Mouse Gene Hoxa11 (ENSMUST00000048026.9) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus homeobox A11 (Hoxa11), mRNA. (from RefSeq NM_010450)
RefSeq Summary (NM_010450): This gene is located in a cluster of developmentally and temporally regulated genes on chromosome 6 encoding proteins involved in pattern formation. These proteins contain a characteristic DNA-binding motif called a homeodomain and function in transcriptional regulation. There are four distinct clusters of related genes on chromosomes 2, 6, 11, and 15. The protein encoded by this gene is important in the development of the skeleton, limbs, and urogenital tract. Expression of this gene may be regulated by overlapping transcription from an adjacent locus on the opposite strand (GeneID: 15397). [provided by RefSeq, Mar 2013]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENSMUST00000048026.9
Gencode Gene: ENSMUSG00000038210.10
Transcript (Including UTRs)
   Position: mm10 chr6:52,242,106-52,245,810 Size: 3,705 Total Exon Count: 2 Strand: -
Coding Region
   Position: mm10 chr6:52,243,360-52,245,719 Size: 2,360 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:52,242,106-52,245,810)mRNA (may differ from genome)Protein (313 aa)
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PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: HXA11_MOUSE
DESCRIPTION: RecName: Full=Homeobox protein Hox-A11; AltName: Full=Homeobox protein Hox-1.9;
FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.
INTERACTION: O88513:Gmnn; NbExp=2; IntAct=EBI-445941, EBI-445922;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the Abd-B 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -26.8091-0.295 Picture PostScript Text
3' UTR -418.601254-0.334 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
IPR021918 - DUF3528
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain
PF12045 - Protein of unknown function (DUF3528)

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P31311
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
      
      

-  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:0001501 skeletal system development
GO:0001656 metanephros development
GO:0001658 branching involved in ureteric bud morphogenesis
GO:0001759 organ induction
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007338 single fertilization
GO:0007501 mesodermal cell fate specification
GO:0008584 male gonad development
GO:0009952 anterior/posterior pattern specification
GO:0009953 dorsal/ventral pattern formation
GO:0009954 proximal/distal pattern formation
GO:0010468 regulation of gene expression
GO:0010720 positive regulation of cell development
GO:0030326 embryonic limb morphogenesis
GO:0032330 regulation of chondrocyte differentiation
GO:0032332 positive regulation of chondrocyte differentiation
GO:0035115 embryonic forelimb morphogenesis
GO:0042733 embryonic digit morphogenesis
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048589 developmental growth
GO:0060065 uterus development
GO:0060272 embryonic skeletal joint morphogenesis
GO:0060348 bone development
GO:0060351 cartilage development involved in endochondral bone morphogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0032991 macromolecular complex
GO:0032993 protein-DNA complex


-  Descriptions from all associated GenBank mRNAs
  U20370 - Mus musculus homeobox protein (Hoxa11) mRNA, complete cds.
BC052232 - Mus musculus cDNA clone IMAGE:6504963.
AK133481 - Mus musculus 11 days pregnant adult female ovary and uterus cDNA, RIKEN full-length enriched library, clone:5031409E18 product:homeo box A11, full insert sequence.
BC119302 - Mus musculus homeo box A11, mRNA (cDNA clone MGC:155618 IMAGE:8734051), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: Hox-1.9, Hoxa-11, HXA11_MOUSE, NM_010450, P31311, Q3V026, uc009byn.1, uc009byn.2, uc009byn.3
UCSC ID: uc009byn.3
RefSeq Accession: NM_010450
Protein: P31311 (aka HXA11_MOUSE or HXAB_MOUSE)
CCDS: CCDS20148.1

-  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.