LMO3 (LIM domain only 3)

Gene

• Entrez ID: 55885
• Gene name: LIM domain only 3
• Gene symbol: LMO3
• Synonyms (NCBI Gene): RBTN3, RBTNL2, RHOM3, Rhom-3
• Chromosome: 12
• Chromosome location: 12p12.3
• Summary: The protein encoded by this gene belongs to the rhombotin family of cysteine-rich LIM domain oncogenes. This gene is predominantly expressed in the brain. Related family members, LMO1 and LMO2 on chromosome 11, have been reported to be involved in chromos

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017853	hsa-miR-335-5p	Microarray	18185580
MIRT1111879	hsa-miR-1226	CLIP-seq
MIRT1111880	hsa-miR-1236	CLIP-seq
MIRT1111881	hsa-miR-1305	CLIP-seq
MIRT1111882	hsa-miR-141	CLIP-seq
MIRT1111883	hsa-miR-200a	CLIP-seq
MIRT1111884	hsa-miR-219-5p	CLIP-seq
MIRT1111885	hsa-miR-27a	CLIP-seq
MIRT1111886	hsa-miR-27b	CLIP-seq
MIRT1111887	hsa-miR-28-3p	CLIP-seq
MIRT1111888	hsa-miR-3140-3p	CLIP-seq
MIRT1111889	hsa-miR-338-3p	CLIP-seq
MIRT1111890	hsa-miR-3674	CLIP-seq
MIRT1111891	hsa-miR-375	CLIP-seq
MIRT1111892	hsa-miR-4310	CLIP-seq
MIRT1111893	hsa-miR-4422	CLIP-seq
MIRT1111894	hsa-miR-4445	CLIP-seq
MIRT1111895	hsa-miR-4659a-3p	CLIP-seq
MIRT1111896	hsa-miR-4659b-3p	CLIP-seq
MIRT1111897	hsa-miR-4699-5p	CLIP-seq
MIRT1111898	hsa-miR-4753-3p	CLIP-seq
MIRT1111899	hsa-miR-4768-5p	CLIP-seq
MIRT1111900	hsa-miR-4777-5p	CLIP-seq
MIRT1111901	hsa-miR-4778-3p	CLIP-seq
MIRT1111902	hsa-miR-4782-3p	CLIP-seq
MIRT1111903	hsa-miR-508-3p	CLIP-seq
MIRT1111904	hsa-miR-5096	CLIP-seq
MIRT1111905	hsa-miR-513a-5p	CLIP-seq
MIRT1111906	hsa-miR-518d-5p	CLIP-seq
MIRT1111907	hsa-miR-519b-5p	CLIP-seq
MIRT1111908	hsa-miR-519c-5p	CLIP-seq
MIRT1111909	hsa-miR-520c-5p	CLIP-seq
MIRT1111910	hsa-miR-526a	CLIP-seq
MIRT1111911	hsa-miR-548aa	CLIP-seq
MIRT1111912	hsa-miR-548p	CLIP-seq
MIRT1111913	hsa-miR-634	CLIP-seq
MIRT1111914	hsa-miR-4712-3p	CLIP-seq
MIRT1920589	hsa-miR-205	CLIP-seq
MIRT1920590	hsa-miR-2682	CLIP-seq
MIRT1920591	hsa-miR-449c	CLIP-seq
MIRT1920592	hsa-miR-940	CLIP-seq
MIRT1920589	hsa-miR-205	CLIP-seq
MIRT1920590	hsa-miR-2682	CLIP-seq
MIRT1920591	hsa-miR-449c	CLIP-seq
MIRT1920592	hsa-miR-940	CLIP-seq
MIRT2031232	hsa-miR-3143	CLIP-seq
MIRT2031233	hsa-miR-3607-3p	CLIP-seq
MIRT2031234	hsa-miR-3686	CLIP-seq
MIRT2031235	hsa-miR-4775	CLIP-seq
MIRT2031236	hsa-miR-543	CLIP-seq
MIRT2031237	hsa-miR-590-3p	CLIP-seq
MIRT2262026	hsa-miR-3145-3p	CLIP-seq
MIRT1111903	hsa-miR-508-3p	CLIP-seq
MIRT2465552	hsa-miR-2113	CLIP-seq
MIRT2465553	hsa-miR-218	CLIP-seq
MIRT2465554	hsa-miR-338-5p	CLIP-seq
MIRT2465555	hsa-miR-3671	CLIP-seq
MIRT2465556	hsa-miR-3977	CLIP-seq
MIRT2465557	hsa-miR-607	CLIP-seq
MIRT2465558	hsa-miR-636	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
NKX2-1	Unknown	23322301

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003713	Function	Transcription coactivator activity	IBA
GO:0005515	Function	Protein binding	IPI	16189514, 20211142, 25416956, 27107012, 31515488, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005737	Component	Cytoplasm	IDA	23823477
GO:0035360	Process	Positive regulation of peroxisome proliferator activated receptor signaling pathway	IDA	23823477
GO:0045600	Process	Positive regulation of fat cell differentiation	IMP	23823477
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0070373	Process	Negative regulation of ERK1 and ERK2 cascade	IDA	23823477
GO:0140297	Function	DNA-binding transcription factor binding	IBA
GO:2000324	Process	Positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway	IDA	23823477

Other IDs

• MIM: 180386
• HGNC: 6643
• e!Ensembl: ENSG00000048540

Protein

• UniProt ID: Q8TAP4
• Protein name: LIM domain only protein 3 (LMO-3) (Neuronal-specific transcription factor DAT1) (Rhombotin-3)
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00412	LIM	13 → 71	LIM domain	Domain
  PF00412	LIM	77 → 134	LIM domain	Domain

• Sequence:

  MLSVQPDTKPKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANL
  ILCRRDYLRLFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFL
  KNNMILCQTDYEEGLMKEGYAPQVR

• Sequence length: 145

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
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRRITABLE BOWEL SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	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
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	23322301, 31646571		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	33980985	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	38366633	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	30219064	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	38366633	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	22011669	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	38366633	Inhibit	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	30884196		★☆☆☆☆ Found in Text Mining only
Diffuse Large B-Cell Lymphoma	Diffuse Lymphoma	BEFREE	27184832		★☆☆☆☆ Found in Text Mining only
Disturbance in mood	Mood Disorder	BEFREE	31707294		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	36581816	Associate	★☆☆☆☆ Found in Text Mining only
Ewings sarcoma	Ewing sarcoma	BEFREE	31488873		★☆☆☆☆ Found in Text Mining only
Gilles de la Tourette syndrome	Tourette Syndrome	GWASCAT_DG	30818990		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	25829251	Associate	★☆☆☆☆ Found in Text Mining only
Hurthle Cell Tumor	Tumor	BEFREE	28986304		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30219064		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	29436606		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21124317		★☆☆☆☆ Found in Text Mining only
Meningioma	Meningioma	Pubtator	23840654	Associate	★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	23840654	Associate	★☆☆☆☆ Found in Text Mining only
Mood Disorders	Mood Disorder	BEFREE	31707294		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16915569, 31488873		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	15930276, 19995558, 21573214		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	21573214, 36037157	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	23823477		★☆☆☆☆ Found in Text Mining only
Oxyphilic Adenoma	Oxyphilic Adenoma	BEFREE	28986304		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	38366633	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of lung	Lung carcinoma	BEFREE	22011669		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	29436606		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	29436606	Stimulate	★☆☆☆☆ Found in Text Mining only
Thyroid Carcinoma Anaplastic	Thyroid cancer	Pubtator	27796151	Associate	★☆☆☆☆ Found in Text Mining only