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 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:102,505,468-102,589,698)mRNA (may differ from genome)Protein (431 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
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.
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="";
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";
WEB RESOURCE: Name=GeneReviews; URL="";
WEB RESOURCE: Name=PAX2 variant database paired box 2 (PAX2); Note=Leiden Open Variation Database (LOVD); URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PAX2
CDC HuGE Published Literature: PAX2
Positive Disease Associations: Alzheimer's Disease , isolated colobomas or colobomas associated , kidney size, newborn
Related Studies:
  1. 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 . [PubMed 19749422]
  2. 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. [PubMed 9783702]
    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.
  3. 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. [PubMed 17513325]
    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.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PAX2
Diseases sorted by gene-association score: papillorenal syndrome* (1712), glomerulosclerosis, focal segmental, 7* (1300), glomerulosclerosis, focal segmental, 1* (157), renal hypodysplasia* (128), renal hypoplasia (28), multicystic dysplastic kidney (27), renal hypoplasia, bilateral* (25), scleral staphyloma (24), focal segmental glomerulosclerosis (23), vesicoureteral reflux (22), denys-drash syndrome (22), coloboma (20), nephrogenic adenoma (18), rete testis adenoma (16), nail-patella syndrome (15), rete testis neoplasm (15), diffuse mesangial sclerosis (13), acro-renal-ocular syndrome (13), nephrogenic adenoma of urinary bladder (11), endocervical adenocarcinoma (11), childhood endodermal sinus tumor (11), bladder benign neoplasm (11), cervix endometriosis (11), wilms tumor susceptibility-5 (9), branchiootorenal syndrome (9), renal hypodysplasia/aplasia 1 (9), clear cell adenocarcinoma (9), adenocarcinoma in situ (9), spermatocele (9), kidney benign neoplasm (8), oxyphilic adenoma (8), prostatic acinar adenocarcinoma (7), childhood kidney cell carcinoma (7), retinal hemangioblastoma (7), nephrogenic adenofibroma (7), renal adenoma (7), renal dysplasia (6), charge syndrome (6), hemangioblastoma (6), bladder diverticulum (6), endometrial mucinous adenocarcinoma (6), congenital aphakia (6), ureteral disease (5), kidney disease (5), mayer-rokitansky-kuster-hauser syndrome (5), axenfeld-rieger syndrome, type 1 (5), split-hand/foot malformation 3 (4), duane-radial ray syndrome (4), deafness, autosomal dominant 10 (4), split hand-foot malformation 2 (4), ovarian brenner tumor (3), renal cell carcinoma (3), kallmann syndrome (1)
* = Manually curated disease association

-  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: 36.86 RPKM in Kidney - Cortex
Total median expression: 40.71 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 -242.20550-0.440 Picture PostScript Text
3' UTR -924.222258-0.409 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
IPR009057 - Homeodomain-like
IPR001523 - Paired_dom
IPR022130 - Pax2_C
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00292 - 'Paired box' domain
PF12403 - Paired-box protein 2 C terminal

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q02962
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  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

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005764 lysosome
GO:0005794 Golgi apparatus
GO:0005815 microtubule organizing center
GO:0032991 macromolecular complex
GO:0032993 protein-DNA complex
GO:0034451 centriolar satellite

-  Descriptions from all associated GenBank mRNAs
  L25597 - Homo sapiens paired box protein mRNA, complete cds.
M89470 - Human paired-box protein (PAX2) mRNA, complete cds.
JD395544 - Sequence 376568 from Patent EP1572962.
JD460915 - Sequence 441939 from Patent EP1572962.
JD387880 - Sequence 368904 from Patent EP1572962.
JD393253 - Sequence 374277 from Patent EP1572962.
JD456952 - Sequence 437976 from Patent EP1572962.
JD086424 - Sequence 67448 from Patent EP1572962.
JD121861 - Sequence 102885 from Patent EP1572962.
JD312739 - Sequence 293763 from Patent EP1572962.
AB463994 - Synthetic construct DNA, clone: pF1KB9716, Homo sapiens PAX2 gene for paired box 2, without stop codon, in Flexi system.
BC141452 - Synthetic construct Homo sapiens clone IMAGE:100014752, MGC:175366 paired box 2 (PAX2) mRNA, encodes complete protein.
BC148710 - Synthetic construct Homo sapiens clone IMAGE:100015741, MGC:183161 paired box 2 (PAX2) mRNA, encodes complete protein.
LF213819 - JP 2014500723-A/21322: Polycomb-Associated Non-Coding RNAs.
AY153483 - Homo sapiens paired box transcription factor (PAX2) mRNA, partial cds, alternatively spliced.
AY153484 - Homo sapiens paired box transcription factor (PAX2) mRNA, partial cds, alternatively spliced.
LF211342 - JP 2014500723-A/18845: Polycomb-Associated Non-Coding RNAs.
JD339178 - Sequence 320202 from Patent EP1572962.
JD389899 - Sequence 370923 from Patent EP1572962.
JD540015 - Sequence 521039 from Patent EP1572962.
JD457030 - Sequence 438054 from Patent EP1572962.
JD387800 - Sequence 368824 from Patent EP1572962.
JD097000 - Sequence 78024 from Patent EP1572962.
JD461853 - Sequence 442877 from Patent EP1572962.
LF345768 - JP 2014500723-A/153271: Polycomb-Associated Non-Coding RNAs.
JD289216 - Sequence 270240 from Patent EP1572962.
JD465915 - Sequence 446939 from Patent EP1572962.
JD216217 - Sequence 197241 from Patent EP1572962.
JD127529 - Sequence 108553 from Patent EP1572962.
JD060030 - Sequence 41054 from Patent EP1572962.
JD555295 - Sequence 536319 from Patent EP1572962.
JD252258 - Sequence 233282 from Patent EP1572962.
JD256889 - Sequence 237913 from Patent EP1572962.
JD398943 - Sequence 379967 from Patent EP1572962.
JD253115 - Sequence 234139 from Patent EP1572962.
JD216674 - Sequence 197698 from Patent EP1572962.
JD524633 - Sequence 505657 from Patent EP1572962.
JD392869 - Sequence 373893 from Patent EP1572962.
JD541510 - Sequence 522534 from Patent EP1572962.
JD541511 - Sequence 522535 from Patent EP1572962.
JD081793 - Sequence 62817 from Patent EP1572962.
JD107925 - Sequence 88949 from Patent EP1572962.
JD125327 - Sequence 106351 from Patent EP1572962.
JD240351 - Sequence 221375 from Patent EP1572962.
JD289236 - Sequence 270260 from Patent EP1572962.
JD566626 - Sequence 547650 from Patent EP1572962.
JD270818 - Sequence 251842 from Patent EP1572962.
JD191513 - Sequence 172537 from Patent EP1572962.
JD392217 - Sequence 373241 from Patent EP1572962.
JD132838 - Sequence 113862 from Patent EP1572962.
JD259294 - Sequence 240318 from Patent EP1572962.
JD418556 - Sequence 399580 from Patent EP1572962.
MA581345 - JP 2018138019-A/153271: Polycomb-Associated Non-Coding RNAs.
MA449396 - JP 2018138019-A/21322: Polycomb-Associated Non-Coding RNAs.
MA446919 - JP 2018138019-A/18845: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003990, NP_003981, PAX2_HUMAN, Q02962, Q15105, Q15110, Q15837, Q5SZP2, Q5SZP3
UCSC ID: uc001krk.4
RefSeq Accession: NM_003990
Protein: Q02962 (aka PAX2_HUMAN)
CCDS: CCDS53569.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PAX2:
papr (PAX2-Related Disorder)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_003990.3
exon count: 11CDS single in 3' UTR: no RNA size: 4104
ORF size: 1299CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 2732.00frame shift in genome: no % Coverage: 100.00
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.