LIME1 (Lck interacting transmembrane adaptor 1)

Gene

• Entrez ID: 54923
• Gene name: Lck interacting transmembrane adaptor 1
• Gene symbol: LIME1
• Synonyms (NCBI Gene): LIME, dJ583P15.4
• Chromosome: 20
• Chromosome location: 20q13.33
• Summary: This gene encodes a transmembrane adaptor protein that links the T and B-cell receptor stimulation to downstream signaling pathways via its association with the Src family kinases Lck and Lyn, respectively. Alternative splicing of this gene results in mul

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2030526	hsa-miR-3659	CLIP-seq
MIRT2030527	hsa-miR-4658	CLIP-seq
MIRT2030528	hsa-miR-4758-5p	CLIP-seq
MIRT2030529	hsa-miR-574-5p	CLIP-seq
MIRT2261277	hsa-miR-1294	CLIP-seq
MIRT2261278	hsa-miR-1908	CLIP-seq
MIRT2261279	hsa-miR-3180	CLIP-seq
MIRT2261280	hsa-miR-3180-3p	CLIP-seq
MIRT2261281	hsa-miR-3196	CLIP-seq
MIRT2261282	hsa-miR-3197	CLIP-seq
MIRT2261283	hsa-miR-4316	CLIP-seq
MIRT2261284	hsa-miR-663	CLIP-seq
MIRT2261285	hsa-miR-744	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002250	Process	Adaptive immune response	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	32296183, 33961781
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005886	Component	Plasma membrane	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0016020	Component	Membrane	IEA
GO:0019815	Component	B cell receptor complex	IBA
GO:0019815	Component	B cell receptor complex	IEA
GO:0019901	Function	Protein kinase binding	IBA
GO:0019901	Function	Protein kinase binding	IEA
GO:0043122	Process	Regulation of canonical NF-kappaB signal transduction	IEA
GO:0050852	Process	T cell receptor signaling pathway	IEA
GO:0050853	Process	B cell receptor signaling pathway	IBA
GO:0050853	Process	B cell receptor signaling pathway	IEA
GO:0050853	Process	B cell receptor signaling pathway	IEA
GO:0051279	Process	Regulation of release of sequestered calcium ion into cytosol	IEA
GO:0051896	Process	Regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA
GO:1901222	Process	Regulation of non-canonical NF-kappaB signal transduction	IEA

Other IDs

• MIM: 609809
• HGNC: 26016
• e!Ensembl: ENSG00000203896

Protein

• UniProt ID: Q9H400
• Protein name: Lck-interacting transmembrane adapter 1 (Lck-interacting membrane protein) (Lck-interacting molecule)
• Protein function: Involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and TCR (T-cell antigen receptor)-mediated T-cell signaling in T-cells. In absence of TCR signaling, may be involved in CD4-mediated inhibition of T-cell activation. Couples
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15332	LIME1	27 → 259	Lck-interacting transmembrane adapter 1	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed in peripheral blood lymphocytes, lymphoid tissues, and liver. Present in T-cells and plasma cells, and in various hematopoietic cell lines (at protein level). {ECO:0000269|PubMed:14610044, ECO:0000269|PubMed:14610046, ECO:000
• Sequence:

  MGLPVSWAPPALWVLGCCALLLSLWALCTACRRPEDAVAPRKRARRQRARLQGSATAAEA
  SLLRRTHLCSLSKSDTRLHELHRGPRSSRALRPASMDLLRPHWLEVSRDITGPQAAPSAF
  PHQELPRALPAAAATAGCAGLEATYSNVGLAALPGVSLAASPVVAEYARVQKRKGTHRSP
  QEPQQGKTEVTPAAQVDVLYSRVCKPKRRDPGPTTDPLDPKGQGAILALAGDLAYQTLPL
  RALDVDSGPLENVYESIRELGDPAGRSSTCGAGTPPASSCPSLGRGWRPLPASLP

• Sequence length: 295

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
DERMATOMYCOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DERMATOPHYTOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	34449791	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral Palsy	Cerebral palsy	Pubtator	29484035	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28263391		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	16160011	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	31932686	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28263391		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	27067812		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	34449791	Associate	★☆☆☆☆ Found in Text Mining only