Human Gene PHOX2A (ENST00000298231.5) from GENCODE V44
  Description: Homo sapiens paired like homeobox 2A (PHOX2A), mRNA. (from RefSeq NM_005169)
RefSeq Summary (NM_005169): The protein encoded by this gene contains a paired-like homeodomain most similar to that of the Drosophila aristaless gene product. The encoded protein plays a central role in development of the autonomic nervous system. It regulates the expression of tyrosine hydroxylase and dopamine beta-hydroxylase, two catecholaminergic biosynthetic enzymes essential for the differentiation and maintenance of the noradrenergic neurotransmitter phenotype. The encoded protein has also been shown to regulate transcription of the alpha3 nicotinic acetylcholine receptor gene. Mutations in this gene have been associated with autosomal recessive congenital fibrosis of the extraocular muscles. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000298231.5
Gencode Gene: ENSG00000165462.5
Transcript (Including UTRs)
   Position: hg38 chr11:72,239,077-72,244,176 Size: 5,100 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr11:72,239,749-72,244,004 Size: 4,256 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:72,239,077-72,244,176)mRNA (may differ from genome)Protein (284 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired mesoderm homeobox protein 2A; AltName: Full=ARIX1 homeodomain protein; AltName: Full=Aristaless homeobox protein homolog; AltName: Full=Paired-like homeobox 2A;
FUNCTION: May be involved in regulating the specificity of expression of the catecholamine biosynthetic genes. Acts as a transcription activator/factor. Could maintain the noradrenergic phenotype.
SUBCELLULAR LOCATION: Nucleus (By similarity).
DISEASE: Defects in PHOX2A are the cause of congenital fibrosis of extraocular muscles type 2 (CFEOM2) [MIM:602078]. CFEOM encompasses several different inherited strabismus syndromes characterized by congenital restrictive ophthalmoplegia affecting extraocular muscles innervated by the oculomotor and/or trochlear nerves. CFEOM is characterized clinically by anchoring of the eyes in downward gaze, ptosis, and backward tilt of the head. CFEOM2 may result from the aberrant development of the oculomotor (nIII), trochlear (nIV) and abducens (nVI) cranial nerve nuclei.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
WEB RESOURCE: Name=GeneReviews; URL="";

-  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: PHOX2A
Diseases sorted by gene-association score: fibrosis of extraocular muscles, congenital, 2* (1252), tukel syndrome* (219), phox2a-related congenital fibrosis of the extraocular muscles* (200), brown syndrome (12), hypotropia (10), exotropia (9), ocular motility disease (8), strabismus (7), ptosis (7), paralytic squint (7), kearns-sayre syndrome (5), central hypoventilation syndrome, congenital (5), moebius syndrome (5), cranial nerve disease (5), facial nerve disease (5), sudden infant death syndrome (4), autonomic nervous system disease (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: 0.71 RPKM in Colon - Sigmoid
Total median expression: 2.14 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 -81.20172-0.472 Picture PostScript Text
3' UTR -238.70672-0.355 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
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on O14813
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
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:0003357 noradrenergic neuron differentiation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0021523 somatic motor neuron differentiation
GO:0021623 oculomotor nerve formation
GO:0021642 trochlear nerve formation
GO:0021703 locus ceruleus development
GO:0030901 midbrain development
GO:0043576 regulation of respiratory gaseous exchange
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048485 sympathetic nervous system development
GO:0048486 parasympathetic nervous system development
GO:0071542 dopaminergic neuron differentiation

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC041564 - Homo sapiens paired-like homeobox 2a, mRNA (cDNA clone MGC:52227 IMAGE:5923445), complete cds.
AK290645 - Homo sapiens cDNA FLJ76024 complete cds, highly similar to Homo sapiens paired-like (aristaless) homeobox 2a (PHOX2A), mRNA.
EU446462 - Synthetic construct Homo sapiens clone IMAGE:100069949; IMAGE:100011671; FLH257061.01L paired-like homeobox 2a (PHOX2A) gene, encodes complete protein.
JD128752 - Sequence 109776 from Patent EP1572962.
JD124743 - Sequence 105767 from Patent EP1572962.
JD210315 - Sequence 191339 from Patent EP1572962.
JD555213 - Sequence 536237 from Patent EP1572962.
JD306821 - Sequence 287845 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3N0, ARIX, ENST00000298231.1, ENST00000298231.2, ENST00000298231.3, ENST00000298231.4, NM_005169, O14813, PHX2A_HUMAN, PMX2A, Q8IVZ2, uc001osh.1, uc001osh.2, uc001osh.3, uc001osh.4
UCSC ID: ENST00000298231.5
RefSeq Accession: NM_005169
Protein: O14813 (aka PHX2A_HUMAN)
CCDS: CCDS8214.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PHOX2A:
cfeom (Congenital Fibrosis of the Extraocular Muscles Overview)

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