Human Gene HES3 (ENST00000377898.4) from GENCODE V44
  Description: Homo sapiens hes family bHLH transcription factor 3 (HES3), mRNA. (from RefSeq NM_001024598)
Gencode Transcript: ENST00000377898.4
Gencode Gene: ENSG00000173673.9
Transcript (Including UTRs)
   Position: hg38 chr1:6,244,179-6,245,578 Size: 1,400 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr1:6,244,366-6,245,507 Size: 1,142 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:6,244,179-6,245,578)mRNA (may differ from genome)Protein (186 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Transcription factor HES-3; AltName: Full=Class B basic helix-loop-helix protein 43; Short=bHLHb43; AltName: Full=Hairy and enhancer of split 3;
FUNCTION: Transcriptional repressor of genes that require a bHLH protein for their transcription (By similarity).
SUBUNIT: Transcription repression requires formation of a complex with a corepressor protein of the Groucho/TLE family (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
DOMAIN: Has a particular type of basic domain (presence of a helix-interrupting proline) that binds to the N-box (CACNAG), rather than the canonical E-box (CANNTG).
DOMAIN: The C-terminal WRPW motif is a transcriptional repression domain necessary for the interaction with Groucho/TLE family members, transcriptional corepressors recruited to specific target DNA by Hairy-related proteins (By similarity).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 Orange domain.
SEQUENCE CAUTION: Sequence=CAI19439.1; Type=Erroneous gene model prediction;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.19 RPKM in Testis
Total median expression: 0.19 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 -23.7078-0.304 Picture PostScript Text
3' UTR -16.0071-0.225 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

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q5TGS1
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     
Protein SequenceProtein Sequence    

-  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:0003677 DNA binding
GO:0008134 transcription factor binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001701 in utero embryonic development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0021555 midbrain-hindbrain boundary morphogenesis
GO:0021557 oculomotor nerve development
GO:0021558 trochlear nerve development
GO:0021575 hindbrain morphogenesis
GO:0021915 neural tube development
GO:0030901 midbrain development
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050767 regulation of neurogenesis
GO:0060164 regulation of timing of neuron differentiation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC156115 - Synthetic construct Homo sapiens clone IMAGE:100062350, MGC:190476 hairy and enhancer of split 3 (Drosophila) (HES3) mRNA, encodes complete protein.
BC156912 - Synthetic construct Homo sapiens clone IMAGE:100062770, MGC:190609 hairy and enhancer of split 3 (Drosophila) (HES3) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHB43, ENST00000377898.1, ENST00000377898.2, ENST00000377898.3, HES3_HUMAN, NM_001024598, Q5TGS0, Q5TGS1, uc009vly.1, uc009vly.2, uc009vly.3
UCSC ID: ENST00000377898.4
RefSeq Accession: NM_001024598
Protein: Q5TGS1 (aka HES3_HUMAN)
CCDS: CCDS41238.1

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