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

Gene ID: 8553, updated on 12-Oct-2019

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
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

Genomic context

See BHLHE40 in Genome Data Viewer
Location:
3p26.1
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (4979420..4985323)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5021097..5026866)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene inositol 1,4,5-trisphosphate receptor type 1 Neighboring gene uncharacterized LOC105376933 Neighboring gene eosinophil granule ontogeny transcript Neighboring gene BHLHE40 antisense RNA 1 Neighboring gene uncharacterized LOC105376934 Neighboring gene ring finger protein 10 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI 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.
NHGRI GWA Catalog

Pathways from BioSystems

  • BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystem (from REACTOME)
    BMAL1:CLOCK,NPAS2 activates circadian gene expression, organism-specific biosystemAs inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et...
  • Circadian Clock, organism-specific biosystem (from REACTOME)
    Circadian Clock, organism-specific biosystemAt the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by b...
  • Circadian rhythm, organism-specific biosystem (from KEGG)
    Circadian rhythm, organism-specific biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Circadian rhythm, conserved biosystem (from KEGG)
    Circadian rhythm, conserved biosystemCircadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of ...
  • Circadian rhythm pathway, organism-specific biosystem (from Pathway Interaction Database)
    Circadian rhythm pathway, organism-specific biosystem
    Circadian rhythm pathway
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • HIF-1-alpha transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    HIF-1-alpha transcription factor network, organism-specific biosystem
    HIF-1-alpha transcription factor network
  • HIF-2-alpha transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    HIF-2-alpha transcription factor network, organism-specific biosystem
    HIF-2-alpha transcription factor network
  • Heart Development, organism-specific biosystem (from WikiPathways)
    Heart Development, organism-specific biosystemThis pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impa...
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ99214

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
MRF binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II activating transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II distal enhancer sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bHLH transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
circadian regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
circadian regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
circadian rhythm IDA
Inferred from Direct Assay
more info
PubMed 
entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of neurogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

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)

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)

  1. NM_003670.3NP_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
    UniProtKB/TrEMBL
    Q6IB83
    Related
    ENSP00000256495.3, ENST00000256495.4
    Conserved Domains (2) summary
    smart00511
    Location:140184
    ORANGE; Orange domain
    cd00083
    Location:50111
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    4979420..4985323
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453798.1XP_024309566.1  class E basic helix-loop-helix protein 40 isoform X1

    Conserved Domains (1) summary
    smart00511
    Location:144
    ORANGE; Orange domain
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