BHLHE40 basic helix-loop-helix family member e40 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BHLHE40provided by HGNC
Official Full Name: basic helix-loop-helix family member e40provided by HGNC
Primary source: HGNC:HGNC:1046
See related: Ensembl:ENSG00000134107 MIM:604256; AllianceGenome:HGNC:1046
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DEC1; HLHB2; BHLHB2; Clast5; SHARP2; STRA13; Stra14; SHARP-2
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 believed to be involved in the control of circadian rhythm and cell differentiation. [provided by RefSeq, Feb 2014]
Annotation information: Note: DEC1 (Gene ID: 50514) and BHLHE40 (Gene ID: 8553) share the DEC1 symbol/alias in common. DEC1 (differentially expressed in chondrocytes 1) is a widely used alternative name for basic helix-loop-helix family member e40 (BHLHE40), which can be confused with the official symbol for deleted in esophageal cancer 1 (DEC1). [23 May 2018]
Expression: Ubiquitous expression in esophagus (RPKM 152.7), liver (RPKM 106.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p26.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (4979437..4985323)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (4970406..4979102)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (5021122..5027008)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer.
Title: Single-Cell and Spatial Transcriptome Profiling Identifies the Transcription Factor BHLHE40 as a Driver of EMT in Metastatic Colorectal Cancer.
BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer's disease and other disorders of lipid-rich tissues.
Title: BHLHE40/41 regulate microglia and peripheral macrophage responses associated with Alzheimer's disease and other disorders of lipid-rich tissues.
LncRNA H19 Influences Cellular Activities via the miR-454-3p/BHLHE40 Axis in Anaplastic Thyroid Carcinoma.
Title: LncRNA H19 Influences Cellular Activities via the miR-454-3p/BHLHE40 Axis in Anaplastic Thyroid Carcinoma.
DEC1 is involved in circadian rhythm disruption-exacerbated pulmonary fibrosis.
Title: DEC1 is involved in circadian rhythm disruption-exacerbated pulmonary fibrosis.
The BHLHE40-PPM1F-AMPK pathway regulates energy metabolism and is associated with the aggressiveness of endometrial cancer.
Title: The BHLHE40‒PPM1F‒AMPK pathway regulates energy metabolism and is associated with the aggressiveness of endometrial cancer.
BHLHE40, a potential immune therapy target, regulated by FGD5-AS1/miR-15a-5p in pancreatic cancer.
Title: BHLHE40, a potential immune therapy target, regulated by FGD5-AS1/miR-15a-5p in pancreatic cancer.
High expression of BHLHE40 promotes immune infiltration and tumor progression in thyroid cancer.
Title: High expression of BHLHE40 promotes immune infiltration and tumor progression in thyroid cancer.
HIF-1alpha contributes to metastasis in choriocarcinoma by regulating DEC1 expression.
Title: HIF-1α contributes to metastasis in choriocarcinoma by regulating DEC1 expression.
Overcoming ABCB1-mediated multidrug resistance by transcription factor BHLHE40.
Title: Overcoming ABCB1-mediated multidrug resistance by transcription factor BHLHE40.
Single-cell RNA-seq analysis reveals BHLHE40-driven pro-tumour neutrophils with hyperactivated glycolysis in pancreatic tumour microenvironment.
Title: Single-cell RNA-seq analysis reveals BHLHE40-driven pro-tumour neutrophils with hyperactivated glycolysis in pancreatic tumour microenvironment.

Submit: New GeneRIF Correction See all GeneRIFs (92)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3912 (e-PCR)
- UniSTS:76598

SHGC-37025 (e-PCR)
- UniSTS:10298

D3S2920E (e-PCR)
- UniSTS:150904

BHLHB2_2101 (e-PCR)
- UniSTS:280460

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables E-box binding	IDA Inferred from Direct Assay more info	PubMed
enables E-box binding	IEA Inferred from Electronic Annotation more info
enables MRF binding	IEA Inferred from Electronic Annotation more info
enables MRF binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISS Inferred from Sequence or Structural Similarity more info
enables bHLH transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in circadian regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in circadian regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in circadian rhythm	IDA Inferred from Direct Assay more info	PubMed
involved_in circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in entrainment of circadian clock by photoperiod	IEA Inferred from Electronic Annotation more info
involved_in entrainment of circadian clock by photoperiod	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in regulation of circadian rhythm	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neurogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: class E basic helix-loop-helix protein 40

Names: basic helix-loop-helix domain containing, class B, 2; class B basic helix-loop-helix protein 2; differentially expressed in chondrocytes 1; differentially expressed in chondrocytes protein 1; differentiated embryo chondrocyte expressed gene 1; enhancer-of-split and hairy-related protein 2; stimulated by retinoic acid gene 13 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_003670.3 → NP_003661.1 class E basic helix-loop-helix protein 40

See identical proteins and their annotated locations for NP_003661.1

Status: REVIEWED

Source sequence(s)

AA632164, AC090955, BC068292, BC082238, BI962730, DB144350

Consensus CDS

CCDS2565.1

UniProtKB/Swiss-Prot

O14503, Q96TD3

UniProtKB/TrEMBL

A0A024R2D0, Q6IB83

Related

ENSP00000256495.3, ENST00000256495.4

Conserved Domains (2) summary

smart00511
Location:140 → 184

ORANGE; Orange domain

cd19749
Location:40 → 129

bHLH-O_DEC1; basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein 1 (DEC1) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

4979437..4985323

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

4970406..4979102

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348161.1 → XP_054204136.1 class E basic helix-loop-helix protein 40 isoform X1

UniProtKB/Swiss-Prot

O14503, Q96TD3

UniProtKB/TrEMBL

A0A024R2D0, Q6IB83
XM_054348162.1 → XP_054204137.1 class E basic helix-loop-helix protein 40 isoform X1

UniProtKB/Swiss-Prot

O14503, Q96TD3

UniProtKB/TrEMBL

A0A024R2D0, Q6IB83
XM_054348160.1 → XP_054204135.1 class E basic helix-loop-helix protein 40 isoform X1

UniProtKB/Swiss-Prot

O14503, Q96TD3

UniProtKB/TrEMBL

A0A024R2D0, Q6IB83