Human Gene HOXB4 (ENST00000332503.6_7) from GENCODE V47lift37
  Description: homeobox B4 (from RefSeq NM_024015.5)
Gencode Transcript: ENST00000332503.6_7
Gencode Gene: ENSG00000182742.6_10
Transcript (Including UTRs)
   Position: hg19 chr17:46,652,869-46,655,712 Size: 2,844 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:46,654,084-46,655,681 Size: 1,598 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:46,652,869-46,655,712)mRNA (may differ from genome)Protein (251 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HXB4_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Hox-B4; AltName: Full=Homeobox protein Hox-2.6; AltName: Full=Homeobox protein Hox-2F;
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.
DEVELOPMENTAL STAGE: Expressed in whole embryos and fetuses at 5-9 weeks from conception.
SIMILARITY: Belongs to the Antp homeobox family. Deformed 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           more ... click here to view the complete list

+  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: 14.50 RPKM in Esophagus - Gastroesophageal Junction
Total median expression: 158.33 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 -6.3031-0.203 Picture PostScript Text
3' UTR -456.901215-0.376 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
IPR017995 - Homeobox_antennapedia
IPR001827 - Homeobox_Antennapedia_CS
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeodomain

SCOP Domains:
101447 - Formin homology 2 domain (FH2 domain)
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P17483
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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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0002011 morphogenesis of an epithelial sheet
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0008283 cell proliferation
GO:0009952 anterior/posterior pattern specification
GO:0030097 hemopoiesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048103 somatic stem cell division
GO:0048536 spleen development
GO:0048539 bone marrow development
GO:0048704 embryonic skeletal system morphogenesis
GO:0048705 skeletal system morphogenesis
GO:0060216 definitive hemopoiesis
GO:0060218 hematopoietic stem cell differentiation
GO:2000738 positive regulation of stem cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005813 centrosome


-  Descriptions from all associated GenBank mRNAs
  AL137449 - Homo sapiens mRNA; cDNA DKFZp434G0128 (from clone DKFZp434G0128); partial cds.
BC049204 - Homo sapiens homeobox B4, mRNA (cDNA clone MGC:54130 IMAGE:5533346), complete cds.
DQ579259 - Homo sapiens piRNA piR-47371, complete sequence.
JD322140 - Sequence 303164 from Patent EP1572962.
JD306845 - Sequence 287869 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P17483 (Reactome details) participates in the following event(s):

R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000332503.1, ENST00000332503.2, ENST00000332503.3, ENST00000332503.4, ENST00000332503.5, HOX2F, HXB4_HUMAN, NM_024015, P17483, Q9NTA0, uc317tlm.1, uc317tlm.2
UCSC ID: ENST00000332503.6_7
RefSeq Accession: NM_024015.5
Protein: P17483 (aka HXB4_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.