PAR-CLIP	20371350
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	20371350
MIRT463791	hsa-miR-379-5p	PAR-CLIP	24398324
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	24398324
MIRT463787	hsa-miR-8069	PAR-CLIP	24398324
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	24398324
MIRT341355	hsa-miR-4451	PAR-CLIP	24398324
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	24398324
MIRT463791	hsa-miR-379-5p	PAR-CLIP	23592263
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	23592263
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	23592263
MIRT463788	hsa-miR-6831-3p	PAR-CLIP	23592263
MIRT463787	hsa-miR-8069	PAR-CLIP	23592263
MIRT341357	hsa-miR-6744-5p	PAR-CLIP	23592263
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	23592263
MIRT341355	hsa-miR-4451	PAR-CLIP	23592263
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	23592263
MIRT731079	hsa-miR-382-5p	qRT-PCR, Luciferase reporter assay, Western blot	25292190
MIRT731079	hsa-miR-382-5p	qRT-PCR, Luciferase reporter assay, Western blot	25292190
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	26701625
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	26701625
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	26701625
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	26701625
MIRT463791	hsa-miR-379-5p	PAR-CLIP	26701625
MIRT463791	hsa-miR-379-5p	PAR-CLIP	26701625
MIRT341355	hsa-miR-4451	PAR-CLIP	26701625
MIRT341355	hsa-miR-4451	PAR-CLIP	26701625
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	26701625
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	26701625
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	26701625
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	26701625
MIRT463787	hsa-miR-8069	PAR-CLIP	26701625
MIRT463787	hsa-miR-8069	PAR-CLIP	26701625
MIRT731079	hsa-miR-382-5p	qRT-PCR	31417288
MIRT463791	hsa-miR-379-5p	PAR-CLIP	20371350
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	20371350
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	20371350
MIRT463787	hsa-miR-8069	PAR-CLIP	20371350
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	20371350
MIRT341355	hsa-miR-4451	PAR-CLIP	20371350
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	20371350
MIRT463791	hsa-miR-379-5p	PAR-CLIP	24398324
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	24398324
MIRT463787	hsa-miR-8069	PAR-CLIP	24398324
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	24398324
MIRT341355	hsa-miR-4451	PAR-CLIP	24398324
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	24398324
MIRT463791	hsa-miR-379-5p	PAR-CLIP	23592263
MIRT463790	hsa-miR-3529-5p	PAR-CLIP	23592263
MIRT463789	hsa-miR-1537-3p	PAR-CLIP	23592263
MIRT463788	hsa-miR-6831-3p	PAR-CLIP	23592263
MIRT463787	hsa-miR-8069	PAR-CLIP	23592263
MIRT341357	hsa-miR-6744-5p	PAR-CLIP	23592263
MIRT463786	hsa-miR-4650-3p	PAR-CLIP	23592263
MIRT341355	hsa-miR-4451	PAR-CLIP	23592263
MIRT341358	hsa-miR-6832-5p	PAR-CLIP	23592263
MIRT1498323	hsa-miR-1206	CLIP-seq
MIRT1498324	hsa-miR-1255a	CLIP-seq
MIRT1498325	hsa-miR-1255b	CLIP-seq
MIRT1498326	hsa-miR-1273f	CLIP-seq
MIRT1498327	hsa-miR-1279	CLIP-seq
MIRT1498328	hsa-miR-1287	CLIP-seq
MIRT1498329	hsa-miR-129-5p	CLIP-seq
MIRT1498330	hsa-miR-1537	CLIP-seq
MIRT1498331	hsa-miR-208a	CLIP-seq
MIRT1498332	hsa-miR-208b	CLIP-seq
MIRT1498333	hsa-miR-30a	CLIP-seq
MIRT1498334	hsa-miR-30b	CLIP-seq
MIRT1498335	hsa-miR-30c	CLIP-seq
MIRT1498336	hsa-miR-30d	CLIP-seq
MIRT1498337	hsa-miR-30e	CLIP-seq
MIRT1498338	hsa-miR-3119	CLIP-seq
MIRT1498339	hsa-miR-3135b	CLIP-seq
MIRT1498340	hsa-miR-3529	CLIP-seq
MIRT1498341	hsa-miR-3658	CLIP-seq
MIRT1498342	hsa-miR-3667-5p	CLIP-seq
MIRT1498343	hsa-miR-375	CLIP-seq
MIRT1498344	hsa-miR-379	CLIP-seq
MIRT1498345	hsa-miR-382	CLIP-seq
MIRT1498346	hsa-miR-4327	CLIP-seq
MIRT1498347	hsa-miR-4461	CLIP-seq
MIRT1498348	hsa-miR-4477a	CLIP-seq
MIRT1498349	hsa-miR-4659a-3p	CLIP-seq
MIRT1498350	hsa-miR-4659b-3p	CLIP-seq
MIRT1498351	hsa-miR-4778-3p	CLIP-seq
MIRT1498352	hsa-miR-499-5p	CLIP-seq
MIRT1498353	hsa-miR-520d-5p	CLIP-seq
MIRT1498354	hsa-miR-524-5p	CLIP-seq
MIRT1498355	hsa-miR-539	CLIP-seq
MIRT1498356	hsa-miR-548aa	CLIP-seq
MIRT1498357	hsa-miR-548ac	CLIP-seq
MIRT1498358	hsa-miR-548c-3p	CLIP-seq
MIRT1498359	hsa-miR-548d-3p	CLIP-seq
MIRT1498360	hsa-miR-548z	CLIP-seq
MIRT1498361	hsa-miR-552	CLIP-seq
MIRT1498362	hsa-miR-556-3p	CLIP-seq
MIRT1498363	hsa-miR-578	CLIP-seq
MIRT1498364	hsa-miR-579	CLIP-seq
MIRT1498365	hsa-miR-580	CLIP-seq
MIRT1498366	hsa-miR-636	CLIP-seq
MIRT1498367	hsa-miR-653	CLIP-seq
MIRT1498368	hsa-miR-764	CLIP-seq
MIRT1498369	hsa-miR-95	CLIP-seq
MIRT1498358	hsa-miR-548c-3p	CLIP-seq
MIRT1498324	hsa-miR-1255a	CLIP-seq
MIRT1498325	hsa-miR-1255b	CLIP-seq
MIRT1498326	hsa-miR-1273f	CLIP-seq
MIRT2150092	hsa-miR-153	CLIP-seq
MIRT1498330	hsa-miR-1537	CLIP-seq
MIRT2150093	hsa-miR-3126-3p	CLIP-seq
MIRT2150094	hsa-miR-3168	CLIP-seq
MIRT1498340	hsa-miR-3529	CLIP-seq
MIRT2150095	hsa-miR-3663-5p	CLIP-seq
MIRT1498344	hsa-miR-379	CLIP-seq
MIRT1498349	hsa-miR-4659a-3p	CLIP-seq
MIRT1498350	hsa-miR-4659b-3p	CLIP-seq
MIRT1498351	hsa-miR-4778-3p	CLIP-seq
MIRT1498357	hsa-miR-548ac	CLIP-seq
MIRT2150096	hsa-miR-548ae	CLIP-seq
MIRT2150097	hsa-miR-548aj	CLIP-seq
MIRT2150098	hsa-miR-548am	CLIP-seq
MIRT1498359	hsa-miR-548d-3p	CLIP-seq
MIRT2150099	hsa-miR-548x	CLIP-seq
MIRT1498360	hsa-miR-548z	CLIP-seq
MIRT2150100	hsa-miR-577	CLIP-seq
MIRT1498363	hsa-miR-578	CLIP-seq
MIRT1498369	hsa-miR-95	CLIP-seq
MIRT2150092	hsa-miR-153	CLIP-seq
MIRT2150093	hsa-miR-3126-3p	CLIP-seq
MIRT2150095	hsa-miR-3663-5p	CLIP-seq
MIRT1498346	hsa-miR-4327	CLIP-seq
MIRT1498358	hsa-miR-548c-3p	CLIP-seq
MIRT1498361	hsa-miR-552	CLIP-seq
MIRT2150100	hsa-miR-577	CLIP-seq
MIRT1498366	hsa-miR-636	CLIP-seq
MIRT1498367	hsa-miR-653	CLIP-seq
MIRT1498368	hsa-miR-764	CLIP-seq
MIRT1498369	hsa-miR-95	CLIP-seq
MIRT1498327	hsa-miR-1279	CLIP-seq
MIRT1498346	hsa-miR-4327	CLIP-seq
MIRT1498348	hsa-miR-4477a	CLIP-seq
MIRT1498349	hsa-miR-4659a-3p	CLIP-seq
MIRT1498350	hsa-miR-4659b-3p	CLIP-seq
MIRT1498351	hsa-miR-4778-3p	CLIP-seq
MIRT1498361	hsa-miR-552	CLIP-seq
MIRT1498363	hsa-miR-578	CLIP-seq
MIRT1498366	hsa-miR-636	CLIP-seq
MIRT1498367	hsa-miR-653	CLIP-seq
MIRT1498368	hsa-miR-764	CLIP-seq
MIRT1498338	hsa-miR-3119	CLIP-seq
MIRT1498347	hsa-miR-4461	CLIP-seq
MIRT2663964	hsa-miR-4484	CLIP-seq
MIRT2663965	hsa-miR-494	CLIP-seq
MIRT1498355	hsa-miR-539	CLIP-seq
MIRT1498356	hsa-miR-548aa	CLIP-seq
MIRT1498357	hsa-miR-548ac	CLIP-seq
MIRT2150096	hsa-miR-548ae	CLIP-seq
MIRT2150097	hsa-miR-548aj	CLIP-seq
MIRT2150098	hsa-miR-548am	CLIP-seq
MIRT2663966	hsa-miR-548an	CLIP-seq
MIRT1498359	hsa-miR-548d-3p	CLIP-seq
MIRT2150099	hsa-miR-548x	CLIP-seq
MIRT1498360	hsa-miR-548z	CLIP-seq
MIRT1498365	hsa-miR-580	CLIP-seq
MIRT1498347	hsa-miR-4461	CLIP-seq
MIRT2663964	hsa-miR-4484	CLIP-seq
MIRT2663965	hsa-miR-494	CLIP-seq
MIRT1498355	hsa-miR-539	CLIP-seq
MIRT1498356	hsa-miR-548aa	CLIP-seq
MIRT1498357	hsa-miR-548ac	CLIP-seq
MIRT2150096	hsa-miR-548ae	CLIP-seq
MIRT2150097	hsa-miR-548aj	CLIP-seq
MIRT2150098	hsa-miR-548am	CLIP-seq
MIRT2663966	hsa-miR-548an	CLIP-seq
MIRT1498359	hsa-miR-548d-3p	CLIP-seq
MIRT2150099	hsa-miR-548x	CLIP-seq
MIRT1498360	hsa-miR-548z	CLIP-seq
MIRT1498365	hsa-miR-580	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
TWIST1	Activation	21876555
TWIST1	Unknown	19318582

Show/Hide all(64)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000932	Component	P-body	IEA
GO:0001701	Process	In utero embryonic development	IEA
GO:0003676	Function	Nucleic acid binding	IBA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	2977358, 3174636, 8188694
GO:0003682	Function	Chromatin binding	IEA
GO:0003690	Function	Double-stranded DNA binding	TAS	1738588
GO:0003697	Function	Single-stranded DNA binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IDA	19561594, 28341602
GO:0003723	Function	RNA binding	IEA
GO:0003729	Function	MRNA binding	IEA
GO:0005515	Function	Protein binding	IPI	12674497, 15229244, 16797541, 17289661, 17572683, 17932509, 18335541, 18809583, 18851979, 19174163, 20856196, 21145461, 21653829, 21849455, 22118625, 22365833, 23986595, 24965446, 24981860, 25497084, 26184334, 26845719, 27607350, 31358969, 32814053, 33961781, 35271311
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	3174636
GO:0005654	Component	Nucleoplasm	TAS
GO:0005689	Component	U12-type spliceosomal complex	IDA	15146077
GO:0005737	Component	Cytoplasm	IDA	24965446
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005829	Component	Cytosol	IDA	19029303
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0006355	Process	Regulation of DNA-templated transcription	IDA	18809583
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0008544	Process	Epidermis development	IEA
GO:0008544	Process	Epidermis development	ISS
GO:0010468	Process	Regulation of gene expression	IBA
GO:0010494	Component	Cytoplasmic stress granule	IDA	18335541
GO:0017148	Process	Negative regulation of translation	ISS
GO:0035198	Function	MiRNA binding	IDA	27559612
GO:0045202	Component	Synapse	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	18809583
GO:0048255	Process	MRNA stabilization	IDA	31358969
GO:0048598	Process	Embryonic morphogenesis	ISS
GO:0050658	Process	RNA transport	IMP	29073095
GO:0051020	Function	GTPase binding	IPI	24337748
GO:0051031	Process	TRNA transport	IMP	29073095
GO:0051154	Process	Negative regulation of striated muscle cell differentiation	IEA
GO:0051781	Process	Positive regulation of cell division	IEA
GO:0062153	Function	C5-methylcytidine-containing RNA reader activity	IDA	31358969
GO:0070062	Component	Extracellular exosome	HDA	20458337
GO:0070062	Component	Extracellular exosome	IDA	27559612, 28341602
GO:0070934	Process	CRD-mediated mRNA stabilization	IDA	19029303
GO:0070934	Process	CRD-mediated mRNA stabilization	IMP	19029303
GO:0070937	Component	CRD-mediated mRNA stability complex	IDA	19029303
GO:0070937	Component	CRD-mediated mRNA stability complex	IPI	19029303
GO:0071204	Component	Histone pre-mRNA 3'end processing complex	IEA
GO:0071204	Component	Histone pre-mRNA 3'end processing complex	ISS
GO:0098761	Process	Cellular response to interleukin-7	IEA
GO:1900152	Process	Negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IDA	19029303
GO:1903608	Process	Protein localization to cytoplasmic stress granule	IMP	24965446
GO:1990428	Process	MiRNA transport	IDA	27559612
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990904	Component	Ribonucleoprotein complex	IDA	17289661
GO:2000767	Process	Positive regulation of cytoplasmic translation	IDA	19029303
GO:2000773	Process	Negative regulation of cellular senescence	IEA
GO:2000773	Process	Negative regulation of cellular senescence	ISS

MIM	HGNC	e!Ensembl
154030	8014	ENSG00000065978

Protein

UniProt ID

P67809

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)

Protein function

DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:3

PDB

1H95 , 5YTS , 5YTT , 5YTV , 5YTX , 6A6L , 6KTC , 6KUG , 6LMR , 6LMS

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00313	CSD	59 → 128		Domain

Sequence

MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVL
GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGA
EAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEG
QAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRG
YRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDG
KETKAADPPAENSSAPEAEQGGAE

Sequence length

324

Interactions

View interactions

	Reactome
			mRNA Splicing - Major Pathway mRNA Splicing - Minor Pathway Noncanonical activation of NOTCH3

YBX1 (Y-box binding protein 1)