Human Gene HOXA2 (ENST00000222718.7) from GENCODE V44
  Description: Homo sapiens homeobox A2 (HOXA2), mRNA. (from RefSeq NM_006735)
RefSeq Summary (NM_006735): In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000222718.7
Gencode Gene: ENSG00000105996.7
Transcript (Including UTRs)
   Position: hg38 chr7:27,100,354-27,102,683 Size: 2,330 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg38 chr7:27,100,726-27,102,500 Size: 1,775 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:27,100,354-27,102,683)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HXA2_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Hox-A2; AltName: Full=Homeobox protein Hox-1K;
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.
DISEASE: Defects in HOXA2 are a cause of microtia hearing impairment and cleft palate (MHICP) [MIM:612290]. Microtia is a congenital deformity of the outer ear and occurs in approximately one in 8'000-10'000 births. It is characterized by a small, abnormally shaped outer ear. It can be unilateral or bilateral. Syndromic forms of microtia occur in conjunction with other abnormalities. The most common associated malformations is the cleft palate, a congenital fissure of the soft and/or hard palate due to faulty fusion. Defects in HOXA2 are a cause of autosomal- recessive bilateral microtia, mixed symmetrical severe to profound hearing impairment and partial cleft palate.
SIMILARITY: Belongs to the Antp homeobox family. Proboscipedia 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.
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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: HOXA2
Diseases sorted by gene-association score: microtia, hearing impairment, and cleft palate* (1730), microtia* (389), bamforth-lazarus syndrome (11), facial nerve disease (8), hemifacial microsomia (8), skin tag (8), facial paralysis (7), poland syndrome (7), branchiootorenal syndrome (5), cleft soft palate (5), treacher collins syndrome 1 (5), renal hypodysplasia/aplasia 1 (4)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.95 RPKM in Fallopian Tube
Total median expression: 58.66 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 -51.60183-0.282 Picture PostScript Text
3' UTR -76.20372-0.205 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
IPR001827 - Homeobox_Antennapedia_CS
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on O43364
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-  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
Genome BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein Sequence Protein Sequence   
Alignment Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific 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:0001709 cell fate determination
GO:0002076 osteoblast development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007379 segment specification
GO:0007389 pattern specification process
GO:0008045 motor neuron axon guidance
GO:0009952 anterior/posterior pattern specification
GO:0009953 dorsal/ventral pattern formation
GO:0021568 rhombomere 2 development
GO:0021569 rhombomere 3 development
GO:0021658 rhombomere 3 morphogenesis
GO:0035284 brain segmentation
GO:0042474 middle ear morphogenesis
GO:0045165 cell fate commitment
GO:0045665 negative regulation of neuron differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048703 embryonic viscerocranium morphogenesis
GO:0048704 embryonic skeletal system morphogenesis
GO:0071300 cellular response to retinoic acid

Cellular Component:
GO:0005634 nucleus
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  BC130571 - Homo sapiens homeobox A2, mRNA (cDNA clone MGC:163443 IMAGE:40146602), complete cds.
BC136500 - Homo sapiens homeobox A2, mRNA (cDNA clone MGC:168112 IMAGE:9020489), complete cds.
JD442729 - Sequence 423753 from Patent EP1572962.
JD392435 - Sequence 373459 from Patent EP1572962.
JD036466 - Sequence 17490 from Patent EP1572962.
AK096742 - Homo sapiens cDNA FLJ39423 fis, clone PROST1000322, highly similar to HOMEOBOX PROTEIN HOX-A2.
AL079274 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 345330.
KJ891376 - Synthetic construct Homo sapiens clone ccsbBroadEn_00770 HOXA2 gene, encodes complete protein.
AB464572 - Synthetic construct DNA, clone: pF1KB8980, Homo sapiens HOXA2 gene for homeobox A2, without stop codon, in Flexi system.
AK291164 - Homo sapiens cDNA FLJ78348 complete cds.
JD310198 - Sequence 291222 from Patent EP1572962.

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

Protein O43364 (Reactome details) participates in the following event(s):

R-HSA-9010503 HOXA2 binds ROBO2 gene promoter
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-376176 Signaling by ROBO receptors
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A1L4K3, B2RMW3, ENST00000222718.1, ENST00000222718.2, ENST00000222718.3, ENST00000222718.4, ENST00000222718.5, ENST00000222718.6, HOX1K, HXA2_HUMAN, NM_006735, O43364, uc003syh.1, uc003syh.2, uc003syh.3, uc003syh.4, uc003syh.5
UCSC ID: ENST00000222718.7
RefSeq Accession: NM_006735
Protein: O43364 (aka HXA2_HUMAN)
CCDS: CCDS5403.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.