YBX3 (Y-box binding protein 3)

Gene

• Entrez ID: 8531
• Gene name: Y-box binding protein 3
• Gene symbol: YBX3
• Synonyms (NCBI Gene): CSDA, CSDA1, DBPA, ZONAB
• Chromosome: 12
• Chromosome location: 12p13.2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT020521	hsa-miR-155-5p	Proteomics	18668040
MIRT022125	hsa-miR-124-3p	Proteomics	18668037
MIRT028402	hsa-miR-30a-5p	Proteomics	18668040
MIRT031397	hsa-miR-16-5p	Proteomics	18668040
MIRT050665	hsa-miR-18a-5p	CLASH	23622248
MIRT049114	hsa-miR-92a-3p	CLASH	23622248
MIRT048561	hsa-miR-100-5p	CLASH	23622248
MIRT041350	hsa-miR-193b-3p	CLASH	23622248
MIRT039503	hsa-miR-652-3p	CLASH	23622248
MIRT054166	hsa-miR-191-5p	Immunoprecipitation, In situ hybridization, Luciferase assay, Microarray, Northern blot, QRTPCR, Western blot	23505378
0	hsa-miR-191-5p	Immunoprecipitation, In situ hybridization, Luciferase assay, Microarray, Northern blot, QRTPCR, Western blot	23505378

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	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:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003730	Function	MRNA 3'-UTR binding	IEA
GO:0003730	Function	MRNA 3'-UTR binding	ISS	22711822
GO:0005515	Function	Protein binding	IPI	25593058, 37608570
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS	22711822
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	7628487
GO:0005829	Component	Cytosol	IDA
GO:0005923	Component	Bicellular tight junction	ISS	22711822
GO:0006915	Process	Apoptotic process	IEA
GO:0007283	Process	Spermatogenesis	IEA
GO:0008584	Process	Male gonad development	IEA
GO:0009566	Process	Fertilization	IEA
GO:0010468	Process	Regulation of gene expression	IBA
GO:0031267	Function	Small GTPase binding	ISS
GO:0035234	Process	Ectopic germ cell programmed cell death	IEA
GO:0043021	Function	Ribonucleoprotein complex binding	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0045202	Component	Synapse	IEA
GO:0046622	Process	Positive regulation of organ growth	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	ISS	22711822
GO:0048642	Process	Negative regulation of skeletal muscle tissue development	IEA
GO:0051093	Process	Negative regulation of developmental process	IEA
GO:0060546	Process	Negative regulation of necroptotic process	IMP	22711822
GO:0070935	Process	3'-UTR-mediated mRNA stabilization	IC	22711822
GO:0071356	Process	Cellular response to tumor necrosis factor	IMP	22711822
GO:0071474	Process	Cellular hyperosmotic response	IMP	22711822
GO:1902219	Process	Negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress	IMP	22711822
GO:2000242	Process	Negative regulation of reproductive process	IEA
GO:2000767	Process	Positive regulation of cytoplasmic translation	ISS	22711822

Other IDs

• MIM: 603437
• HGNC: 2428
• e!Ensembl: ENSG00000060138

Protein

• UniProt ID: P16989
• Protein name: Y-box-binding protein 3 (Cold shock domain-containing protein A) (DNA-binding protein A) (Single-strand DNA-binding protein NF-GMB)
• Protein function: Binds to the GM-CSF promoter. Seems to act as a repressor. Also binds to full-length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression (By similarity).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00313	CSD	91 → 160		Domain

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in skeletal muscle and heart.
• Sequence:

  MSEAGEATTTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAAAPAPAAHVAGNPGGDA
  APAATGTAAAASLATAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQ
  TAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRG
  YYGRRRGPPRNYAGEEEEEGSGSSEGFDPPATDRQFSGARNQLRRPQYRPQYRQRRFPPY
  HVGQTFDRRSRVLPHPNRIQAGEIGEMKDGVPEGAQLQGPVHRNPTYRPRYRSRGPPRPR
  PAPAVGEAEDKENQQATSGPNQPSVRRGYRRPYNYRRRPRPPNAPSQDGKEAKAGEAPTE
  NPAPPTQQSSAE

• Sequence length: 372

Pathways

KEGG:

Tight junction

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenomatous Polyposis Coli	Multiple polyposis syndrome	BEFREE	19749785		★☆☆☆☆ Found in Text Mining only
Arthritis Juvenile	Juvenile arthritis	Pubtator	38243323	Associate	★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet disease	Pubtator	35941595	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	18179684		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	32627826	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	30214570		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	24885929, 33229623, 37418046	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	27569444		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34965023, 36059530	Associate	★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	20133480		★☆☆☆☆ Found in Text Mining only
Cystinosis	Cystinosis	BEFREE	29806776		★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	25220401	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	25220401		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	18179684		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	30214570		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	19749785		★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	BEFREE	25220401		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24885929		★☆☆☆☆ Found in Text Mining only
Peripheral Arterial Diseases	Vascular Diseases	BEFREE	21473684		★☆☆☆☆ Found in Text Mining only
Peripheral Vascular Diseases	Vascular Diseases	BEFREE	21473684		★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	29721182		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	19749785		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	19749785	Associate	★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	33282635	Associate	★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Uveal melanoma	Pubtator	20861479	Associate	★☆☆☆☆ Found in Text Mining only