Human Gene HOXB5 (uc002inr.3) Description and Page Index
  Description: Homo sapiens homeobox B5 (HOXB5), mRNA.
RefSeq Summary (NM_002147): This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in lung and gut development. Increased expression of this gene is associated with a distinct biologic subset of acute myeloid leukemia (AML) and the occurrence of bronchopulmonary sequestration (BPS) and congenital cystic adenomatoid malformation (CCAM) tissue. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BI766494.1, M92299.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1966682, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:46,668,619-46,671,103 Size: 2,485 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:46,669,571-46,671,044 Size: 1,474 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:46,668,619-46,671,103)mRNA (may differ from genome)Protein (269 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: HXB5_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Hox-B5; AltName: Full=Homeobox protein HHO.C10; AltName: Full=Homeobox protein Hox-2A; AltName: Full=Homeobox protein Hu-1;
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.
TISSUE SPECIFICITY: Spinal cord.
DEVELOPMENTAL STAGE: Embryo.
SIMILARITY: Belongs to the Antp homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAA52681.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HOXB5
CDC HuGE Published Literature: HOXB5
Positive Disease Associations: Obesity
Related Studies:
  1. Obesity
    Jonathan P Bradfield et al. Nature genetics 2012, A genome-wide association meta-analysis identifies new childhood obesity loci., Nature genetics. [PubMed 22484627]

-  MalaCards Disease Associations
  MalaCards Gene Search: HOXB5
Diseases sorted by gene-association score: ovarian serous carcinoma (7), hirschsprung disease 1 (1)

-  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: 12.68 RPKM in Colon - Transverse
Total median expression: 73.27 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.8659-0.133 Picture PostScript Text
3' UTR -314.51952-0.330 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 - Homeobox domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P09067
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001205 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0009653 anatomical structure morphogenesis
GO:0009952 anterior/posterior pattern specification
GO:0045446 endothelial cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048704 embryonic skeletal system morphogenesis
GO:0048706 embryonic skeletal system development

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF209285 - JP 2014500723-A/16788: Polycomb-Associated Non-Coding RNAs.
X03794 - Human embryonic mRNA 3' end with homoeo box (clone HHOc10).
M92299 - Human homeobox 2.1 protein (HOX2A) mRNA, complete cds.
BC004454 - Homo sapiens homeobox B5, mRNA (cDNA clone IMAGE:2819487).
BC008940 - Homo sapiens homeobox B5, mRNA (cDNA clone IMAGE:2819487).
JD565172 - Sequence 546196 from Patent EP1572962.
JD305062 - Sequence 286086 from Patent EP1572962.
JD054186 - Sequence 35210 from Patent EP1572962.
JD519969 - Sequence 500993 from Patent EP1572962.
JD103235 - Sequence 84259 from Patent EP1572962.
JD349485 - Sequence 330509 from Patent EP1572962.
JD486825 - Sequence 467849 from Patent EP1572962.
JD545905 - Sequence 526929 from Patent EP1572962.
JD398039 - Sequence 379063 from Patent EP1572962.
JD113585 - Sequence 94609 from Patent EP1572962.
JD310818 - Sequence 291842 from Patent EP1572962.
JD280093 - Sequence 261117 from Patent EP1572962.
JD494975 - Sequence 475999 from Patent EP1572962.
JD253540 - Sequence 234564 from Patent EP1572962.
LF212442 - JP 2014500723-A/19945: Polycomb-Associated Non-Coding RNAs.
BC117247 - Homo sapiens homeobox B5, mRNA (cDNA clone MGC:150856 IMAGE:40125798), complete cds.
JD120791 - Sequence 101815 from Patent EP1572962.
JD357411 - Sequence 338435 from Patent EP1572962.
M86726 - Human homeobox protein (HOX-2.1) mRNA, 3' end.
JD078844 - Sequence 59868 from Patent EP1572962.
JD429578 - Sequence 410602 from Patent EP1572962.
JD114641 - Sequence 95665 from Patent EP1572962.
JD416028 - Sequence 397052 from Patent EP1572962.
JD114409 - Sequence 95433 from Patent EP1572962.
JD393197 - Sequence 374221 from Patent EP1572962.
JD210435 - Sequence 191459 from Patent EP1572962.
JD209792 - Sequence 190816 from Patent EP1572962.
AK314964 - Homo sapiens cDNA, FLJ95879, Homo sapiens homeo box B5 (HOXB5), mRNA.
KJ891381 - Synthetic construct Homo sapiens clone ccsbBroadEn_00775 HOXB5 gene, encodes complete protein.
AB464575 - Synthetic construct DNA, clone: pF1KB8922, Homo sapiens HOXB5 gene for homeobox B5, without stop codon, in Flexi system.
JD250766 - Sequence 231790 from Patent EP1572962.
MA444862 - JP 2018138019-A/16788: Polycomb-Associated Non-Coding RNAs.
MA448019 - JP 2018138019-A/19945: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RC69, HOX2A, HXB5_HUMAN, NM_002147, NP_002138, P09067, P09069, Q17RP4
UCSC ID: uc002inr.3
RefSeq Accession: NM_002147
Protein: P09067 (aka HXB5_HUMAN)
CCDS: CCDS11530.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002147.3
exon count: 2CDS single in 3' UTR: no RNA size: 1830
ORF size: 810CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1720.00frame shift in genome: no % Coverage: 99.51
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.