U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 8553, updated on 17-Jun-2024

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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See BHLHE40 in Genome Data Viewer
Location:
3p26.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (4979437..4985323)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4970406..4979102)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5021122..5027008)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene inositol 1,4,5-trisphosphate receptor type 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19354 Neighboring gene Sharpr-MPRA regulatory region 7157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:4824730-4825689 Neighboring gene eosinophil granule ontogeny transcript Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 Neighboring gene uncharacterized LOC124906209 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4859780-4860166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:4866229-4866729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14019 Neighboring gene small nucleolar RNA U13 Neighboring gene BHLHE40 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:4947837-4948542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:4958477-4959105 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4987703-4987867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14021 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5021511-5022105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024435-5024994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024995-5025554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5027373-5028270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5028271-5029168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5030786-5031286 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5036716-5037915 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5043965-5044466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5054312-5055114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5055115-5055916 Neighboring gene CRISPRi-validated cis-regulatory element chr3.91 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5064405-5065604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5073333-5073834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19375 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:5119481-5119626 Neighboring gene ring finger protein 10 pseudogene 1 Neighboring gene UBTF like 8 (pseudogene)

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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ99214

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 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 E-box binding IDA
Inferred from Direct Assay
more info
PubMed 
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-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 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 
Component Evidence Code Pubs
part_of 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 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)

NEW Try the new Transcript table

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, Q96TD3
    UniProtKB/TrEMBL
    A0A024R2D0, Q6IB83
    Related
    ENSP00000256495.3, ENST00000256495.4
    Conserved Domains (2) summary
    smart00511
    Location:140184
    ORANGE; Orange domain
    cd19749
    Location:40129
    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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    4979437..4985323
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    4970406..4979102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    O14503, Q96TD3
    UniProtKB/TrEMBL
    A0A024R2D0, Q6IB83
  2. XM_054348162.1XP_054204137.1  class E basic helix-loop-helix protein 40 isoform X1

    UniProtKB/Swiss-Prot
    O14503, Q96TD3
    UniProtKB/TrEMBL
    A0A024R2D0, Q6IB83
  3. XM_054348160.1XP_054204135.1  class E basic helix-loop-helix protein 40 isoform X1

    UniProtKB/Swiss-Prot
    O14503, Q96TD3
    UniProtKB/TrEMBL
    A0A024R2D0, Q6IB83