Human Gene PAX6 (ENST00000640613.1) from GENCODE V44
  Description: Homo sapiens paired box 6 (PAX6), transcript variant 48, mRNA. (from RefSeq NM_001368927)
RefSeq Summary (NM_001368925): This gene encodes paired box protein Pax-6, one of many human homologs of the Drosophila melanogaster gene prd. In addition to a conserved paired box domain, a hallmark feature of this gene family, the encoded protein also contains a homeobox domain. Both domains are known to bind DNA and function as regulators of gene transcription. Activity of this protein is key in the development of neural tissues, particularly the eye. This gene is regulated by multiple enhancers located up to hundreds of kilobases distant from this locus. Mutations in this gene or in the enhancer regions can cause ocular disorders such as aniridia and Peter's anomaly. Use of alternate promoters and alternative splicing results in multiple transcript variants encoding different isoforms. Interestingly, inclusion of a particular alternate coding exon has been shown to increase the length of the paired box domain and alter its DNA binding specificity. Consequently, isoforms that carry the shorter paired box domain regulate a different set of genes compared to the isoforms carrying the longer paired box domain. [provided by RefSeq, Mar 2019].
Gencode Transcript: ENST00000640613.1
Gencode Gene: ENSG00000007372.25
Transcript (Including UTRs)
   Position: hg38 chr11:31,789,938-31,811,118 Size: 21,181 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg38 chr11:31,789,938-31,806,411 Size: 16,474 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
GeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:31,789,938-31,811,118)mRNA (may differ from genome)Protein (368 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  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: PAX6
Diseases sorted by gene-association score: coloboma of optic nerve* (1729), optic nerve hypoplasia* (1680), coloboma, ocular* (1628), foveal hypoplasia 1* (1579), aniridia* (1385), keratitis* (1298), anterior segment dysgenesis 5, multiple subtypes* (1200), coloboma* (804), peters-plus syndrome* (627), o donnell pappas syndrome* (500), isolated aniridia* (468), gillespie syndrome* (331), coloboma of eye lens* (247), coloboma of eyelid* (247), cataract 9, multiple types* (148), pax6-related anophthalmia* (100), wagr syndrome* (44), keratopathy (24), iris hypoplasia (20), iris disease (20), stromal keratitis (19), congenital nystagmus (19), coloboma of iris (18), arrhinia (18), retinal perforation (17), axenfeld-rieger syndrome (16), ectropion (13), aniridia 2 (13), morning glory syndrome (13), dopamine beta-hydroxylase deficiency (13), large cell medulloblastoma (12), ablepharon-macrostomia syndrome (12), scleral staphyloma (11), microphthalmia (11), pseudopapilledema (10), intestinal atresia (9), papillorenal syndrome (9), glaucoma 3a, primary open angle, congenital, juvenile, or adult onset (9), chiasmal syndrome (8), fryns microphthalmia syndrome (8), pathologic nystagmus (8), wilms tumor susceptibility-5 (8), congenital aphakia (8), anophthalmia/microphthalmia (7), eye disease (7), lens disease (6), waardenburg's syndrome (6), persistent hyperplastic primary vitreous (6), anterior segment dysgenesis 1, multiple subtypes (6), conjunctival degeneration (5), hypocalciuric hypercalcemia, type ii (5), juvenile glaucoma (5), hereditary wilms' tumor (5), pinguecula (4), axenfeld-rieger syndrome, type 1 (4), poland syndrome (4), ethylmalonic encephalopathy (4), myopia (4), frasier syndrome (4), maturity-onset diabetes of the young (2), microcephaly (2), schizophrenia (1)
* = 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: 28.57 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 85.91 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 -96.82419-0.231 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.

-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Descriptions from all associated GenBank mRNAs
  AB593092 - Homo sapiens PAX6 mRNA for paired box protein Pax-6, complete cds, clone: HP06376-ARe92D06.
AB593093 - Homo sapiens PAX6 mRNA for paired box protein Pax-6, complete cds, clone: HP06376-ARh11B12.
AB593094 - Homo sapiens PAX6 mRNA for paired box protein Pax-6, complete cds, clone: HP06376-ARi61A11.
M77844 - Homo sapiens oculorhombin (PAX6) mRNA, complete cds, alternatively spliced.
M93650 - Human paired box gene (PAX6) homologue, complete cds.
BC011953 - Homo sapiens paired box 6, mRNA (cDNA clone MGC:17209 IMAGE:3880468), complete cds.
BX640762 - Homo sapiens mRNA; cDNA DKFZp686B14266 (from clone DKFZp686B14266).
AY707088 - Homo sapiens paired box gene 6 isoform a mRNA, complete cds.
AY047583 - Homo sapiens paired box protein PAX6 (PAX6) mRNA, complete cds.
AK314470 - Homo sapiens cDNA, FLJ95274.
DQ891436 - Synthetic construct clone IMAGE:100004066; FLH176929.01X; RZPDo839B01124D paired box gene 6 (aniridia, keratitis) (PAX6) gene, encodes complete protein.
AK094172 - Homo sapiens cDNA FLJ36853 fis, clone ASTRO2014498, highly similar to PAIRED BOX PROTEIN PAX-6.
AK094249 - Homo sapiens cDNA FLJ36930 fis, clone BRACE2005251, highly similar to PAIRED BOX PROTEIN PAX-6.
DQ894612 - Synthetic construct Homo sapiens clone IMAGE:100009072; FLH176926.01L; RZPDo839B01123D paired box gene 6 (aniridia, keratitis) (PAX6) gene, encodes complete protein.
AK074881 - Homo sapiens cDNA FLJ90400 fis, clone NT2RP2005941, highly similar to Paired box protein Pax-6.
AB209177 - Homo sapiens mRNA for paired box gene 6 isoform a variant protein.
AB528383 - Synthetic construct DNA, clone: pF1KB7983, Homo sapiens PAX6 gene for paired box 6, without stop codon, in Flexi system.
GQ141695 - Homo sapiens paired box protein 6 isoform c (PAX6) mRNA, complete cds, alternatively spliced.
CU680128 - Synthetic construct Homo sapiens gateway clone IMAGE:100017234 5' read PAX6 mRNA.
KP255960 - UNVERIFIED: Homo sapiens paired box 6-like mRNA, complete sequence.
JD242206 - Sequence 223230 from Patent EP1572962.
JD037394 - Sequence 18418 from Patent EP1572962.
JD493110 - Sequence 474134 from Patent EP1572962.
JD053733 - Sequence 34757 from Patent EP1572962.
KM609512 - Homo sapiens clone S3 paired box protein Pax-6 (PAX6) mRNA, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04950 - Maturity onset diabetes of the young

-  Other Names for This Gene
  Alternate Gene Symbols: A0A1W2PRG3, NM_001368927, uc058acc.1, uc058acc.2
UCSC ID: ENST00000640613.1
RefSeq Accession: NM_001368925

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PAX6:
aniridia (PAX6-Related Aniridia)

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