Details for: YBX3

Gene ID: 8531

Symbol: YBX3

Ensembl ID: ENSG00000060138

Description: Y-box binding protein 3

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: polychromatophilic erythroblast (CL0000550)
    Fold Change: 355.5236
    Cell Significance Index: -55.3000
  • Cell Name: hematopoietic oligopotent progenitor cell (CL0002032)
    Fold Change: 255.9893
    Cell Significance Index: -64.9300
  • Cell Name: embryonic stem cell (CL0002322)
    Fold Change: 174.0513
    Cell Significance Index: -71.7000
  • Cell Name: smooth muscle fiber of ileum (CL1000278)
    Fold Change: 166.5033
    Cell Significance Index: -78.6100
  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 161.5726
    Cell Significance Index: -65.6400
  • Cell Name: peripheral blood mononuclear cell (CL2000001)
    Fold Change: 145.6107
    Cell Significance Index: -74.9000
  • Cell Name: ileal goblet cell (CL1000326)
    Fold Change: 117.7159
    Cell Significance Index: -78.9900
  • Cell Name: ciliated cell of the bronchus (CL0002332)
    Fold Change: 68.5420
    Cell Significance Index: -65.4400
  • Cell Name: orthochromatic erythroblast (CL0000552)
    Fold Change: 52.6540
    Cell Significance Index: -64.9200
  • Cell Name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell (CL0000796)
    Fold Change: 28.8668
    Cell Significance Index: -77.3300
  • Cell Name: stromal cell of bone marrow (CL0010001)
    Fold Change: 20.6662
    Cell Significance Index: -81.5500
  • Cell Name: CD8-positive, alpha-beta regulatory T cell (CL0000795)
    Fold Change: 20.3747
    Cell Significance Index: -62.5800
  • Cell Name: epidermal Langerhans cell (CL0002457)
    Fold Change: 16.1154
    Cell Significance Index: -35.2700
  • Cell Name: prostate gland microvascular endothelial cell (CL2000059)
    Fold Change: 15.9394
    Cell Significance Index: 114.4800
  • Cell Name: vascular lymphangioblast (CL0005022)
    Fold Change: 13.2469
    Cell Significance Index: 234.0900
  • Cell Name: type II muscle cell (CL0002212)
    Fold Change: 11.5697
    Cell Significance Index: 186.6800
  • Cell Name: type I muscle cell (CL0002211)
    Fold Change: 10.2146
    Cell Significance Index: 249.2300
  • Cell Name: fibroblast of mammary gland (CL0002555)
    Fold Change: 7.5543
    Cell Significance Index: 216.5500
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: 5.9364
    Cell Significance Index: 382.9900
  • Cell Name: oral mucosa squamous cell (CL1001576)
    Fold Change: 5.7966
    Cell Significance Index: 49.8100
  • Cell Name: luminal hormone-sensing cell of mammary gland (CL4033058)
    Fold Change: 5.0925
    Cell Significance Index: 31.3400
  • Cell Name: basal cell of prostate epithelium (CL0002341)
    Fold Change: 5.0523
    Cell Significance Index: 137.5200
  • Cell Name: peg cell (CL4033014)
    Fold Change: 4.9941
    Cell Significance Index: 115.3800
  • Cell Name: retinal rod cell (CL0000604)
    Fold Change: 4.8546
    Cell Significance Index: 57.8700
  • Cell Name: perivascular cell (CL4033054)
    Fold Change: 4.6608
    Cell Significance Index: 21.5200
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: 4.5331
    Cell Significance Index: 337.8500
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: 4.3578
    Cell Significance Index: 204.8100
  • Cell Name: endothelial cell of venule (CL1000414)
    Fold Change: 4.1178
    Cell Significance Index: 46.7800
  • Cell Name: lactocyte (CL0002325)
    Fold Change: 4.0481
    Cell Significance Index: 522.9900
  • Cell Name: stem cell of epidermis (CL1000428)
    Fold Change: 3.9744
    Cell Significance Index: 11.8200
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: 3.7460
    Cell Significance Index: 514.4300
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: 3.7333
    Cell Significance Index: 194.4600
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: 3.5625
    Cell Significance Index: 438.0400
  • Cell Name: mesonephric nephron tubule epithelial cell (CL1000022)
    Fold Change: 3.4046
    Cell Significance Index: 118.3100
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: 3.1235
    Cell Significance Index: 145.6300
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 3.0992
    Cell Significance Index: 1692.5400
  • Cell Name: hair follicular keratinocyte (CL2000092)
    Fold Change: 3.0956
    Cell Significance Index: 1368.6200
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: 3.0088
    Cell Significance Index: 542.3900
  • Cell Name: sebum secreting cell (CL0000317)
    Fold Change: 2.8181
    Cell Significance Index: 199.3100
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: 2.0943
    Cell Significance Index: 108.8000
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 2.0528
    Cell Significance Index: 55.0100
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: 1.9274
    Cell Significance Index: 50.6800
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: 1.8005
    Cell Significance Index: 113.4800
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: 1.7612
    Cell Significance Index: 49.2200
  • Cell Name: skeletal muscle satellite stem cell (CL0008011)
    Fold Change: 1.6988
    Cell Significance Index: 17.7400
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: 1.6801
    Cell Significance Index: 44.8600
  • Cell Name: umbrella cell of urothelium (CL4030056)
    Fold Change: 1.1473
    Cell Significance Index: 10.5700
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 1.1058
    Cell Significance Index: 84.8600
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 1.0134
    Cell Significance Index: 110.2300
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.9627
    Cell Significance Index: 156.5800
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.9043
    Cell Significance Index: 26.0600
  • Cell Name: cardiac endothelial cell (CL0010008)
    Fold Change: 0.7495
    Cell Significance Index: 10.7800
  • Cell Name: epithelial cell of urethra (CL1000296)
    Fold Change: 0.6746
    Cell Significance Index: 4.1800
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: 0.6200
    Cell Significance Index: 12.1000
  • Cell Name: endothelial cell of placenta (CL0009092)
    Fold Change: 0.5296
    Cell Significance Index: 3.2000
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: 0.5268
    Cell Significance Index: 26.6200
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.5253
    Cell Significance Index: 23.8100
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 0.5119
    Cell Significance Index: 325.1200
  • Cell Name: CD14-positive, CD16-negative classical monocyte (CL0002057)
    Fold Change: 0.4556
    Cell Significance Index: 8.4200
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 0.4392
    Cell Significance Index: 87.1600
  • Cell Name: skeletal muscle myoblast (CL0000515)
    Fold Change: 0.4323
    Cell Significance Index: 4.7000
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.3956
    Cell Significance Index: 8.5700
  • Cell Name: cardiac muscle cell (CL0000746)
    Fold Change: 0.3644
    Cell Significance Index: 5.3800
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: 0.3517
    Cell Significance Index: 9.0400
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: 0.3483
    Cell Significance Index: 59.4700
  • Cell Name: odontoblast (CL0000060)
    Fold Change: 0.2623
    Cell Significance Index: 33.6200
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.1974
    Cell Significance Index: 371.7400
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.1906
    Cell Significance Index: 36.2800
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.1327
    Cell Significance Index: 119.8600
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: 0.1182
    Cell Significance Index: 181.9200
  • Cell Name: pulmonary alveolar epithelial cell (CL0000322)
    Fold Change: 0.1112
    Cell Significance Index: 84.1400
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: 0.0963
    Cell Significance Index: 177.5200
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0645
    Cell Significance Index: 2.2700
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.0581
    Cell Significance Index: 5.7500
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: -0.0165
    Cell Significance Index: -12.0700
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: -0.0253
    Cell Significance Index: -34.4100
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.0413
    Cell Significance Index: -4.2200
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0616
    Cell Significance Index: -27.9400
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0691
    Cell Significance Index: -19.8900
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: -0.0924
    Cell Significance Index: -63.8800
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.1071
    Cell Significance Index: -79.3100
  • Cell Name: pancreatic PP cell (CL0002275)
    Fold Change: -0.1402
    Cell Significance Index: -87.5200
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.1487
    Cell Significance Index: -83.8700
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.1937
    Cell Significance Index: -28.1600
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: -0.1951
    Cell Significance Index: -69.9800
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: -0.2196
    Cell Significance Index: -3.6800
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: -0.2309
    Cell Significance Index: -3.1500
  • Cell Name: neutrophil progenitor cell (CL0000834)
    Fold Change: -0.3017
    Cell Significance Index: -8.0700
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: -0.3119
    Cell Significance Index: -62.5600
  • Cell Name: pro-T cell (CL0000827)
    Fold Change: -0.3425
    Cell Significance Index: -8.7500
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: -0.3599
    Cell Significance Index: -41.9400
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: -0.3932
    Cell Significance Index: -9.8300
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.4221
    Cell Significance Index: -88.9100
  • Cell Name: microcirculation associated smooth muscle cell (CL0008035)
    Fold Change: -0.4643
    Cell Significance Index: -3.9000
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.4982
    Cell Significance Index: -51.8700
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.5090
    Cell Significance Index: -58.3200
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: -0.5236
    Cell Significance Index: -61.7500
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: -0.6868
    Cell Significance Index: -22.0000
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.7831
    Cell Significance Index: -62.0200
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: -0.9445
    Cell Significance Index: -53.0000

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** 1. **Expression pattern:** YBX3 is highly expressed in various cell types, including pancreatic acinar cells, fibroblasts, and immune cells. 2. **Function:** YBX3 regulates mRNA stability, transcription, and translation, as well as apoptosis and cell growth. 3. **Regulatory mechanisms:** YBX3 is regulated by multiple pathways, including 3'-utr-mediated mRNA stabilization, apoptotic process, and stress responses. 4. **Cellular localization:** YBX3 is primarily localized to the nucleus, cytosol, and perinuclear region of the cytoplasm. **Pathways and Functions:** 1. **3'-utr-mediated mRNA stabilization:** YBX3 binds to the 3' untranslated region (3'-utr) of mRNAs, stabilizing them and regulating their translation. 2. **Apoptotic process:** YBX3 regulates apoptosis by modulating the intrinsic apoptotic signaling pathway in response to osmotic stress. 3. **Negative regulation of intrinsic apoptotic signaling pathway:** YBX3 inhibits the intrinsic apoptotic signaling pathway, preventing excessive apoptosis. 4. **Negative regulation of necroptotic process:** YBX3 also regulates necroptosis, preventing excessive cell death. 5. **Regulation of gene expression:** YBX3 regulates gene expression by binding to the transcriptional regulatory region of genes, modulating their expression. 6. **Regulation of translation:** YBX3 regulates translation by binding to mRNAs, modulating their translation efficiency. 7. **Response to stress:** YBX3 responds to stress by regulating gene expression, apoptosis, and cell growth. **Clinical Significance:** 1. **Cancer:** YBX3 is overexpressed in various types of cancer, including pancreatic cancer, breast cancer, and prostate cancer. 2. **Neurological disorders:** YBX3 is involved in the regulation of gene expression in neurological disorders, such as Alzheimer's disease and Parkinson's disease. 3. **Inflammatory diseases:** YBX3 is involved in the regulation of gene expression in inflammatory diseases, such as rheumatoid arthritis and atherosclerosis. 4. **Regenerative medicine:** YBX3 may play a role in tissue regeneration and repair, making it a potential target for regenerative therapies. In conclusion, YBX3 is a multifaceted gene involved in regulating various cellular processes, including mRNA stabilization, apoptosis, and transcription regulation. Its expression is regulated by multiple pathways, including those involved in stress responses. Understanding the functions and regulation of YBX3 can provide insights into the pathogenesis of various diseases and the development of novel therapeutic strategies.

Genular Protein ID: 836134128

Symbol: YBOX3_HUMAN

Name: Y-box-binding protein 3

UniProtKB Accession Codes:

P16989 B2RBW6 Q14121 Q969N6 Q96B76

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 BMRB 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CDD 1 CORUM 1 CPTAC 2 CTD 1 ChEMBL 1 ChiTaRS 1 DIP 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 18 Ensembl 2 ExpressionAtlas 1 GO 29 Gene3D 1 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 5 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 MetOSite 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PIR 2 PRINTS 1 PRO 1 PROSITE 2 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 3 Pumba 1 RNAct 1 RefSeq 2 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 2977358

Title: Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology.

PubMed ID: 2977358

DOI: 10.1016/0378-1119(88)90514-8

PubMed ID: 7628487

Title: Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain.

PubMed ID: 7628487

DOI: 10.1111/j.1432-1033.1995.tb20672.x

PubMed ID: 8710501

Title: Cold shock domain proteins repress transcription from the GM-CSF promoter.

PubMed ID: 8710501

DOI: 10.1093/nar/24.12.2311

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 19413330

Title: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

PubMed ID: 19413330

DOI: 10.1021/ac9004309

PubMed ID: 19710015

Title: The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor.

PubMed ID: 19710015

DOI: 10.1074/jbc.m109.023457

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 21406692

Title: System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.

PubMed ID: 21406692

DOI: 10.1126/scisignal.2001570

PubMed ID: 22223895

Title: Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features.

PubMed ID: 22223895

DOI: 10.1074/mcp.m111.015131

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 24129315

Title: Immunoaffinity enrichment and mass spectrometry analysis of protein methylation.

PubMed ID: 24129315

DOI: 10.1074/mcp.o113.027870

Sequence Information:

  • Length: 372
  • Mass: 40090
  • Checksum: AA8517AC3B7D35CC
  • Sequence:
    • MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA HVAGNPGGDA 
APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV RNGYGFINRN DTKEDVFVHQ 
TAIKKNNPRK YLRSVGDGET VEFDVVEGEK GAEAANVTGP DGVPVEGSRY AADRRRYRRG 
YYGRRRGPPR NYAGEEEEEG SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY 
HVGQTFDRRS RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR 
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK EAKAGEAPTE 
NPAPPTQQSS AE

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.