TRIM40 (tripartite motif containing 40)

Gene

• Entrez ID: 135644
• Gene name: Tripartite motif containing 40
• Gene symbol: TRIM40
• Synonyms (NCBI Gene): RNF35
• Chromosome: 6
• Chromosome location: 6p22.1
• Summary: This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that enc

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017261	hsa-miR-335-5p	Microarray	18185580
MIRT1454731	hsa-miR-1293	CLIP-seq
MIRT1454732	hsa-miR-1301	CLIP-seq
MIRT1454733	hsa-miR-3153	CLIP-seq
MIRT1454734	hsa-miR-4483	CLIP-seq
MIRT1454735	hsa-miR-4652-3p	CLIP-seq
MIRT1454736	hsa-miR-4668-5p	CLIP-seq
MIRT1454737	hsa-miR-5047	CLIP-seq
MIRT2136201	hsa-miR-4742-5p	CLIP-seq
MIRT2434363	hsa-miR-224	CLIP-seq
MIRT2434364	hsa-miR-664	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21474709
GO:0005737	Component	Cytoplasm	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008385	Component	IkappaB kinase complex	IDA	21474709
GO:0016740	Function	Transferase activity	IEA
GO:0030308	Process	Negative regulation of cell growth	IEA
GO:0032088	Process	Negative regulation of NF-kappaB transcription factor activity	IDA	21474709
GO:0042177	Process	Negative regulation of protein catabolic process	IDA	21474709
GO:0045087	Process	Innate immune response	IBA
GO:0045116	Process	Protein neddylation	IDA	21474709
GO:0046872	Function	Metal ion binding	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IBA
GO:0061630	Function	Ubiquitin protein ligase activity	IEA
GO:1900181	Process	Negative regulation of protein localization to nucleus	IDA	21474709
GO:1901223	Process	Negative regulation of non-canonical NF-kappaB signal transduction	NAS	21474709

Other IDs

• MIM: 616976
• HGNC: 18736
• e!Ensembl: ENSG00000204614

Protein

• UniProt ID: Q6P9F5
• Protein name: E3 ubiquitin ligase TRIM40 (EC 2.3.2.27) (Probable E3 NEDD8-protein ligase) (RING finger protein 35)
• Protein function: E3 ubiquitin-protein ligase that plays a role in the limitation of the innate immune response (PubMed:21474709, PubMed:29117565). Mediates inhibition of the RLR signaling pathway by ubiquitinating RIGI and IFIH1 receptors, leading to their prote
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13445	zf-RING_UBOX	14 → 54	RING-type zinc-finger	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in normal gastrointestinal epithelia but that is down-regulated in gastrointestinal carcinomas and chronic inflammatory lesions of the gastrointestinal tract. {ECO:0000269|PubMed:21474709}.
• Sequence:

  MIPLQKDNQEEGVCPICQESLKEAVSTNCGHLFCRVCLTQHVEKASASGVFCCPLCRKPC
  SEEVLGTGYICPNHQKRVCRFCEESRLLLCVECLVSPEHMSHHELTIENALSHYKERLNR
  RSRKLRKDIAELQRLKAQQEKKLQALQFQVDHGNHRLEAGPESQHQTREQLGALPQQWLG
  QLEHMPAEAARILDISRAVTQLRSLVIDLERTAKELDTNTLKNAGDLLNRSAPQKLEVIY
  PQLEKGVSELLLQPPQKL

• Sequence length: 258

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
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC INTERSTITIAL CYSTITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DERMATITIS, IRRITANT	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARKINSON DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	40244264	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	21682861	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	21474709	Inhibit	★☆☆☆☆ Found in Text Mining only
Chronic Disease	Chronic disease	Pubtator	21474709	Inhibit	★☆☆☆☆ Found in Text Mining only
Dermatitis, Irritant	Dermatitis	CTD_human_DG	27258892		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	GWASDB_DG	17632545		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Diseases	Gastrointestinal disease	Pubtator	21474709	Associate	★☆☆☆☆ Found in Text Mining only
Gastrointestinal Neoplasms	Gastrointestinal neoplasm	Pubtator	21474709	Inhibit	★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	27699474		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	GWASDB_DG	17804836, 19503088		★★☆☆☆ Found in Text Mining + Unknown/Other Associations