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

    Gene ID: 8553, updated on 9-Dec-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_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_000003.12Genomic 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
    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 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_2024_08

    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