Human Gene PAX2 (uc001krk.4) Description and Page Index
Description: Homo sapiens paired box 2 (PAX2), transcript variant e, mRNA. RefSeq Summary (NM_003990): PAX2 encodes paired box gene 2, one of many human homologues of the Drosophila melanogaster gene prd. The central feature of this transcription factor gene family is the conserved DNA-binding paired box domain. PAX2 is believed to be a target of transcriptional supression by the tumor suppressor gene WT1. Mutations within PAX2 have been shown to result in optic nerve colobomas and renal hypoplasia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2014]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. 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## RNAseq introns :: single sample supports all introns SAMEA1970526, SAMEA2145774 [ECO:0000348] ##Evidence-Data-END## Transcript (Including UTRs) Position: hg19 chr10:102,505,468-102,589,698 Size: 84,231 Total Exon Count: 11 Strand: + Coding Region Position: hg19 chr10:102,506,018-102,587,440 Size: 81,423 Coding Exon Count: 11
ID:PAX2_HUMAN DESCRIPTION: RecName: Full=Paired box protein Pax-2; FUNCTION: Probable transcription factor that may have a role in kidney cell differentiation. Has a critical role in the development of the urogenital tract, the eyes, and the CNS. SUBUNIT: Interacts with ELGN3; the interaction targets PAX2 for destruction. SUBCELLULAR LOCATION: Nucleus. TISSUE SPECIFICITY: Expressed in primitive cells of the kidney, ureter, eye, ear and central nervous system. DEVELOPMENTAL STAGE: Mainly in fetal kidney and juvenile nephrogenic rests. DISEASE: Defects in PAX2 are the cause of renal-coloboma syndrome (RCS) [MIM:120330]; also known as papillorenal syndrome or optic nerve coloboma with renal disease. RCS is an autosomal dominant disease characterized by the association of renal hypoplasia, vesicoureteral reflux and dysplasia of the retina and optic disk. DISEASE: Note=Defects in PAX2 can be responsible for isolated renal hypodysplasia and oligomeganephronia (OMN). This is a rare congenital and usually sporadic anomaly characterized by bilateral renal hypoplasia, with a reduced number of enlarged nephrons and without urinary tract abnormalities. SIMILARITY: Contains 1 paired domain. WEB RESOURCE: Name=PAX2 mutation db; URL="http://www.hgu.mrc.ac.uk/Softdata/PAX2/"; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PAX2ID41642ch10q24.html"; WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PAX2"; WEB RESOURCE: Name=PAX2 variant database paired box 2 (PAX2); Note=Leiden Open Variation Database (LOVD); URL="http://grenada.lumc.nl/LOVD2/PAX2/home.php?select_db=PAX2";
Genetic Association Studies of Complex Diseases and Disorders
Alzheimer's Disease Heinzen ,et al. 2009, Genome-Wide Scan of Copy Number Variation in Late-Onset Alzheimer's Disease, Journal of Alzheimers disease : JAD 2009 .
isolated colobomas or colobomas associated Cunliffe HE et al. 1998, The prevalence of PAX2 mutations in patients with isolated colobomas or colobomas associated with urogenital anomalies., Journal of medical genetics. 1998 Oct;35(10):806-12.
We conclude that PAX2 mutations are unlikely to be common in patients with ocular colobomas in isolation or in patients with ocular colobomas and associated anomalies, except for patients with typical renal-coloboma syndrome where PAX2 is known to be the aetiological cause.
kidney size, newborn Quinlan, J. et al. 2007, A Common Variant of the PAX2 Gene Is Associated with Reduced Newborn Kidney Size, J Am Soc Nephrol 2007.
Subtle renal hypoplasia in normal newborns may be partially due to a common variant of the PAX2 gene that reduces mRNA expression during kidney development.
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.
ModBase Predicted Comparative 3D Structure on Q02962
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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.
Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function: GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0000987 core promoter proximal region sequence-specific DNA binding GO:0003677 DNA binding GO:0005515 protein binding GO:0008134 transcription factor binding GO:0016175 superoxide-generating NADPH oxidase activity GO:0044212 transcription regulatory region DNA binding
Biological Process: GO:0001655 urogenital system development GO:0001658 branching involved in ureteric bud morphogenesis GO:0001709 cell fate determination GO:0001823 mesonephros development GO:0001843 neural tube closure GO:0002072 optic cup morphogenesis involved in camera-type eye development GO:0003337 mesenchymal to epithelial transition involved in metanephros morphogenesis GO:0003406 retinal pigment epithelium development 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:0007409 axonogenesis GO:0007501 mesodermal cell fate specification GO:0007568 aging GO:0007601 visual perception GO:0008284 positive regulation of cell proliferation GO:0010001 glial cell differentiation GO:0021554 optic nerve development GO:0021631 optic nerve morphogenesis GO:0021633 optic nerve structural organization GO:0021650 vestibulocochlear nerve formation GO:0030154 cell differentiation GO:0031667 response to nutrient levels GO:0035566 regulation of metanephros size GO:0035799 ureter maturation GO:0039003 pronephric field specification GO:0042472 inner ear morphogenesis GO:0043010 camera-type eye development GO:0043066 negative regulation of apoptotic process GO:0043069 negative regulation of programmed cell death GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process GO:0043491 protein kinase B signaling GO:0045892 negative regulation of transcription, DNA-templated GO:0045893 positive regulation of transcription, DNA-templated GO:0045918 negative regulation of cytolysis GO:0045944 positive regulation of transcription from RNA polymerase II promoter GO:0048513 animal organ development GO:0048793 pronephros development GO:0048854 brain morphogenesis GO:0048863 stem cell differentiation GO:0050679 positive regulation of epithelial cell proliferation GO:0055114 oxidation-reduction process GO:0060231 mesenchymal to epithelial transition GO:0061360 optic chiasma development GO:0070301 cellular response to hydrogen peroxide GO:0071300 cellular response to retinoic acid GO:0071333 cellular response to glucose stimulus GO:0071364 cellular response to epidermal growth factor stimulus GO:0072075 metanephric mesenchyme development GO:0072108 positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis GO:0072162 metanephric mesenchymal cell differentiation GO:0072179 nephric duct formation GO:0072189 ureter development GO:0072205 metanephric collecting duct development GO:0072207 metanephric epithelium development GO:0072221 metanephric distal convoluted tubule development GO:0072289 metanephric nephron tubule formation GO:0072300 positive regulation of metanephric glomerulus development GO:0072305 negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis GO:0072307 regulation of metanephric nephron tubule epithelial cell differentiation GO:0072593 reactive oxygen species metabolic process GO:0090102 cochlea development GO:0090103 cochlea morphogenesis GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis GO:1900212 negative regulation of mesenchymal cell apoptotic process involved in metanephros development GO:1900215 negative regulation of apoptotic process involved in metanephric collecting duct development GO:1900218 negative regulation of apoptotic process involved in metanephric nephron tubule development GO:2000378 negative regulation of reactive oxygen species metabolic process GO:2000594 positive regulation of metanephric DCT cell differentiation GO:2000597 positive regulation of optic nerve formation