Human Gene HAND1 (ENST00000231121.3) from GENCODE V43
  Description: Homo sapiens heart and neural crest derivatives expressed 1 (HAND1), mRNA. (from RefSeq NM_004821)
RefSeq Summary (NM_004821): The protein encoded by this gene belongs to the basic helix-loop-helix family of transcription factors. This gene product is one of two closely related family members, the HAND proteins, which are asymmetrically expressed in the developing ventricular chambers and play an essential role in cardiac morphogenesis. Working in a complementary fashion, they function in the formation of the right ventricle and aortic arch arteries, implicating them as mediators of congenital heart disease. In addition, it has been suggested that this transcription factor may be required for early trophoblast differentiation. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000231121.3
Gencode Gene: ENSG00000113196.3
Transcript (Including UTRs)
   Position: hg38 chr5:154,474,972-154,478,227 Size: 3,256 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr5:154,475,806-154,478,008 Size: 2,203 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:154,474,972-154,478,227)mRNA (may differ from genome)Protein (215 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Heart- and neural crest derivatives-expressed protein 1; AltName: Full=Class A basic helix-loop-helix protein 27; Short=bHLHa27; AltName: Full=Extraembryonic tissues, heart, autonomic nervous system and neural crest derivatives-expressed protein 1; Short=eHAND;
FUNCTION: Transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. In the adult, could be required for ongoing expression of cardiac-specific genes. Binds the DNA sequence 5'- NRTCTG-3' (non-canonical E-box) (By similarity).
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Forms homodimers and heterodimers with TCF3 gene products E12 and E47, HAND2 and HEY1, HEY2 and HEYL (hairy-related transcription factors). Interacts with MDFIC (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleoplasm (By similarity). Nucleus, nucleolus (By similarity). Note=Interaction with MDFIC sequesters it into the nucleolus, preventing the transcription factor activity. Phosphorylation by PLK4 disrupts the interaction with MDFIC and releases it from the nucleolus, leading to transcription factor activity (By similarity).
PTM: Phosphorylation by PLK4 disrupts the interaction with MDFIC and leads to tranlocation into the nucleoplasm, allowing dimerization and transcription factor activity (By similarity).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) 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

-  MalaCards Disease Associations
  MalaCards Gene Search: HAND1
Diseases sorted by gene-association score: hypoplastic left heart syndrome (10), tetralogy of fallot (5), heart disease (4)

-  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: 50.76 RPKM in Colon - Sigmoid
Total median expression: 80.11 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 -86.00219-0.393 Picture PostScript Text
3' UTR -228.80834-0.274 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 O96004
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:0003713 transcription coactivator activity
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019899 enzyme binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043425 bHLH transcription factor binding
GO:0043565 sequence-specific DNA binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001525 angiogenesis
GO:0001701 in utero embryonic development
GO:0001707 mesoderm formation
GO:0001824 blastocyst development
GO:0001829 trophectodermal cell differentiation
GO:0001947 heart looping
GO:0003144 embryonic heart tube formation
GO:0003218 cardiac left ventricle formation
GO:0003219 cardiac right ventricle formation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007507 heart development
GO:0030154 cell differentiation
GO:0035050 embryonic heart tube development
GO:0042475 odontogenesis of dentin-containing tooth
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0055010 ventricular cardiac muscle tissue morphogenesis
GO:0060411 cardiac septum morphogenesis
GO:0060485 mesenchyme development
GO:0060536 cartilage morphogenesis
GO:0060707 trophoblast giant cell differentiation
GO:0061371 determination of heart left/right asymmetry
GO:1903026 negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0090575 RNA polymerase II transcription factor complex

-  Descriptions from all associated GenBank mRNAs
  BC021190 - Homo sapiens heart and neural crest derivatives expressed 1, mRNA (cDNA clone MGC:1826 IMAGE:3162118), complete cds.
AF061756 - Homo sapiens Hand1 protein mRNA, complete cds.
JD549698 - Sequence 530722 from Patent EP1572962.
JD307742 - Sequence 288766 from Patent EP1572962.
JD259993 - Sequence 241017 from Patent EP1572962.
JD414320 - Sequence 395344 from Patent EP1572962.
JD061876 - Sequence 42900 from Patent EP1572962.
JD542116 - Sequence 523140 from Patent EP1572962.
JD475269 - Sequence 456293 from Patent EP1572962.
JD141658 - Sequence 122682 from Patent EP1572962.
JD395066 - Sequence 376090 from Patent EP1572962.
JD417164 - Sequence 398188 from Patent EP1572962.
JD530321 - Sequence 511345 from Patent EP1572962.
JD254545 - Sequence 235569 from Patent EP1572962.
JD075748 - Sequence 56772 from Patent EP1572962.
CU676862 - Synthetic construct Homo sapiens gateway clone IMAGE:100023295 5' read HAND1 mRNA.
KJ905377 - Synthetic construct Homo sapiens clone ccsbBroadEn_14938 HAND1 gene, encodes complete protein.
EU446688 - Synthetic construct Homo sapiens clone IMAGE:100069799; IMAGE:100011897; FLH258592.01L heart and neural crest derivatives expressed 1 (HAND1) gene, encodes complete protein.
AB464562 - Synthetic construct DNA, clone: pF1KB8892, Homo sapiens HAND1 gene for heart and neural crest derivatives expressed 1, without stop codon, in Flexi system.
JD191072 - Sequence 172096 from Patent EP1572962.
JD125269 - Sequence 106293 from Patent EP1572962.
JD461918 - Sequence 442942 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_nfatPathway - NFAT and Hypertrophy of the heart (Transcription in the broken heart)

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHA27, EHAND, ENST00000231121.1, ENST00000231121.2, HAND1_HUMAN, NM_004821, O96004, uc003lvn.1, uc003lvn.2, uc003lvn.3, uc003lvn.4
UCSC ID: ENST00000231121.3
RefSeq Accession: NM_004821
Protein: O96004 (aka HAND1_HUMAN or HAN1_HUMAN)
CCDS: CCDS4327.1

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