Mouse Gene Rhox13 (ENSMUST00000152730.3) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus reproductive homeobox 13 (Rhox13), mRNA. (from RefSeq NM_001185002)
Gencode Transcript: ENSMUST00000152730.3
Gencode Gene: ENSMUSG00000050197.5
Transcript (Including UTRs)
   Position: mm10 chrX:38,121,219-38,129,967 Size: 8,749 Total Exon Count: 3 Strand: +
Coding Region
   Position: mm10 chrX:38,121,290-38,129,861 Size: 8,572 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:38,121,219-38,129,967)mRNA (may differ from genome)Protein (232 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: F6YCR7_MOUSE
DESCRIPTION: SubName: Full=Protein Rhox13;
SUBCELLULAR LOCATION: Nucleus (By similarity).
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -28.0071-0.394 Picture PostScript Text
3' UTR -19.10106-0.180 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 F6YCR7
FrontTopSide
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     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0071300 cellular response to retinoic acid

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK007253 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:1700123J19 product:hypothetical Homeobox domain containing protein, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: F6YCR7, F6YCR7_MOUSE, NM_001185002, uc009szo.1, uc009szo.2, uc009szo.3
UCSC ID: uc009szo.3
RefSeq Accession: NM_001185002
Protein: F6YCR7 CCDS: CCDS57754.1

-  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.