Gene Report

Basic Information

Approved Symbol	YBX1
Approved Name	Y box binding protein 1
Previous Symbol	NSEP1
Previous Name	"nuclease sensitive element binding protein 1"
Symbol Alias	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2
Location	1p34
Position	chr1:43167652-43168020 (+)
External Links	Entrez Gene: 4904 Ensembl: ENSG00000065978 UCSC: uc001chs.3 HGNC ID: 8014
No. of Studies (Positive/Negative)	1(1/0)
Type	Literature-origin

Positive relationships between YBX1 and MDD (count: 1)

Name in Literature	Reference	Research Type	Statistical Result	Relation Description
Y-box-binding protein 1	Shelton, 2011	patients and normal controls		The results strongly implicate increased apoptotic stress in...... The results strongly implicate increased apoptotic stress in the samples from the MDD group. Three anti-apoptotic factors, Y-box-binding protein 1, caspase-1 dominant-negative inhibitor pseudo-ICE, and the putative apoptosis inhibitor FKGS2, were over-expressed More...

Positive relationships between YBX1 and other components at different levels (count: 0)

Positive relationship network of YBX1 in MK4MDD

Network loading ...

Note:
1. The different color of the nodes denotes the level of the nodes.

Genetic/Epigenetic Locus	Protein and Other Molecule	Cell and Molecular Pathway	Neural System	Cognition and Behavior	Symptoms and Signs	Environment	MDD

2. Besides the component related relationships from literature, gene mapped protein and protein mapped gene are also shown in the network. If the mapped gene or protein is not from literature, square node would be used instead of Circle node. Accordingly, the relationship is marked with dot line.
2. User can drag the nodes to rearrange the layout of the network. Click the node will enter the report page of the node. Right-click will show also the menus to link to the report page of the node and remove the node and related edges. Hover the node will show the level of the node and hover the edge will show the evidence/description of the edge.
3. The network is generated using Cytoscape Web

Negative relationships between YBX1 and MDD (count: 0)

Negative relationships between YBX1 and other components at different levels (count: 0)

YBX1 related SNPs in MK4MDD (count: 0)

YBX1 related proteins in MK4MDD (count: 0)

YBX1 related GO terms (count: 43)

ID	Name	Type	Evidence
Gene mapped GO terms
GO:1903608	protein localization to cytoplasmic stress granule	biological process	IMP[24965446]
GO:0030425	dendrite	cellular component	IEA
GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	molecular function	IDA[18809583]
GO:0010467	gene expression	biological process	TAS
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[18809583]
GO:0070934	CRD-mediated mRNA stabilization	biological process	IMP[19029303]
GO:0005689	U12-type spliceosomal complex	cellular component	IDA[15146077]
GO:0003690	double-stranded DNA binding	molecular function	TAS[1738588]
GO:0005654	nucleoplasm	cellular component	TAS
GO:0006355	regulation of transcription, DNA-templated	biological process	IDA[18809583]
GO:0010494	cytoplasmic stress granule	cellular component	IDA[18335541]
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	IEA
GO:0051020	GTPase binding	molecular function	IPI[24337748]
GO:0051154	negative regulation of striated muscle cell differentiation	biological process	IEA
GO:0008134	transcription factor binding	molecular function	IEA
GO:0006366	transcription from RNA polymerase II promoter	biological process	TAS[3174636]
GO:0003682	chromatin binding	molecular function	IEA
GO:0001701	in utero embryonic development	biological process	IEA
GO:0005737	cytoplasm	cellular component	IDA[24965446]
GO:0070062	extracellular exosome	cellular component	IDA[20458337]
GO:0071204	histone pre-mRNA 3'end processing complex	cellular component	ISS
GO:0070937	CRD-mediated mRNA stability complex	cellular component	IDA[19029303]
GO:0003677	DNA binding	molecular function	IDA[18809583]; TAS[2977358\|8188694]
GO:0044822	poly(A) RNA binding	molecular function	IDA[22658674\|22681889]
GO:0008380	RNA splicing	biological process	TAS
GO:0043231	intracellular membrane-bounded organelle	cellular component	IDA
GO:1990124	messenger ribonucleoprotein complex	cellular component	IEA
GO:0002039	p53 binding	molecular function	IEA
GO:0003700	transcription factor activity, sequence-specific DNA binding	molecular function	TAS[3174636]
GO:0000398	mRNA splicing, via spliceosome	biological process	TAS
GO:0031965	nuclear membrane	cellular component	IDA
GO:0003729	mRNA binding	molecular function	IEA
GO:0048471	perinuclear region of cytoplasm	cellular component	IEA
GO:0005634	nucleus	cellular component	TAS[3174636]
GO:0046627	negative regulation of insulin receptor signaling pathway	biological process	IEA
GO:0008284	positive regulation of cell proliferation	biological process	IEA
GO:0043066	negative regulation of apoptotic process	biological process	IEA
GO:0005515	protein binding	molecular function	IPI[12674497\|15229244\|16797541\|17289661\|17932509\|18335541\|18809583\|18851979\|19174163\|20856196\|21849455\|22118625\|22365833\|23986595\|24965446\|25497084]
GO:0003723	RNA binding	molecular function	IDA[19561594]
GO:0030529	intracellular ribonucleoprotein complex	cellular component	IDA[17289661]
GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	molecular function	IDA[18809583]
GO:0003697	single-stranded DNA binding	molecular function	IEA
GO:0051781	positive regulation of cell division	biological process	IEA

YBX1 related KEGG pathways (count: 0)

YBX1 related BioCarta pathways (count: 0)

YBX1 related Reactome pathways (count: 5)

ID	Name	Description
Gene mapped Reactome pathways
REACT_71	gene expression	Gene Expression covers the process of transcription of mRNA ...... Gene Expression covers the process of transcription of mRNA genes, the processing of pre-mRNA, and its subsequent translation to result in a protein. The expression of non-protein-coding genes is not included in this section yet. However, the transcription of RNAs other than mRNA is described in the section on transcription; in the sections 'RNA Polymerase I Transcription', and 'RNA Polymerase III Transcription'. More...
REACT_2039	formation and_maturation_of_mrna_transcript	Before a gene transcript is ready to be transported out of t...... Before a gene transcript is ready to be transported out of the nucleus, it has to undergo three major processing events to produce a fully translatable mRNA. These comprise capping, splicing out of introns from within the body of the pre-mRNA, and the generation of a 3' end, by cleavage, and except in the case of histone pre-mRNAs, polyadenylation. Although each of these reactions is a biochemically distinct process, these processes are interlinked and hence, influence one another's specificity and efficiency. On the other hand, most mRNA processing reactions occur co-transcriptionally. This is particularly important in very long genes where a strictly post-transcriptional processing would imply the existence of extremely long primary transcript molecules that would be susceptible to degradation. The co-transcriptional nature of pre-mRNA processing does not necessarily imply a functional coupling between the transcription and mRNA processing machineries. In some cases it may simply reflect that processing reactions occur during transcription because they are relatively fast compared with the time it takes to transcribe a gene to its end. In other cases a tight link exists between a particular processing reaction and the transcription process, due to the ability of the carboxy-terminal (CTD) of RNA polymerase II largest subunit to bind or recruit processing factors. The CTD consists of 52 heptad repeats (YSPTSPS). Specific phosphorylation/dephosphorylation patterns of serines 2 and 5 are critical for CTD function in coupling. CTD deletions that do not inactivate transcription significantly decrease the efficiency of capping, splicing and polyadenylation. The export of mRNA from the nucleus and mRNA splicing are also coupled. Mature mRNAs generated by splicing are more efficiently exported than their identical counterparts transcribed from a complementary DNA (cDNA). This effect of splicing on export is due to the recruitment of the mRNA export factor ALY to the mRNA during the splicing reaction, which in turn delivers the mRNP to the nuclear pore for export. More...
REACT_1021	elongation and_processing_of_capped_transcripts
REACT_1735	mrna splicing	The process in which excision of introns from the primary tr...... The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing. Most of the mRNA is spliced by the major pathway, involving the U1, U2, U4, U5 and U6 snRNPs. A minor fraction, about 1 %, of the mRNAs are spliced via the U12 dependent pathway. More...
REACT_125	processing of_capped_intron_containing_pre_mrna	Any covalent change in a primary (nascent) mRNA transcript i...... Any covalent change in a primary (nascent) mRNA transcript is mRNA Processing. For successful gene expression, the primary mRNA transcript needs to be converted to a mature mRNA prior to its translation into polypeptide. Eucaryotic mRNAs undergo a series of complex processing reactions; these begin on nascent transcripts as soon as a few ribonucleotides have been synthesized during transcription by RNA Polymerase II, through the export of the mature mRNA to the cytoplasm, and culminate with mRNA turnover in the cytoplasm. More...

YBX1 related interactors from protein-protein interaction data in HPRD (count: 25)

Gene	Interactor	Interactor in MK4MDD?	Experiment Type	PMID
YBX1	TP53	No	in vitro;in vivo	11175333 , 11973333
YBX1	FMR1	No	in vivo	11162447
YBX1	CTCF	No	in vitro;in vivo	10906122 , 15229244
YBX1	ANKRD2	No	in vitro;in vivo	15136035
YBX1	FUS	No	in vitro;yeast 2-hybrid	12168660
YBX1	YBX1	Yes	in vitro;in vivo;yeast 2-hybrid	12192037
YBX1	HNRNPK	No	in vitro;in vivo;yeast 2-hybrid	10809782
YBX1	SMAD3	No	in vitro;in vivo	12917425
YBX1	IREB2	No	in vitro;in vivo;yeast 2-hybrid	12192037
YBX1	RBBP6	No	in vitro;in vivo;yeast 2-hybrid	18851979
YBX1	HNRNPD	No	in vitro;in vivo;yeast 2-hybrid	12674497
YBX1	SFRS9	No	in vivo;yeast 2-hybrid	12604611
YBX1	TFAP2A	No	in vitro;in vivo	9830047 , 11973333
YBX1	SLC6A4	Yes	in vitro;in vivo;yeast 2-hybrid	15229244
YBX1	PURA	No	in vitro;in vivo	10318844 , 11751932
YBX1	VEGFA	Yes	in vitro	16198352
YBX1	AKT1	No	in vitro;in vivo	16354698
YBX1	PCBP2	Yes	yeast 2-hybrid	8871564
YBX1	NFYB	No	in vitro	7651426
YBX1	SFRS12	No	in vitro;in vivo;yeast 2-hybrid	14559993
YBX1	GSK3B	Yes	in vitro	16198352
YBX1	MAPK1	Yes	in vitro	16198352
YBX1	HABP4	No	yeast 2-hybrid	16455055
YBX1	PCNA	No	in vitro;in vivo	9927044
YBX1	FBXO33	No	in vitro;in vivo	16797541

Gene Report

Gene mapped GO terms

Gene mapped Reactome pathways