Human Gene NKX2-6 (ENST00000325017.4) from GENCODE V44
  Description: Homo sapiens NK2 homeobox 6 (NKX2-6), mRNA. (from RefSeq NM_001136271)
RefSeq Summary (NM_001136271): This gene encodes a homeobox-containing protein that belongs to the NK-2 homeobox family. This protein is a vertebrate homolog of Drosophila homeobox-containing protein called 'tinman', which has been shown to be essential for development of the heart-like dorsal vessel. In conjunction with related gene, NKX2-5, this gene may play a role in both pharyngeal and cardiac embryonic development. Mutations in this gene are associated with persistent truncus arteriosus.[provided by RefSeq, Aug 2011].
Gencode Transcript: ENST00000325017.4
Gencode Gene: ENSG00000180053.8
Transcript (Including UTRs)
   Position: hg38 chr8:23,701,740-23,706,756 Size: 5,017 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr8:23,702,451-23,706,598 Size: 4,148 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq 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 (chr8:23,701,740-23,706,756)mRNA (may differ from genome)Protein (301 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein Nkx-2.6; AltName: Full=Homeobox protein NK-2 homolog F;
FUNCTION: In conjunction with NKX2-5, may play a role in both pharyngeal and cardiac embryonic development (By similarity).
DISEASE: Defects in NKX2-6 may be a cause of conotruncal heart malformations (CTHM) [MIM:217095]. CTHM defines a group of congenital heart defects involving the outflow tracts. Examples include truncus arteriosus communis, double-outlet right ventricle and transposition of great arteries. Truncus arteriosus communis is characterized by a single outflow tract instead of a separate aorta and pulmonary artery. In transposition of the great arteries, the aorta arises from the right ventricle and the pulmonary artery from the left ventricle. In double outlet of the right ventricle, both the pulmonary artery and aorta arise from the right ventricle.
SIMILARITY: Belongs to the NK-2 homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding 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: NKX2-6
Diseases sorted by gene-association score: conotruncal heart malformations* (894), tricuspid valve disease (13), total anomalous pulmonary venous return 1 (13), ventricular septal defect (12), pulmonary valve disease (12), pulmonary valve insufficiency (12), familial atrial fibrillation* (11), tetralogy of fallot* (11), heart septal defect (10), aortic valve insufficiency (9), tricuspid atresia (9), aortic valve disease 1 (9), dextro-looped transposition of the great arteries (8), endocardium disease (8), pulmonary valve stenosis (7), transposition of the great arteries (7), ebstein anomaly (7), mediastinitis (7), atrial heart septal defect (7), esophageal atresia/tracheoesophageal fistula (6), chromosomal deletion syndrome (5), atrioventricular septal defect (5), tricuspid valve stenosis (5), diaphragmatic eventration (5), cloacal exstrophy (5), hypoplastic left heart syndrome (4), aortic valve disease 2 (4), heart disease (4), velocardiofacial syndrome (1), patent foramen ovale (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.55 RPKM in Minor Salivary Gland
Total median expression: 1.12 RPKM

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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -70.50158-0.446 Picture PostScript Text
3' UTR -265.30711-0.373 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
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on A6NCS4
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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007507 heart development
GO:0008284 positive regulation of cell proliferation
GO:0021854 hypothalamus development
GO:0030154 cell differentiation
GO:0035050 embryonic heart tube development
GO:0043066 negative regulation of apoptotic process
GO:0043586 tongue development
GO:0048565 digestive tract development
GO:0055014 atrial cardiac muscle cell development
GO:0055015 ventricular cardiac muscle cell development
GO:0060037 pharyngeal system development
GO:0060039 pericardium development

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AB464642 - Synthetic construct DNA, clone: pF1KB8942, Homo sapiens NKX2-6 gene for NK2 transcription factor related, locus 6, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NCS4, ENST00000325017.1, ENST00000325017.2, ENST00000325017.3, NKX26_HUMAN, NKX2F, NM_001136271, uc011kzy.1, uc011kzy.2, uc011kzy.3, uc011kzy.4
UCSC ID: ENST00000325017.4
RefSeq Accession: NM_001136271
Protein: A6NCS4 (aka NKX26_HUMAN)

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