Human Gene PAX2 (ENST00000355243.8) from GENCODE V43
  Description: Homo sapiens paired box 2 (PAX2), transcript variant b, mRNA. (from RefSeq NM_000278)
RefSeq Summary (NM_000278): 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. CCDS Note: The coding region has been updated to add an additional glycine residue in the protein C-terminal region, supported by the available transcript and conservation data.
Gencode Transcript: ENST00000355243.8
Gencode Gene: ENSG00000075891.24
Transcript (Including UTRs)
   Position: hg38 chr10:100,745,582-100,829,944 Size: 84,363 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg38 chr10:100,746,261-100,827,619 Size: 81,359 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-02-17 22:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:100,745,582-100,829,944)mRNA (may differ from genome)Protein (394 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode

-  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="";

-  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: 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

-  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 -302.00679-0.445 Picture PostScript Text
3' UTR -913.502325-0.393 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

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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  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.
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.
MA449396 - JP 2018138019-A/21322: Polycomb-Associated Non-Coding RNAs.
AY153483 - Homo sapiens paired box transcription factor (PAX2) mRNA, partial cds, alternatively spliced.
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.
AY153484 - Homo sapiens paired box transcription factor (PAX2) mRNA, partial cds, alternatively spliced.
LF211342 - JP 2014500723-A/18845: Polycomb-Associated Non-Coding RNAs.
MA446919 - JP 2018138019-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.
MA581345 - JP 2018138019-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.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000355243.1, ENST00000355243.2, ENST00000355243.3, ENST00000355243.4, ENST00000355243.5, ENST00000355243.6, ENST00000355243.7, NM_000278, PAX2_HUMAN, Q02962, Q15105, Q15110, Q15837, Q5SZP2, Q5SZP3, uc001kro.1, uc001kro.2, uc001kro.3, uc001kro.4, uc001kro.5
UCSC ID: ENST00000355243.8
RefSeq Accession: NM_000278
Protein: Q02962 (aka PAX2_HUMAN)
CCDS: CCDS41561.1

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

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