Mouse Gene Nkx1-2 (ENSMUST00000054562.3) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus NK1 homeobox 2 (Nkx1-2), mRNA. (from RefSeq NM_009123)
Gencode Transcript: ENSMUST00000054562.3
Gencode Gene: ENSMUSG00000048528.7
Transcript (Including UTRs)
   Position: mm10 chr7:132,594,878-132,599,637 Size: 4,760 Total Exon Count: 2 Strand: -
Coding Region
   Position: mm10 chr7:132,597,113-132,599,526 Size: 2,414 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:132,594,878-132,599,637)mRNA (may differ from genome)Protein (305 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=NK1 transcription factor-related protein 2; AltName: Full=Homeobox protein SAX-1; AltName: Full=NKX-1.1;
FUNCTION: May function in cell specification, particularly in the CNS.
SUBUNIT: Interacts with HIPK1, HIPK2, and HIPK3.
TISSUE SPECIFICITY: Expression detected in adult brain, testis and spleen. In the testis, expressed in the germ cells of the seminiferous epithelium, in elongating spermatids and in spermatozoa. Expressed throughout the brain with highest levels in regions of the cerebral cortex, hippocampus, diencephalon, pons, medulla and cerebellum. In the embryo, expressed in the developing posterior central nervous system. First seen in the ectoderm lateral to the primitive streak, later it encompasses the neural plate. Starting at day 9.5 pc, expressed in distinct areas of spinal cord, hindbrain, midbrain and forebrain.
DEVELOPMENTAL STAGE: In the embryo, expressed at highest levels at day 10 with levels decreasing during further development.
PTM: Phosphorylated by HIPK2 in vitro.
SIMILARITY: Belongs to the NK-1 homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAF43670.1; Type=Erroneous gene model prediction; Sequence=AAF43672.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact; Sequence=AAF43674.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.50111-0.428 Picture PostScript Text
3' UTR -680.702235-0.305 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

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P42580
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.
HumanRatZebrafishD. 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:0003677 DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AF222442 - Mus musculus Nkx-1.2 gene, 3' untranslated region, partial sequence.
AF222444 - Mus musculus homeodomain protein (Nkx-1.2) mRNA, complete cds.
BC139757 - Mus musculus NK1 transcription factor related, locus 2 (Drosophila), mRNA (cDNA clone MGC:149930 IMAGE:40047346), complete cds.
X75384 - M.musculus mRNA for Sax-1 gene encoded protein.
AF222445 - Mus musculus homeobox protein Nkx1.2E427 (Nkx-1.2) mRNA, alternatively spliced, complete cds.
AF223361 - Mus musculus homeodomain protein Nkx-1.2E4.29 (Nkx-1.2) mRNA, partial cds.
AF223363 - Mus musculus homeodomain protein Nkx-1.2T5.1 (Nkx-1.2) mRNA, partial cds.
AF223675 - Mus musculus homeodomain protein Nkx-1.2T5.17 (Nkx-1.2) mRNA, partial cds.
AF223674 - Mus musculus homeodomain protein Nkx-1.2T5.18 (Nkx-1.2) mRNA, partial cds.
AF223362 - Mus musculus homeodomain protein Nkx1.2T8.7 (Nkx1.2) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: A4QPC3, Nkx1.1, NKX12_MOUSE, NM_009123, P42580, Q9JHF2, Q9JKW5, Q9JKW6, Q9JKW9, Q9JKX0, Q9JKX1, Sax1, uc009kcc.1, uc009kcc.2
UCSC ID: uc009kcc.2
RefSeq Accession: NM_009123
Protein: P42580 (aka NKX12_MOUSE or SAX1_MOUSE)
CCDS: CCDS21924.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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