Human Gene BHLHE41 (ENST00000242728.5) from GENCODE V44
  Description: Homo sapiens basic helix-loop-helix family member e41 (BHLHE41), mRNA. (from RefSeq NM_030762)
RefSeq Summary (NM_030762): 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. Defects in this gene are associated with the short sleep phenotype. [provided by RefSeq, Feb 2014].
Gencode Transcript: ENST00000242728.5
Gencode Gene: ENSG00000123095.6
Transcript (Including UTRs)
   Position: hg38 chr12:26,120,030-26,125,037 Size: 5,008 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr12:26,122,066-26,124,779 Size: 2,714 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:26,120,030-26,125,037)mRNA (may differ from genome)Protein (482 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BHE41_HUMAN
DESCRIPTION: RecName: Full=Class E basic helix-loop-helix protein 41; Short=bHLHe41; AltName: Full=Class B basic helix-loop-helix protein 3; Short=bHLHb3; AltName: Full=Differentially expressed in chondrocytes protein 2; Short=hDEC2; AltName: Full=Enhancer-of-split and hairy-related protein 1; Short=SHARP-1;
FUNCTION: May be a transcriptional repressor that represses both basal and activated transcription.
SUBUNIT: Homodimerize.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Highly expressed in skeletal muscle and brain, moderately expressed in pancreas and heart, weakly expressed in placenta, lung, liver and kidney.
POLYMORPHISM: Genetic variations in BHLHE41 are associated with the short sleep phenotype [MIM:612975]. Individuals with this trait require less sleep in any 24-hour period than is typical for their age group.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 Orange domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.99 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 341.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -79.80258-0.309 Picture PostScript Text
3' UTR -479.702036-0.236 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom
IPR003650 - Orange
IPR018352 - Orange_subgr

Pfam Domains:
PF07527 - Hairy Orange
PF00010 - Helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q9C0J9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding
GO:0003677 DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0042803 protein homodimerization activity
GO:0042826 histone deacetylase binding
GO:0043425 bHLH transcription factor binding
GO:0043426 MRF binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity
GO:0070888 E-box binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007623 circadian rhythm
GO:0008283 cell proliferation
GO:0009887 animal organ morphogenesis
GO:0010832 negative regulation of myotube differentiation
GO:0010944 negative regulation of transcription by competitive promoter binding
GO:0030154 cell differentiation
GO:0032922 circadian regulation of gene expression
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048511 rhythmic process

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  LF207466 - JP 2014500723-A/14969: Polycomb-Associated Non-Coding RNAs.
MA443043 - JP 2018138019-A/14969: Polycomb-Associated Non-Coding RNAs.
AK094422 - Homo sapiens cDNA FLJ37103 fis, clone BRACE2019327.
AB044088 - Homo sapiens mRNA for bHLH protein DEC2, complete cds.
AY665466 - Homo sapiens clone A10-B11 basic helix-loop-helix protein 3 isoform 2 (BHLHB3) mRNA, complete cds, alternatively spliced.
JD284230 - Sequence 265254 from Patent EP1572962.
AY665467 - Homo sapiens clone D11-G10 basic helix-loop-helix protein 3 isoform 1 (BHLHB3) mRNA, complete cds, alternatively spliced.
BC025968 - Homo sapiens basic helix-loop-helix family, member e41, mRNA (cDNA clone MGC:39365 IMAGE:4650325), complete cds.
JD553211 - Sequence 534235 from Patent EP1572962.
JD145324 - Sequence 126348 from Patent EP1572962.
JD200797 - Sequence 181821 from Patent EP1572962.
JD258679 - Sequence 239703 from Patent EP1572962.
JD227310 - Sequence 208334 from Patent EP1572962.
AJ270695 - Homo sapiens partial unknown mRNA from drug-resistant melanoma cells, 3'UTR, clone DMS-11.
JD554549 - Sequence 535573 from Patent EP1572962.
JD313860 - Sequence 294884 from Patent EP1572962.
LF366492 - JP 2014500723-A/173995: Polycomb-Associated Non-Coding RNAs.
MA602069 - JP 2018138019-A/173995: Polycomb-Associated Non-Coding RNAs.
JD284109 - Sequence 265133 from Patent EP1572962.
AK311258 - Homo sapiens cDNA, FLJ18300.
LF366493 - JP 2014500723-A/173996: Polycomb-Associated Non-Coding RNAs.
MA602070 - JP 2018138019-A/173996: Polycomb-Associated Non-Coding RNAs.
JD553923 - Sequence 534947 from Patent EP1572962.
JD196639 - Sequence 177663 from Patent EP1572962.
JD244042 - Sequence 225066 from Patent EP1572962.
AK303677 - Homo sapiens cDNA FLJ61743 complete cds, highly similar to Class B basic helix-loop-helix protein 3.
JD045746 - Sequence 26770 from Patent EP1572962.
JD502291 - Sequence 483315 from Patent EP1572962.
JD075572 - Sequence 56596 from Patent EP1572962.
JD315791 - Sequence 296815 from Patent EP1572962.
JD438236 - Sequence 419260 from Patent EP1572962.
LF213913 - JP 2014500723-A/21416: Polycomb-Associated Non-Coding RNAs.
MA449490 - JP 2018138019-A/21416: Polycomb-Associated Non-Coding RNAs.
JD304482 - Sequence 285506 from Patent EP1572962.
JD056235 - Sequence 37259 from Patent EP1572962.
JD458584 - Sequence 439608 from Patent EP1572962.
LF212079 - JP 2014500723-A/19582: Polycomb-Associated Non-Coding RNAs.
MA447656 - JP 2018138019-A/19582: Polycomb-Associated Non-Coding RNAs.
LF213067 - JP 2014500723-A/20570: Polycomb-Associated Non-Coding RNAs.
MA448644 - JP 2018138019-A/20570: Polycomb-Associated Non-Coding RNAs.
LF366494 - JP 2014500723-A/173997: Polycomb-Associated Non-Coding RNAs.
MA602071 - JP 2018138019-A/173997: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04710 - Circadian rhythm - mammal

Reactome (by CSHL, EBI, and GO)

Protein Q9C0J9 (Reactome details) participates in the following event(s):

R-HSA-1368108 BMAL1:CLOCK,NPAS2 activates circadian gene expression
R-HSA-400253 Circadian Clock

-  Other Names for This Gene
  Alternate Gene Symbols: A2I2N8, BHE41_HUMAN, BHLHB3, DEC2, ENST00000242728.1, ENST00000242728.2, ENST00000242728.3, ENST00000242728.4, NM_030762, Q9C0J9, SHARP1, uc001rhb.1, uc001rhb.2, uc001rhb.3, uc001rhb.4, uc001rhb.5
UCSC ID: ENST00000242728.5
RefSeq Accession: NM_030762
Protein: Q9C0J9 (aka BHE41_HUMAN)
CCDS: CCDS8706.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.