Mouse Gene Uncx (ENSMUST00000172997.2) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus UNC homeobox (Uncx), mRNA. (from RefSeq NM_013702)
Gencode Transcript: ENSMUST00000172997.2
Gencode Gene: ENSMUSG00000029546.12
Transcript (Including UTRs)
   Position: mm10 chr5:139,543,494-139,548,179 Size: 4,686 Total Exon Count: 3 Strand: +
Coding Region
   Position: mm10 chr5:139,543,994-139,547,774 Size: 3,781 Coding Exon Count: 3 

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 (chr5:139,543,494-139,548,179)mRNA (may differ from genome)Protein (530 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein unc-4 homolog; AltName: Full=Homeobox protein Uncx4.1;
FUNCTION: Transcription factor involved in somitogenesis and neurogenesis. Required for the maintenance and differentiation of particular elements of the axial skeleton. May act upstream of PAX9. Plays a role in controlling the development of connections of hypothalamic neurons to pituitary elements, allowing central neurons to reach the peripheral blood circulation and to deliver hormones for control of peripheral functions.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Expressed in the paraxial mesoderm, in the developing kidney and central nervous system. In the somite, it is restricted to the caudal half of the newly formed somite and sclerotome. In the central nervous system, it is detected in the developing spinal cord, hindbrain, mesencephalon and telencephalon. Expressed in adult and embryonic magnocellular neurons of the hypothalamo-neurohypophysial system.
DISRUPTION PHENOTYPE: Mice die perinatally and exhibit severe malformations of the axial skeleton. Pedicles of the neural arches and proximal ribs are not formed. In addition, dorsal root ganglia are disorganized. In the hypothalamo-neurohypophysial system, neurons are viable and able to express neuropeptides; however, the connectivity of magnocellular neurons with posterior pituitary elements is compromised.
MISCELLANEOUS: Marker of antero-posterior subdivisions of the somite.
SIMILARITY: Belongs to the paired homeobox family. Unc-4 subfamily.
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

-  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 -201.00500-0.402 Picture PostScript Text
3' UTR -97.50405-0.241 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
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on O08934
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 orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001502 cartilage condensation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0007399 nervous system development
GO:0010468 regulation of gene expression
GO:0021516 dorsal spinal cord development
GO:0021889 olfactory bulb interneuron differentiation
GO:0030154 cell differentiation
GO:0035726 common myeloid progenitor cell proliferation
GO:0045595 regulation of cell differentiation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  S83543 - Cer-1=cerebellar-expressed gene/granule neuron differentiation-associated gene [mice, cerebellum, granule neurons, mRNA Partial, 622 nt].
AK082472 - Mus musculus 0 day neonate cerebellum cDNA, RIKEN full-length enriched library, clone:C230053I05 product:Unc4.1 homeobox (C. elegans), full insert sequence.
AF247550 - Mus musculus UNC4 protein mRNA, complete cds.
Z96107 - Mus musculus mRNA for Uncx4.1.
BC051973 - Mus musculus UNC homeobox, mRNA (cDNA clone MGC:62254 IMAGE:5718115), complete cds.
AJ001116 - Mus musculus mRNA for Uncx4.1 protein.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_013702, O08934, P70457, Q78DU3, uc009agv.1, uc009agv.2, uc009agv.3, UNC4_MOUSE, Uncx4.1
UCSC ID: uc009agv.3
RefSeq Accession: NM_013702
Protein: O08934 (aka UNC4_MOUSE)
CCDS: CCDS19813.1

-  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.