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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PAX6 Gene

protein-coding GIFtS: 67
GCID: GC11M031806

paired box 6

(Previous names: paired box gene 6 (aniridia, keratitis) )
(Previous symbol: AN2)

Explore 89 diseases affiliated with
PAX6 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Paired Box 6¹ ²		MGDA² ⁵
AN2¹ ² ³ ⁵		Paired Box Gene 6 (Aniridia, Keratitis)¹
AN¹ ²		Oculorhombin³
D11S812E¹ ²		Paired Box Homeotic Gene-6²
WAGR¹ ²		Paired Box Protein Pax-6²
Aniridia Type II Protein² ³		Oculorhombin³

External Ids:	HGNC: 8620¹	Entrez Gene: 5080²	Ensembl: ENSG00000007372⁷	OMIM: 607108⁵	UniProtKB: P26367³

Export aliases for PAX6 gene to outside databases

Previous GC identifers: GC11M033407 GC11M032586 GC11M031849 GC11M031775 GC11M031768 GC11M031501

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PAX6:

This gene encodes paired box gene 6, one of many human homologs of the Drosophila melanogaster gene prd. In addition to

the hallmark feature of this gene family, a conserved paired box domain, the encoded protein also contains a homeo box

domain. Both domains are known to bind DNA and function as regulators of gene transcription. This gene is expressed in

the developing nervous system, and in developing eyes. Mutations in this gene are known to cause ocular disorders such

as aniridia and Peter's anomaly. Alternatively spliced transcript variants encoding multiple isoforms have been

observed for this gene. (provided by RefSeq, May 2012)

UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367

Function: Transcription factor with important functions in the development of the eye, nose, central nervous system and

pancreas. Required for the differentiation of pancreatic islet alpha cells (By similarity). Competes with PAX4 in

binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the

ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Isoform 5a appears to function

as a molecular switch that specifies target genes

Gene Wiki entry for PAX6

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000011.9 NC_018922.1 NT_009237.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PAX6 gene promoter:
PPAR-gamma1 PPAR-gamma2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PAX6 promoter sequence

Search SABiosciences Chromatin IP Primers for PAX6

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PAX6

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p13 Ensembl cytogenetic band: 11p13 HGNC cytogenetic band: 11p13

PAX6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PAX6 gene location

GeneLoc information about chromosome 11 GeneLoc Exon Structure

GeneLoc location for GC11M031806: view genomic region (about GC identifiers)

Start:	31,806,340 bp from pter	End:	31,839,509 bp from pter
Size:	33,170 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367 (See protein sequence)

Recommended Name: Paired box protein Pax-6

Size: 422 amino acids; 46683 Da

Subunit: Interacts with MAF and MAFB (By similarity). Interacts with TRIM11; this interaction leads to ubiquitination

and proteasomal degradation, as well as inhibition of transactivation, possibly in part by preventing PAX6 binding to

consensus DNA sequences (By similarity)

Subcellular location: Nucleus

Developmental stage: Expressed in the developing eye and brain

2 PDB 3D structures from and Proteopedia for PAX6:

2CUE (3D)

6PAX (3D)

Secondary accessions: Q6N006 Q99413

Alternative splicing: 3 isoforms: P26367-1 P26367-2 P26367-3

Explore the universe of human proteins at neXtProt for PAX6: NX_P26367

Post-translational modifications:

Ubiquitinated by TRIM11, leading to ubiquitination and proteasomal degradation (By similarity)¹

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P26367

PAX6 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (7 alternative transcripts):

NP_000271.1 NP_001121084.1 NP_001245391.1 NP_001245392.1 NP_001245393.1 NP_001245394.1 NP_001595.2

ENSEMBL proteins:

ENSP00000368427 ENSP00000368424 ENSP00000451885 ENSP00000368401 ENSP00000431961

ENSP00000241001 ENSP00000368410 ENSP00000450579 ENSP00000368406 ENSP00000368418

ENSP00000451901 ENSP00000450775 ENSP00000368403 ENSP00000451372 ENSP00000452202

ENSP00000452558 ENSP00000435884 ENSP00000397384 ENSP00000435975 ENSP00000450552

ENSP00000431585 ENSP00000388132 ENSP00000404356 ENSP00000436365 ENSP00000404100

Human Recombinant Protein Products:

	EMD Millipore Purified and/or Recombinant PAX6 Protein
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells OriGene Protein Over-expression Lysate (see all 2): PAX6 OriGene Custom Protein Services for PAX6
	GenScript Custom Purified and Recombinant Proteins Services for PAX6
	Novus Biologicals PAX6 Proteins Novus Biologicals PAX6 Lysates
	Browse Sino Biological Recombinant Proteins
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for PAX6

Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000790	nuclear chromatin	IDA	--
GO:0005622	intracellular	--	--
GO:0005634	nucleus	IDA	--
GO:0005730	NOT nucleolus	IDA	--
GO:0005737	cytoplasm	IDA	--

PAX6 for ontologies About GeneDecksing

PAX6 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of PAX6
	R&D Systems Antibodies for PAX6
	OriGene Antibodies (see all 2): PAX6 OriGene Custom Antibody Services for PAX6
	GenScript Custom Superior Antibodies Services for PAX6
	Novus Biologicals PAX6 Antibodies
	Abcam antibodies for PAX6
	Uscn Antibodies for PAX6
	ThermoFisher Antibody for PAX6

Assay Products for PAX6:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	Browse R&D Systems for biochemical assays
	GenScript Custom Assay Services for PAX6
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for PAX6

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

PAX6 for domains About GeneDecksing

5 InterPro domains/families:

IPR001523 Paired_dom

IPR011991 WHTH_trsnscrt_rep_DNA-bd_dom

IPR017970 Homeobox_CS

IPR001356 Homeodomain

IPR009057 Homeodomain-like

Graphical View of Domain Structure for InterPro Entry P26367

ProtoNet protein and cluster: P26367

1 Blocks protein family: IPB001523 Paired box protein

UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367

Similarity: Belongs to the paired homeobox family

Similarity: Contains 1 homeobox DNA-binding domain

Similarity: Contains 1 paired domain

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367

Function: Transcription factor with important functions in the development of the eye, nose, central nervous system and

pancreas. Required for the differentiation of pancreatic islet alpha cells (By similarity). Competes with PAX4 in

binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the

ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Isoform 5a appears to function

as a molecular switch that specifies target genes

Genatlas biochemistry entry for PAX6:

paired box (DNA binding) containing protein 6,with homeo domain,expressed in the central nervous system and endocrine

pancreas,key regulator of eye development and regulator of glial precursors in the ventral neural tube

miRNA Products:		OriGene 3'-UTR Clone (see all 3): PAX6 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat PAX6
		8/131 QIAGEN miScript miRNA Assays for microRNAs that regulate PAX6 (see all 131):
		hsa-miR-579 hsa-miR-140-5p hsa-miR-376b hsa-miR-138-2* hsa-miR-4275 hsa-miR-130b hsa-miR-4273 hsa-miR-518a-5p

		SwitchGear 3'UTR luciferase reporter plasmid: PAX6 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PAX6 (see all 7) OriGene shRNA RFP: PAX6 OriGene siRNA: PAX6
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PAX6

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for PAX6

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PAX6 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PAX6 (see all 3) OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 3): PAX6 (NM_001127612)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for PAX6
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PAX6

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for PAX6
		Search LifeMap BioReagents cell lines for PAX6

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PAX6

Gene Ontology (GO): 5/17 molecular function terms (GO ID links to tree view) (see all 17): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	IDA	--
GO:0000981	sequence-specific DNA binding RNA polymerase II transcription factor activity	IDA	--
GO:0003677	DNA binding	TAS	10441571
GO:0003680	AT DNA binding	IEA	--
GO:0003690	double-stranded DNA binding	IEA	--

PAX6 for ontologies           About GeneDecksing

Animal Models:
     Mouse knock-outs for PAX6: Pax6^tm1Lan Pax6^tm1.1Ued Pax6^tm1Gfs
     15/24 MGI mutant phenotypes (inferred from 38 alleles) (MGI details for Pax6) (see all 24):

behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary
embryogenesis	endocrine/exocrine gland	growth/size	hearing/vestibular/ear	homeostasis/metabolism
immune system	integument	mortality/aging	muscle	nervous system

PAX6 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/6 super-pathways (see all 6) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Transcription factors in neurogenesis

Transcription factors in neurogenesis

1.00

Selected targets of Oct-3/4

Selected targets of Oct-3/4

1.00

Transcriptional Regulatory Network in Embryonic Stem Cell

Transcriptional Regulatory Network in Embryonic Stem Cell

1.00

Rho Family GTPases

ERK Signaling

0.61

Regulation of beta-cell development

Maturity onset diabetes of the young

0.56

Pathway sources
See GeneCards unified pathways
Show all pathways

2 EMD Millipore Pathways for PAX6

	Selected targets of Oct-3/4
	Transcription factors in neurogenesis

2 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for PAX6

	ERK Signaling
	Transcriptional Regulatory Network in Embryonic Stem Cell

1 BioSystems Pathway for PAX6

CDC42 signaling events

1 Kegg Pathway (Kegg details for PAX6):

Maturity onset diabetes of the young

PAX6 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for PAX6

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

5/59 Interacting proteins for PAX6 (P26367^{1, 2, 3} ENSP00000368401⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 59)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
RPL9	P32969³	I2D: score=3
RPL9P7	P32969³	I2D: score=3
RPL9P8	P32969³	I2D: score=3
RPL9P9	P32969³	I2D: score=3
IPO13	O94829²^,³, ENSP00000361418⁴	MINT-67030 I2D: score=7 STRING: ENSP00000361418

About this table

Gene Ontology (GO): 5/65 biological process terms (GO ID links to tree view) (see all 65): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001568	blood vessel development	IMP	7550230
GO:0001654	eye development	TAS	10747901
GO:0001709	cell fate determination	IEA	--
GO:0001764	neuron migration	IEA	--
GO:0002052	positive regulation of neuroblast proliferation	IEA	--

PAX6 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

PAX6 for compounds About GeneDecksing

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PAX6
10/12 Novoseek chemical compound relationships for PAX6 gene (see all 12) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
proglucagon	34.6	2	12697711 (1), 16407227 (1)
retinoic acid	34.5	6	10394471 (1), 17525239 (1), 14743441 (1), 9503603 (1) (see all 5)
serine	12.1	7	19917615 (2), 17893655 (1), 9516413 (1), 11553050 (1) (see all 6)
proline	4.32	6	19917615 (2), 10737978 (1), 9516413 (1), 10955655 (1) (see all 5)
oxygen	0.81	2	15193293 (1), 17318412 (1)
glucose	0	23	19034419 (6), 11756345 (5), 15842522 (2), 16079311 (1) (see all 5)
threonine	0	4	19917615 (2), 11309364 (1), 17374606 (1)
bromodeoxyuridine	0	6	17277739 (2), 17291498 (1), 19378256 (1)
alanine	0	1	10737978 (1)
arginine	0	5	10737978 (1), 10955655 (1), 19806579 (1), 10887930 (1) (see all 5)

Search CenterWatch for drugs/clinical trials and news about PAX6

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for PAX6 gene (7 alternative transcripts):

NM_000280.4 NM_001127612.1 NM_001258462.1 NM_001258463.1 NM_001258464.1 NM_001258465.1 NM_001604.5

Unigene Cluster for PAX6:

Paired box 6

Hs.270303 [show with all ESTs]

Unigene Representative Sequence: NM_000280

18/31 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 31):

ENST00000379132 ENST00000379129 ENST00000531633 ENST00000379107 ENST00000464174

ENST00000241001 ENST00000379115 ENST00000474783 ENST00000379111(uc021qfn.1)

ENST00000379123 ENST00000494377 ENST00000470027 ENST00000379109 ENST00000533333

ENST00000532916 ENST00000530373 ENST00000531910 ENST00000471303

miRNA Products:		OriGene 3'-UTR Clone (see all 3): PAX6 Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat PAX6
		8/131 QIAGEN miScript miRNA Assays for microRNAs that regulate PAX6 (see all 131):
		hsa-miR-579 hsa-miR-140-5p hsa-miR-376b hsa-miR-138-2* hsa-miR-4275 hsa-miR-130b hsa-miR-4273 hsa-miR-518a-5p

		SwitchGear 3'UTR luciferase reporter plasmid: PAX6 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PAX6 (see all 7) OriGene shRNA RFP: PAX6 OriGene siRNA: PAX6
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PAX6

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PAX6 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PAX6 (see all 3) OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 3): PAX6 (NM_001127612)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for PAX6
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PAX6

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PAX6 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat PAX6
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PAX6
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PAX6

Additional cDNA sequence:

AB593092.1 AB593093.1 AB593094.1 AK074881.1 AK094249.1 AK314470.1 AY047583.1 AY707088.1

BC011953.1 BX640762.1 GQ141695.1 M77844.1 M93650.1

24/25 DOTS entries (see all 25):

DT.95169354 DT.100784691 DT.101977743 DT.91760372 DT.99988304 DT.99956569 DT.100784690 DT.100028797

DT.97836474 DT.97817296 DT.120745340 DT.97846449 DT.99979680 DT.100028794 DT.100028796 DT.100784689

DT.120745287 DT.75183575 DT.120745294 DT.120745338 DT.120745385 DT.87046009 DT.97800437 DT.97846450

24/145 AceView cDNA sequences (see all 145):

BQ129937 CD513806 BM712394 BU071804 C00607 BM700064 BM565566 BQ129988

BQ636001 BM696268 AY707088 BI962615 BM697312 BQ286267 BM702077 BE786878

BU738294 CD673930 CA397536 BU729510 CD723903 BC011953 AK094172 CD675778

GeneLoc Exon Structure

5/21 Alternative Splicing Database (ASD) splice patterns (SP) for PAX6 (see all 21) About this scheme

ExUns:	1	^	2	^	3a	·	3b	·	3c	^	4	^	5a	·	5b	·	5c	·	5d	^	6a	·	6b	^	7	^	8	^	9a	·	9b	^	10	^	11a	·	11b	^	12	^	13	^	14	^	15a	·	15b	·	15c	·	15d	·
SP1:													-		-						-		-		-						-		-		-		-		-				-
SP2:																					-		-		-						-		-		-		-		-				-
SP3:																															-		-		-		-		-				-
SP4:													-		-						-		-		-						-		-		-		-		-
SP5:																																							-

ExUns:	15e	^	16	^	17a	·	17b	·	17c	^	18	^	19	^	20	^	21a	·	21b	·	21c	^	22a	·	22b	^	23a	·	23b	^	24
SP1:			-		-						-
SP2:			-		-						-
SP3:			-		-						-
SP4:
SP5:			-		-						-

ECgene alternative splicing isoforms for PAX6

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

PAX6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AACAGTCAGC

About this image

PAX6 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

10/65 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 65)

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Ectoderm

Early Retinal Progenitor Cells

Retina

Eye

Neuroblastic Layer

Late Retinal Progenitor Cells

Retina

Eye

Retinal Pigmented Epithelium

Retinal Pigmented Epithelium Progenitor Cells

Retinal Pigmented Epithelium

Pancreas

Dorsal Pancreatic Bud

Alpha Progenitor Cells

Pancreas

Dorsal Pancreatic Bud

Beta/Delta Progenitor Cells

Pancreas

Islets of Langerhans

Delta Cells

Pancreas

Ventral Pancreatic Bud

Alpha Progenitor Cells

Pancreas

Spinal Cord

Motor Neural Progenitor Domain

Motor Neural Progenitor Cells

Motor Neurons

Spinal Cord

V0 Neural Progenitor Domain

V0 Neural Progenitor Cells

Motor Neurons

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 10/45 LifeMap Cells (see all 45)

Name

Category

Neural rosettes (Generation of motor ...)

GABA neuron-like cells (Generation of motor ...)

Brain

bFGF induced cells (Generation of motor ...)

Neural rosettes (Generation of forebr...)

Lateral Ganglionic Eminence progenitors (Generation of forebr...)

Neuroectoderm cells (Generation of human ...)

Pancreatic endoderm/endocrine precursor-like cells (A scalable, suspensi...)

Endocrine progenitors (Generation of pancre...)

Anterior neural specified EBs (Differentiation of h...)

Optic cup structures (Generation of strati...)

See PAX6 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PAX6

SOURCE GeneReport for Unigene cluster: Hs.270303

UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367

Tissue specificity: Fetal eye, brain, spinal cord and olfactory epithelium. Isoform 5a is less abundant than the PAX6

shorter form

SABiosciences Expression via Pathway-Focused PCR Arrays including PAX6 (see all 6):

Notch Signaling Targets in human mouse rat

Neurogenesis in human mouse rat

Stem Cell Transcription Factors in human mouse rat

Embryonic Stem Cells in human mouse rat

Transcription Factors in human mouse rat

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for PAX6 gene from 6/20 species (see all 20) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	PAX6¹	paired box 6	87.54(n) 99.31(a)		395943 NM_205066.1 NP_990397.1
lizard (Anolis carolinensis)	Reptilia	PAX6⁶	--	98(a)	1 ↔ 1	1(60707886-60734555)
African clawed frog (Xenopus laevis)	Amphibia	MGC52531²	similar to paired box gene 6	79.93(n)		U77532.1
zebrafish (Danio rerio)	Actinopterygii	pax6b²	paired box gene 6b	79.96(n)		60639 AF061252.1
fruit fly (Drosophila melanogaster)	Insecta	ey³ toy¹	glia cell migration transcription factor³ twin of eyeless¹	93(a) (best of 4)³ 58.31(n)¹ 65.45(a)¹		4 102C2³ 43833¹ NM_079899.3¹ NP_524638.3¹
worm (Caenorhabditis elegans)	Secernentea	K06B9.5³ vab-3¹	paired box transcription factor³ Protein VAB-3¹	69(a) (best of 5)³ 55.38(n)¹ 56.15(a)¹		IV(4199863-4204573)³ 181251¹ NM_001029399.2¹ NP_001024570.1¹

ENSEMBL Gene Tree for PAX6 (if available)
TreeFam Gene Tree for PAX6 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for PAX6 gene

PAX7² PAX1² PAX3² PAX5² PAX2² PAX8² PAX9² PAX4²

18/32 SIMAP similar genes for PAX6 using alignment to 29 protein entries: PAX6_HUMAN (see all proteins) (see all similar genes):

PAX5 PAX2 PAX9 Pax9 PAX1 PITX2

PHOX2B PAX7B PAX4 PAX8 PAX7 MNX1

PRRX1 SHOX2 NKX2-5 PITX1 PAX3 RAX2

PAX6 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 11 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs3026402^1,2	H	--	31501393(-)	`TGGTTC/TGATAT`	7	--	ds500¹		4		NS EA	420
rs16922475^1,2	C,F,H,	--	31502604(+)	`CTGGGC/GCGGCT`	7	--	ut3¹		9		NA NS EA CSA WA	676
rs3026400^1,2	C	--	31503653(-)	`TTACTA/TTCATC`	7	--	ut3¹		0	--	--	--	--
rs3026399^1,2	C,F,H,	--	31503919(-)	`GGATGG/AAGATT`	7	--	ut3¹		11		NS EA NA	1260
rs3026398^1,2	C,F,O,A,H,	--	31504201(-)	`AGAAGC/TGGCTG`	7	--	ut3¹		28		NS EA NA WA CSA	2978
rs3026397^1,2	O	--	31504402(-)	`CAGTTC/TCGGCC`	7	--	ut3¹		0	--	--	--	--
rs79739975^1,2	C,	--	31504492(+)	`ATAGCC/ACTTCT`	7	--	ut3¹		2		WA	120
rs73477656^1,2	C,F,	--	31504603(+)	`GTGCTC/TACTCC`	7	--	ut3¹		3		WA	122
rs73477658^1,2	C,	--	31504670(+)	`CACATC/ACAAAA`	7	--	ut3¹		1		WA	2
rs3026395^1,2	H	--	31505129(-)	`AAGTGG/AAGGCA`	7	--	ut3¹		4		NS EA	420

HapMap Linkage Disequilibrium report for PAX6 (31806340 - 31839509 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PAX6: --
Human Gene Mutation Database (HGMD): PAX6

Locus Specific Mutation Databases (LSDB): PAX6

SABiosciences Cancer Mutation PCR Assays

1 SABiosciences qBiomarker Copy Number PCR Array containing PAX6:

Birth Defects

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

PAX6 for disorders           About GeneDecksing

OMIM gene information: 607108
OMIM disorders: 106210  604229  604219  148190  136520  120430  165550  120200  206700
UniProtKB/Swiss-Prot: PAX6_HUMAN, P26367

Defects in PAX6 are the cause of aniridia (AN) [MIM:106210]. A congenital, bilateral, panocular disorder

characterized by complete absence of the iris or extreme iris hypoplasia. Aniridia is not just an isolated defect in

iris development but it is associated with macular and optic nerve hypoplasia, cataract, corneal changes, nystagmus.

Visual acuity is generally low but is unrelated to the degree of iris hypoplasia. Glaucoma is a secondary problem

causing additional visual loss over time

Defects in PAX6 are a cause of Peters anomaly (PAN) [MIM:604229]. Peters anomaly consists of a central corneal

leukoma, absence of the posterior corneal stroma and Descemet membrane, and a variable degree of iris and lenticular

attachments to the central aspect of the posterior cornea

Defects in PAX6 are a cause of foveal hypoplasia (FOVHYP) [MIM:136520]. Foveal hypoplasia can be isolated or

associated with presenile cataract. Inheritance is autosomal dominant

Defects in PAX6 are a cause of keratitis hereditary (KERH) [MIM:148190]. An ocular disorder characterized by

corneal opacification, recurrent stromal keratitis and vascularization

Defects in PAX6 are a cause of coloboma of iris choroid and retina (COI) [MIM:120200]; also known as

uveoretinal coloboma. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic

cup and stalk, and the fusion of the fetal fissure (optic fissure). Severe colobomatous malformations may cause as

much as 10% of the childhood blindness. The clinical presentation of ocular coloboma is variable. Some individuals may

present with minimal defects in the anterior iris leaf without other ocular defects. More complex malformations create

a combination of iris, uveoretinal and/or optic nerve defects without or with microphthalmia or even anophthalmia

Defects in PAX6 are a cause of coloboma of optic nerve (COLON) [MIM:120430]

Defects in PAX6 are a cause of bilateral optic nerve hypoplasia (BONH) [MIM:165550]; also known as bilateral

optic nerve aplasia. A congenital anomaly in which the optic disc appears abnormally small. It may be an isolated

finding or part of a spectrum of anatomic and functional abnormalities that includes partial or complete agenesis of

the septum pellucidum, other midline brain defects, cerebral anomalies, pituitary dysfunction, and structural

abnormalities of the pituitary

Defects in PAX6 are a cause of aniridia cerebellar ataxia and mental deficiency (ACAMD) [MIM:206700]; also

known as Gillespie syndrome. A rare condition consisting of partial rudimentary iris, cerebellar impairment of the

ability to perform coordinated voluntary movements, and mental retardation

20/89 diseases for PAX6 (see all 89): About MalaCards

aniridia peters anomaly morning glory disc anomaly keratitis

anterior segment mesenchymal dysgenesis cataract with late-onset corneal dystrophy rubinstein-taybi syndrome aniridia, cerebellar ataxia, and mental retardation

isolated growth hormone deficiency aniridia, cerebellar ataxia and mental deficiency iris hypoplasia cerebellar ataxia with mental retardation

growth hormone deficiency maturity-onset diabetes of the young foveal hypoplasia optic nerve hypoplasia

cerebellar ataxia glucose intolerance corneal dystrophy coloboma

10 diseases from the University of Copenhagen DISEASES database for PAX6:

Aniridia WAGR syndrome Microphthalmia Coloboma

Keratopathy Congenital nystagmus Myopia Glaucoma

Nephroblastoma Intellectual disability

10/48 Novoseek disease relationships for PAX6 gene (see all 48) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
aniridia	97.8	328	17893655 (7), 15740668 (6), 15842522 (6), 8364574 (5) (see all 99)
anomaly peters	91.3	28	8162071 (5), 20405024 (3), 11756345 (2), 10441571 (1) (see all 17)
wagr syndrome	91.2	11	7896291 (2), 8529675 (1), 15779010 (1), 7527372 (1) (see all 10)
eye abnormalities	79.5	16	9415682 (2), 7951315 (1), 8689689 (1), 10412187 (1) (see all 13)
microphthalmia	76.7	7	17406642 (2), 18385072 (1), 17277739 (1), 19004499 (1) (see all 6)
hypoplasia	72.6	20	10441571 (1), 12953159 (1), 15740668 (1), 16803629 (1) (see all 17)
coloboma	69.2	1	11826019 (1)
anophthalmia	67	2	7951315 (1), 18385377 (1)
wilms tumor	66.1	27	12386836 (2), 1334370 (2), 8717056 (1), 15779010 (1) (see all 17)
microcornea	65.5	1	19004499 (1)

GeneTests: PAX6

Aniridia

Genetic Association Database (GAD): PAX6
Human Genome Epidemiology (HuGE) Navigator: PAX6 (19 documents)

Export disorders for PAX6 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for PAX6 gene, integrated from 9 sources (see all 470):
(articles sorted by number of sources associating them with PAX6)

Utopia: connect your pdf to the dynamic
world of online information

Missense mutation at the C-terminus of PAX6 negatively modulates homeodomain function. (PubMed id 11309364)^{1, 2, 9} Singh S.... Saunders G.F. (2001)
Missense mutations in the most ancient residues of the PAX6 paired domain underlie a spectrum of human congenital eye malformations. (PubMed id 9931324)^{1, 2, 9} Hanson I.M.... van Heyningen V. (1999)
Missense mutations in the DNA-binding region and termination codon in PAX6. (PubMed id 12552561)^{1, 2, 9} Chao L.Y....Saunders G.F. (2003)
Missense mutations in the PAX6 gene in aniridia. (PubMed id 9856761)^{1, 2, 9} Azuma N.... Yamada M. (1998)
Mutations at the PAX6 locus are found in heterogeneous anterior segment malformations including Peters' anomaly. (PubMed id 8162071)^{1, 2, 9} Hanson I.M.... van Heyningen V. (1994)
PAX6 mutations in aniridia. (PubMed id 8364574)^{1, 2, 9} Hanson I.M.... van Heyningen V. (1993)
Mutations of the PAX6 gene detected in patients with a variety of optic-nerve malformations. (PubMed id 12721955)^{1, 2, 9} Azuma N....Yamada M. (2003)
Mutational analysis of PAX6: 16 novel mutations including 5 missense mutations with a mild aniridia phenotype. (PubMed id 10234503)^{1, 2, 9} Groenskov K.... Broendum-Nielsen K. (1999)
PAX6 mutations reviewed. (PubMed id 9482572)^{1, 2, 9} Prosser J. and van Heyningen V. (1998)
The human PAX6 gene is mutated in two patients with aniridia. (PubMed id 1302030)^{1, 3, 9} Jordan T....van Heyningen V. (1992)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 5080	HGNC: 8620	AceView: PAX6	Ensembl:ENSG00000007372	euGenes: HUgn5080
ECgene: PAX6	Kegg: 5080	H-InvDB: PAX6

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for PAX6	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for PAX6	Genetics and Cytogenetics in Oncology and Haematology
Human PAX6 allelic variant database web site	http://pax6.hgu.mrc.ac.uk/
GeneReviews	http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PAX6

Intellectual Property for PAX6 gene
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Patent Information for PAX6 gene:
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GeneCards and IP:
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