Tbio YBX1 Nuclease-sensitive element-binding protein 1

Protein Summary

Description

Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates splice site selection. Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Regulates the transcription of numerous genes. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA (in vitro). May play a role in DNA repair. Component of the CRD-mediated complex that promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro. The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation. 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 of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]

Uniprot Accession IDs

• P67809
• P16990
• P16991
• Q14972
• Q15325
• Q5FVF0

Gene Name

• YBX1

Ensembl ID

• ENST00000321358
• ENSP00000361626
• ENSG00000065978

Symbol

• NSEP1
• YB1
• YB1
• BP-8
• CSDB
• DBPB
• YB-1
• CBF-A
• CSDA2
• EFI-A
• NSEP1
• NSEP-1
• MDR-NF1

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
hub protein	1
interacting protein	1
disease perturbation	0.99
ligand (protein) perturbation	0.99
transcription factor perturbation	0.94

Protein Classes

No PANTHER Classes or DTO Classes found

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 898.17   (req: < 5)

Gene RIFs: 250   (req: <= 3)

Antibodies: 504   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 898.17   (req: >= 5)

Gene RIFs: 250   (req: > 3)

Antibodies: 504   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 17

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (423)

Explore Interacting Targets

1 – 10 of 423

• See Interactions on String-DB

RRS1

Tbio

Novelty:  0.01643671

p_int:  0.99310624

p_ni:  0.00689376

Score:  0.286

Data Source:  BioPlex,STRINGDB

RNF151

Tdark

Novelty:  2.0077961

p_int:  0.960169455

p_ni:  0.039830545

Data Source:  BioPlex

ZC3HAV1

Tbio

Novelty:  0.01357759

p_int:  0.949613931

p_ni:  0.050386069

Score:  0.244

Data Source:  BioPlex,STRINGDB

H2AFX

Tbio

Novelty:  0.00048694

p_int:  0.936135517

p_ni:  0.063864483

Score:  0.239

Data Source:  BioPlex,STRINGDB

THAP3

Tdark

Family:  TF

Novelty:  0.52942342

p_int:  0.919063909

p_ni:  0.080936091

Data Source:  BioPlex

BHLHA15

Tbio

Family:  TF

Novelty:  0.02721846

p_int:  0.915780006

p_ni:  0.084219994

Data Source:  BioPlex

E4F1

Tbio

Family:  TF

Novelty:  0.02192338

p_int:  0.907675867

p_ni:  0.092324133

Data Source:  BioPlex

LARP4B

Tbio

Novelty:  0.11363794

p_int:  0.896773165

p_ni:  0.103226835

Score:  0.194

Data Source:  BioPlex,STRINGDB

RPL7A

Tbio

Novelty:  0.01674027

p_int:  0.895157758

p_ni:  0.104842242

Score:  0.435

Data Source:  BioPlex,STRINGDB

ZCRB1

Tdark

Novelty:  0.37592387

p_int:  0.892336467

p_ni:  0.107663533

Score:  0.966

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (16)

Reactome (10)

PathwayCommons (2)

WikiPathways (4)

Metabolism of RNA (R-HSA-8953854)

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1 – 5 of 10

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Metabolism of RNA	686 targets	R-HSA-8953854
Reactome	NOTCH3 Activation and Transmission of Signal to the Nucleus	25 targets	R-HSA-9013507
Reactome	Noncanonical activation of NOTCH3	8 targets	R-HSA-9017802
Reactome	Processing of Capped Intron-Containing Pre-mRNA	241 targets	R-HSA-72203
Reactome	Signal Transduction	2704 targets	R-HSA-162582

Name	Explore in Pharos	Explore in Source
Metabolism of RNA	686 targets	R-HSA-8953854
NOTCH3 Activation and Transmission of Signal to the Nucleus	25 targets	R-HSA-9013507
Noncanonical activation of NOTCH3	8 targets	R-HSA-9017802
Processing of Capped Intron-Containing Pre-mRNA	241 targets	R-HSA-72203
Signal Transduction	2704 targets	R-HSA-162582

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (30)

Functions (9)

Components (13)

Processes (8)

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Items per page:

10

1 – 9 of 9

GO Term	Evidence	Assigned by
DNA binding	Inferred from Direct Assay (IDA)	UniProtKB
proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific	Inferred from Direct Assay (IDA)	NTNU_SB
RNA binding	Inferred from Direct Assay (IDA)	UniProtKB
RNA polymerase II proximal promoter sequence-specific DNA binding	Inferred from Direct Assay (IDA)	NTNU_SB
GTPase binding	Inferred from Physical Interaction (IPI)	UniProtKB
DNA-binding transcription factor activity, RNA polymerase II-specific	Inferred from Sequence Alignment (ISA)	NTNU_SB
DNA-binding transcription factor activity	Traceable Author Statement (TAS)	ProtInc
double-stranded DNA binding	Traceable Author Statement (TAS)	ProtInc
single-stranded DNA binding	Traceable Author Statement (TAS)	ProtInc

Disease Associations ()

No disease associations found

GWAS Traits (0)

No GWAS traits found

Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Activator
Complete proteome
Cytoplasm
Direct protein sequencing
DNA-binding
Isopeptide bond
Mitogen
mRNA processing

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
cellular phenotype
craniofacial phenotype
embryo phenotype
growth/size/body region phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
integument phenotype
liver/biliary system phenotype
mortality/aging

IDG Resources

No IDG generated resources found

Orthologs (12)

1 – 5 of 12

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	nuclease-sensitive element-binding protein 1-like		104004819
Macaque	Y-box binding protein 1		700140
Mouse	Y box protein 1	MGI:99146	22608
Rat	Y box protein 1 related, pseudogene 3	RGD:1590933	29206
Dog	Y-box binding protein 1		607025

Species	Name	OMA	EggNOG	Inparanoid
Chimp	nuclease-sensitive element-binding protein 1-like
Macaque	Y-box binding protein 1
Mouse	Y box protein 1
Rat	Y box protein 1 related, pseudogene 3
Dog	Y-box binding protein 1

Publication Statistics

PubMed Score 898.17

PubMed score by year

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PubTator Score 453.70

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Related Publications

Text Mined References (301)

GeneRif Annotations (250)

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PMID	Year	Title