Human Gene HES2 (ENST00000377834.8) from GENCODE V44
  Description: Homo sapiens hes family bHLH transcription factor 2 (HES2), mRNA. (from RefSeq NM_019089)
Gencode Transcript: ENST00000377834.8
Gencode Gene: ENSG00000069812.11
Transcript (Including UTRs)
   Position: hg38 chr1:6,415,232-6,419,919 Size: 4,688 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr1:6,418,873-6,419,820 Size: 948 Coding Exon Count: 4 

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 (chr1:6,415,232-6,419,919)mRNA (may differ from genome)Protein (173 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Transcription factor HES-2; AltName: Full=Class B basic helix-loop-helix protein 40; Short=bHLHb40; AltName: Full=Hairy and enhancer of split 2;
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).
TISSUE SPECIFICITY: Expressed in placenta, pancreatic cancer, colon cancer with RER, cervical cancer, and in head and neck tumors.
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.

-  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: 11.93 RPKM in Esophagus - Mucosa
Total median expression: 41.35 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 -35.6099-0.360 Picture PostScript Text
3' UTR -1439.003641-0.395 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 Q9Y543
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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein 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:0003690 double-stranded 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:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC012091 - Homo sapiens hairy and enhancer of split 2 (Drosophila), mRNA (cDNA clone IMAGE:4634002), complete cds.
KJ902672 - Synthetic construct Homo sapiens clone ccsbBroadEn_12066 HES2 gene, encodes complete protein.
AK023754 - Homo sapiens cDNA FLJ13692 fis, clone PLACE2000103.
AK091122 - Homo sapiens cDNA FLJ33803 fis, clone CTONG2000561, highly similar to Transcription factor HES-2.
JD256411 - Sequence 237435 from Patent EP1572962.
JD254927 - Sequence 235951 from Patent EP1572962.
JD375453 - Sequence 356477 from Patent EP1572962.
JD181711 - Sequence 162735 from Patent EP1572962.
JD288915 - Sequence 269939 from Patent EP1572962.
JD561199 - Sequence 542223 from Patent EP1572962.
JD225067 - Sequence 206091 from Patent EP1572962.
JD237171 - Sequence 218195 from Patent EP1572962.
JD103849 - Sequence 84873 from Patent EP1572962.
JD181856 - Sequence 162880 from Patent EP1572962.
JD445578 - Sequence 426602 from Patent EP1572962.
JD327202 - Sequence 308226 from Patent EP1572962.
JD041545 - Sequence 22569 from Patent EP1572962.
JD407408 - Sequence 388432 from Patent EP1572962.
JD350169 - Sequence 331193 from Patent EP1572962.
JD048951 - Sequence 29975 from Patent EP1572962.
JD198209 - Sequence 179233 from Patent EP1572962.
JD542834 - Sequence 523858 from Patent EP1572962.
JD174793 - Sequence 155817 from Patent EP1572962.
JD277468 - Sequence 258492 from Patent EP1572962.
JD132168 - Sequence 113192 from Patent EP1572962.
JD405023 - Sequence 386047 from Patent EP1572962.
JD123841 - Sequence 104865 from Patent EP1572962.
JD347147 - Sequence 328171 from Patent EP1572962.
JD408954 - Sequence 389978 from Patent EP1572962.
JD449942 - Sequence 430966 from Patent EP1572962.
JD483922 - Sequence 464946 from Patent EP1572962.
JD417013 - Sequence 398037 from Patent EP1572962.
LF206747 - JP 2014500723-A/14250: Polycomb-Associated Non-Coding RNAs.
MA442324 - JP 2018138019-A/14250: Polycomb-Associated Non-Coding RNAs.
JD074484 - Sequence 55508 from Patent EP1572962.
JD423046 - Sequence 404070 from Patent EP1572962.
JD286141 - Sequence 267165 from Patent EP1572962.
JD173904 - Sequence 154928 from Patent EP1572962.
JD539946 - Sequence 520970 from Patent EP1572962.
JD231509 - Sequence 212533 from Patent EP1572962.
JD252333 - Sequence 233357 from Patent EP1572962.
JD545043 - Sequence 526067 from Patent EP1572962.
LF357509 - JP 2014500723-A/165012: Polycomb-Associated Non-Coding RNAs.
MA593086 - JP 2018138019-A/165012: Polycomb-Associated Non-Coding RNAs.
JD178804 - Sequence 159828 from Patent EP1572962.
JD272396 - Sequence 253420 from Patent EP1572962.
JD566522 - Sequence 547546 from Patent EP1572962.
JD135299 - Sequence 116323 from Patent EP1572962.
JD517831 - Sequence 498855 from Patent EP1572962.
JD418327 - Sequence 399351 from Patent EP1572962.
JD335066 - Sequence 316090 from Patent EP1572962.
JD442777 - Sequence 423801 from Patent EP1572962.
JD532181 - Sequence 513205 from Patent EP1572962.
JD558687 - Sequence 539711 from Patent EP1572962.
JD091847 - Sequence 72871 from Patent EP1572962.
JD183773 - Sequence 164797 from Patent EP1572962.
JD333720 - Sequence 314744 from Patent EP1572962.
JD309241 - Sequence 290265 from Patent EP1572962.
JD292794 - Sequence 273818 from Patent EP1572962.
JD171117 - Sequence 152141 from Patent EP1572962.
JD399308 - Sequence 380332 from Patent EP1572962.
JD322119 - Sequence 303143 from Patent EP1572962.
JD306843 - Sequence 287867 from Patent EP1572962.
JD170039 - Sequence 151063 from Patent EP1572962.
JD529596 - Sequence 510620 from Patent EP1572962.
JD557516 - Sequence 538540 from Patent EP1572962.
JD348289 - Sequence 329313 from Patent EP1572962.
JD037259 - Sequence 18283 from Patent EP1572962.
BC142687 - Homo sapiens hairy and enhancer of split 2 (Drosophila), mRNA (cDNA clone MGC:164997 IMAGE:40148619), complete cds.
JD355179 - Sequence 336203 from Patent EP1572962.
JD420585 - Sequence 401609 from Patent EP1572962.
JD144338 - Sequence 125362 from Patent EP1572962.
JD396842 - Sequence 377866 from Patent EP1572962.
JD196151 - Sequence 177175 from Patent EP1572962.
JD325125 - Sequence 306149 from Patent EP1572962.
JD099477 - Sequence 80501 from Patent EP1572962.
JD277218 - Sequence 258242 from Patent EP1572962.
JD425025 - Sequence 406049 from Patent EP1572962.
JD354750 - Sequence 335774 from Patent EP1572962.
JD350163 - Sequence 331187 from Patent EP1572962.
BC132698 - Homo sapiens hairy and enhancer of split 2 (Drosophila), mRNA (cDNA clone MGC:164329 IMAGE:40146720), complete cds.
BC136963 - Homo sapiens hairy and enhancer of split 2 (Drosophila), mRNA (cDNA clone MGC:168578 IMAGE:9020955), complete cds.
JD218116 - Sequence 199140 from Patent EP1572962.
JD108791 - Sequence 89815 from Patent EP1572962.
JD133220 - Sequence 114244 from Patent EP1572962.
JD424519 - Sequence 405543 from Patent EP1572962.
JD383618 - Sequence 364642 from Patent EP1572962.
JD367862 - Sequence 348886 from Patent EP1572962.
JD487076 - Sequence 468100 from Patent EP1572962.
JD534559 - Sequence 515583 from Patent EP1572962.
JD372749 - Sequence 353773 from Patent EP1572962.
LF211970 - JP 2014500723-A/19473: Polycomb-Associated Non-Coding RNAs.
MA447547 - JP 2018138019-A/19473: Polycomb-Associated Non-Coding RNAs.
JD539819 - Sequence 520843 from Patent EP1572962.
JD543782 - Sequence 524806 from Patent EP1572962.
JD561089 - Sequence 542113 from Patent EP1572962.
JD424401 - Sequence 405425 from Patent EP1572962.
JD239689 - Sequence 220713 from Patent EP1572962.
JD391983 - Sequence 373007 from Patent EP1572962.
AB463714 - Synthetic construct DNA, clone: pF1KB7537, Homo sapiens HES2 gene for hairy and enhancer of split 2, without stop codon, in Flexi system.
LF357508 - JP 2014500723-A/165011: Polycomb-Associated Non-Coding RNAs.
MA593085 - JP 2018138019-A/165011: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RTZ9, BHLHB40, ENST00000377834.1, ENST00000377834.2, ENST00000377834.3, ENST00000377834.4, ENST00000377834.5, ENST00000377834.6, ENST00000377834.7, HES2_HUMAN, NM_019089, Q96EN4, Q9Y542, Q9Y543, uc001amx.1, uc001amx.2, uc001amx.3, uc001amx.4
UCSC ID: ENST00000377834.8
RefSeq Accession: NM_019089
Protein: Q9Y543 (aka HES2_HUMAN)
CCDS: CCDS30574.1

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