BHLHE41 (basic helix-loop-helix family member e41)

Gene

• Entrez ID: 79365
• Gene name: Basic helix-loop-helix family member e41
• Gene symbol: BHLHE41
• Synonyms (NCBI Gene): BHLHB3, DEC2, FNSS1, SHARP1, hDEC2
• Chromosome: 12
• Chromosome location: 12p12.1
• Summary: This gene encodes a basic helix-loop-helix protein expressed in various tissues. The encoded protein can interact with ARNTL or compete for E-box binding sites in the promoter of PER1 and repress CLOCK/ARNTL`s transactivation of PER1. This gene is believe

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018496	hsa-miR-335-5p	Microarray	18185580
MIRT044939	hsa-miR-186-5p	CLASH	23622248
MIRT821326	hsa-miR-105	CLIP-seq
MIRT821327	hsa-miR-1304	CLIP-seq
MIRT821328	hsa-miR-15a	CLIP-seq
MIRT821329	hsa-miR-15b	CLIP-seq
MIRT821330	hsa-miR-16	CLIP-seq
MIRT821331	hsa-miR-1827	CLIP-seq
MIRT821332	hsa-miR-195	CLIP-seq
MIRT821333	hsa-miR-424	CLIP-seq
MIRT821334	hsa-miR-4470	CLIP-seq
MIRT821335	hsa-miR-4661-3p	CLIP-seq
MIRT821336	hsa-miR-4711-3p	CLIP-seq
MIRT821337	hsa-miR-497	CLIP-seq
MIRT821338	hsa-miR-501-3p	CLIP-seq
MIRT821339	hsa-miR-502-3p	CLIP-seq
MIRT821340	hsa-miR-511	CLIP-seq
MIRT821341	hsa-miR-545	CLIP-seq
MIRT1922591	hsa-miR-125a-5p	CLIP-seq
MIRT1922592	hsa-miR-125b	CLIP-seq
MIRT1922593	hsa-miR-3667-3p	CLIP-seq
MIRT1922594	hsa-miR-4319	CLIP-seq
MIRT1922595	hsa-miR-4732-3p	CLIP-seq
MIRT1922596	hsa-miR-670	CLIP-seq
MIRT1942784	hsa-miR-1229	CLIP-seq
MIRT821328	hsa-miR-15a	CLIP-seq
MIRT821329	hsa-miR-15b	CLIP-seq
MIRT821330	hsa-miR-16	CLIP-seq
MIRT821332	hsa-miR-195	CLIP-seq
MIRT1942785	hsa-miR-342-3p	CLIP-seq
MIRT1942786	hsa-miR-3658	CLIP-seq
MIRT821333	hsa-miR-424	CLIP-seq
MIRT821337	hsa-miR-497	CLIP-seq
MIRT821341	hsa-miR-545	CLIP-seq
MIRT1942784	hsa-miR-1229	CLIP-seq
MIRT2181527	hsa-miR-1238	CLIP-seq
MIRT2181528	hsa-miR-1255a	CLIP-seq
MIRT2181529	hsa-miR-1255b	CLIP-seq
MIRT2181530	hsa-miR-1269	CLIP-seq
MIRT2181531	hsa-miR-1269b	CLIP-seq
MIRT2181532	hsa-miR-129-5p	CLIP-seq
MIRT2181533	hsa-miR-3074-3p	CLIP-seq
MIRT2181534	hsa-miR-3145-3p	CLIP-seq
MIRT2181535	hsa-miR-3162-3p	CLIP-seq
MIRT1942785	hsa-miR-342-3p	CLIP-seq
MIRT2181536	hsa-miR-4328	CLIP-seq
MIRT2181537	hsa-miR-4520b-3p	CLIP-seq
MIRT2181538	hsa-miR-4529-3p	CLIP-seq
MIRT821341	hsa-miR-545	CLIP-seq
MIRT2181539	hsa-miR-548p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
CLOCK	Activation	14672706
GLI1	Activation	24165159
GLI2	Unknown	24165159

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	14672706, 15193144
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISS
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	19786558
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	ISS
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	19786558, 22801492
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007623	Process	Circadian rhythm	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IBA
GO:0010832	Process	Negative regulation of myotube differentiation	IEA
GO:0010832	Process	Negative regulation of myotube differentiation	ISS
GO:0010944	Process	Negative regulation of transcription by competitive promoter binding	IEA
GO:0010944	Process	Negative regulation of transcription by competitive promoter binding	ISS
GO:0032922	Process	Circadian regulation of gene expression	IBA
GO:0032922	Process	Circadian regulation of gene expression	IEA
GO:0042803	Function	Protein homodimerization activity	IEA
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0042826	Function	Histone deacetylase binding	IEA
GO:0042826	Function	Histone deacetylase binding	ISS
GO:0043425	Function	BHLH transcription factor binding	IEA
GO:0043425	Function	BHLH transcription factor binding	IPI	15193144
GO:0043425	Function	BHLH transcription factor binding	ISS
GO:0043426	Function	MRF binding	IEA
GO:0043426	Function	MRF binding	ISS
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	ISS
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0046982	Function	Protein heterodimerization activity	IPI	15193144
GO:0046983	Function	Protein dimerization activity	IEA
GO:0048511	Process	Rhythmic process	IEA
GO:0050767	Process	Regulation of neurogenesis	IBA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	ISS
GO:0070888	Function	E-box binding	IDA	14672706, 15193144
GO:0070888	Function	E-box binding	IEA
GO:0070888	Function	E-box binding	ISS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 606200
• HGNC: 16617
• e!Ensembl: ENSG00000123095

Protein

• UniProt ID: Q9C0J9
• Protein name: Class E basic helix-loop-helix protein 41 (bHLHe41) (Class B basic helix-loop-helix protein 3) (bHLHb3) (Differentially expressed in chondrocytes protein 2) (hDEC2) (Enhancer-of-split and hairy-related protein 1) (SHARP-1)
• Protein function: Transcriptional repressor involved in the regulation of the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes (PubMed:11278948, PubMed:14672706, PubMed:15193144, PubMed:15560782, PubMed:18411297
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00010	HLH	45 → 100	Helix-loop-helix DNA-binding domain	Domain
  PF07527	Hairy_orange	130 → 171	Hairy Orange	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in skeletal muscle and brain, moderately expressed in pancreas and heart, weakly expressed in placenta, lung, liver and kidney.
• Sequence:

  MDEGIPHLQERQLLEHRDFIGLDYSSLYMCKPKRSMKRDDTKDTYKLPHRLIEKKRRDRI
  NECIAQLKDLLPEHLKLTTLGHLEKAVVLELTLKHLKALTALTEQQHQKIIALQNGERSL
  KSPIQSDLDAFHSGFQTCAKEVLQYLSRFESWTPREPRCVQLINHLHAVATQFLPTPQLL
  TQQVPLSKGTGAPSAAGSAAAPCLERAGQKLEPLAYCVPVIQRTQPSAELAAENDTDTDS
  GYGGEAEARPDREKGKGAGASRVTIKQEPPGEDSPAPKRMKLDSRGGGSGGGPGGGAAAA
  AAALLGPDPAAAAALLRPDAALLSSLVAFGGGGGAPFPQPAAAAAPFCLPFCFLSPSAAA
  AYVQPFLDKSGLEKYLYPAAAAAPFPLLYPGIPAPAAAAAAAAAAAAAAAAFPCLSSVLS
  PPPEKAGAAAATLLPHEVAPLGAPHPQHPHGRTHLPFAGPREPGNPESSAQEDPSQPGKE
  AP

• Sequence length: 482

Pathways

KEGG:

Circadian rhythm

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
BHLHE41-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOOD DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Short sleep, familial natural, 1	Affects	ClinVar	★★☆☆☆ 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	17194498, 18223678		★☆☆☆☆ Found in Text Mining only
Alveolar Soft Part Sarcoma	Alveolar Sarcoma	BEFREE	21552147		★☆☆☆☆ Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	24165159		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	20072116		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar disorder	Pubtator	36481223	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	20236182, 21327324, 22801492, 25242400		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25242400	Inhibit	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30651373, 32073238, 33101542, 34215221, 40508038	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	18223678		★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	30816499	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	31487856	Associate	★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	27384883, 30816499		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	26710124		★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	40508038	Associate	★☆☆☆☆ Found in Text Mining only
Depressive Disorder Major	Major depressive disorder	Pubtator	23671070	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Carcinoma	Endometrial carcinoma	BEFREE	17342330, 24918449, 24997474, 25884381, 31384392		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	24918449, 26391953	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	28498447, 29890466		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	28498447, 29890466		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	31616182		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	31616182		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	31616182		★☆☆☆☆ Found in Text Mining only
Heart Failure	Heart failure	Pubtator	36699999	Associate	★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	20571087		★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	18345027	Stimulate	★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	20236182, 22572381, 24918449, 30816499, 32073238	Associate	★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	34745571	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	30132511		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	29692408		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung Neoplasms	LHGDN	18223678		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung Neoplasms	Lung Neoplasms	CTD_human_DG	27935865		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	24918449	Inhibit	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic Metastasis	BEFREE	24997474		★☆☆☆☆ Found in Text Mining only
Major Depressive Disorder	Mental Depression	GWASCAT_DG	27622933		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of breast	Breast Cancer	BEFREE	20236182, 21327324, 22801492, 25242400		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of endometrium	Endometrial Cancer	BEFREE	24918449, 24997474, 31384392		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	28498447, 29890466		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	18223678		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	CTD_human_DG	27935865		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	22735690, 24165159		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	27840924, 30106153		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of thyroid	Thyroid cancer	BEFREE	30158530		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21327324, 22735690, 26391953, 27840924, 30816499		★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	37373286	Stimulate	★☆☆☆☆ Found in Text Mining only
Mood Disorders	Mood Disorder	GWASCAT_DG	27622933		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	33544757	Associate	★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	Pubtator	34745571	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	18223678, 21552147, 24918449, 25884381, 29890466		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	25884381, 27095063		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	22735690, 24165159		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	34745571	Associate	★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	27840924, 30106153		★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	27384883		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	26710124		★☆☆☆☆ Found in Text Mining only
Short Sleeper Syndrome	Short Sleeper Syndromes	BEFREE	19679812, 28223099		★☆☆☆☆ Found in Text Mining only
Short Sleeper Syndrome	Short Sleeper Syndromes	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	25083013	Associate	★☆☆☆☆ Found in Text Mining only
Sleep Disorders	Sleep Disorders	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Sleep Wake Disorders	Sleep Wake Disorders	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	28498447		★☆☆☆☆ Found in Text Mining only
Thyroid carcinoma	Thyroid Carcinoma	BEFREE	30158530		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasm	Thyroid Neoplasm	BEFREE	30158530		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	22801492, 23913939		★☆☆☆☆ Found in Text Mining only
Unipolar Depression	Mental Depression	GWASCAT_DG	27622933		★☆☆☆☆ Found in Text Mining only