Human Gene HOXD11 (ENST00000249504.7_4) from GENCODE V47lift37
  Description: homeobox D11 (from RefSeq NM_021192.3)
Gencode Transcript: ENST00000249504.7_4
Gencode Gene: ENSG00000128713.14_8
Transcript (Including UTRs)
   Position: hg19 chr2:176,972,008-176,974,482 Size: 2,475 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr2:176,972,084-176,973,870 Size: 1,787 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:176,972,008-176,974,482)mRNA (may differ from genome)Protein (338 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HXD11_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Hox-D11; AltName: Full=Homeobox protein Hox-4F;
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.
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


-  MalaCards Disease Associations
  MalaCards Gene Search: HOXD11
Diseases sorted by gene-association score: syndactyly, type v (13), synpolydactyly (12), brachydactyly-syndactyly syndrome (9), fraser syndrome 1 (5)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.88 RPKM in Uterus
Total median expression: 12.15 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.7076-0.483 Picture PostScript Text
3' UTR -179.90612-0.294 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 - Homeodomain
PF12045 - Protein of unknown function (DUF3528)

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P31277
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  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:0043565 sequence-specific DNA binding

Biological Process:
GO:0001658 branching involved in ureteric bud morphogenesis
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:0009953 dorsal/ventral pattern formation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC160135 - Synthetic construct Homo sapiens clone IMAGE:100064167, MGC:193250 homeobox D11 (HOXD11) mRNA, encodes complete protein.
LF205724 - JP 2014500723-A/13227: Polycomb-Associated Non-Coding RNAs.
AK309681 - Homo sapiens cDNA, FLJ99722.
LF211810 - JP 2014500723-A/19313: Polycomb-Associated Non-Coding RNAs.
BC109394 - Homo sapiens homeobox D11, mRNA (cDNA clone IMAGE:40068657), complete cds.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JC506674 - Sequence 42 from Patent EP2733220.
JC737786 - Sequence 42 from Patent WO2014075939.
JD211267 - Sequence 192291 from Patent EP1572962.
JD217640 - Sequence 198664 from Patent EP1572962.
JD364798 - Sequence 345822 from Patent EP1572962.
JD418501 - Sequence 399525 from Patent EP1572962.
JD525680 - Sequence 506704 from Patent EP1572962.
JD521488 - Sequence 502512 from Patent EP1572962.
JD145528 - Sequence 126552 from Patent EP1572962.
JD236300 - Sequence 217324 from Patent EP1572962.
MA441301 - JP 2018138019-A/13227: Polycomb-Associated Non-Coding RNAs.
MA447387 - JP 2018138019-A/19313: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NIS4, ENST00000249504.1, ENST00000249504.2, ENST00000249504.3, ENST00000249504.4, ENST00000249504.5, ENST00000249504.6, HOX4F, HXD11_HUMAN, NM_021192, P31277, Q9NS02, uc317ezu.1, uc317ezu.2
UCSC ID: ENST00000249504.7_4
RefSeq Accession: NM_021192.3
Protein: P31277 (aka HXD11_HUMAN or HXDB_HUMAN)

-  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.