id: P26630 gene_symbol: pax6a product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: >- pax6a is one of two zebrafish co-orthologues of vertebrate PAX6, retained from the teleost-specific genome duplication. It encodes a transcription factor with an N-terminal paired domain and a paired-type homeodomain that binds cis-regulatory DNA and activates target genes; alternative splicing produces short and long (exon 5a-containing) isoforms. pax6a is expressed in the developing retina and lens and, more broadly than its paralogue pax6b, in the telencephalon, diencephalon, hindbrain and spinal cord, but not in the pancreas. It is required for habenular neurogenesis in the dorsal diencephalon, acts together with pax6b in anterior eye segment development, in guidance of periocular neural crest and in hindbrain patterning, and promotes proliferation of Muller glia-derived neuronal progenitors during adult retinal regeneration. The two co-orthologues encode proteins with equivalent transactivation activity; their divergence lies mainly in expression, reflecting differential loss of cis-regulatory elements after duplication. alternative_products: - name: Short id: P26630-1 - name: Long id: P26630-2 sequence_note: VSP_002367 existing_annotations: - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0005558 - MGI:MGI:97485 - MGI:MGI:97486 - MGI:MGI:97488 - MGI:MGI:97489 - MGI:MGI:97490 - PANTHER:PTN002552508 - RGD:3258 - RGD:620434 - UniProtKB:P26367 - UniProtKB:Q06710 - WB:WBGene00001204 - WB:WBGene00003938 review: summary: >- Sequence-specific binding of RNA polymerase II cis-regulatory DNA by the paired domain and homeodomain. action: ACCEPT reason: >- Both zebrafish Pax6 co-orthologues retain complete paired domains and homeodomains and activate paired-domain (CD19) and homeodomain (P3) reporter targets at indistinguishable levels in the same assay (PMID:18282108); both act as transcriptional activators and both induce ectopic eyes in Drosophila (PMID:9831649). The molecular function is therefore conserved in both copies and is correctly shared across the pair. Pax6a activates reporters through a homeodomain target (P3) and a paired-domain target (CD19), which requires sequence-specific binding of these sites. supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - reference_id: PMID:9831649 supporting_text: >- The coding sequences of the two genes show 82% identity whereas the deduced amino acid sequences are 95% identical with complete conservation of the paired- and homeodomains. - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0003145 - FB:FBgn0005558 - FB:FBgn0005561 - MGI:MGI:97485 - MGI:MGI:97486 - MGI:MGI:97487 - MGI:MGI:97488 - MGI:MGI:97489 - MGI:MGI:97490 - MGI:MGI:97491 - MGI:MGI:97493 - PANTHER:PTN002552508 - RGD:3258 - RGD:620434 - UniProtKB:O43316 - UniProtKB:P26367 - ZFIN:ZDB-GENE-001031-1 - ZFIN:ZDB-GENE-990415-200 review: summary: >- pax6a encodes a paired/homeodomain sequence-specific DNA-binding transcription factor; transcriptional activation by Pax6a has been directly measured in reporter assays. action: ACCEPT reason: >- Both zebrafish Pax6 co-orthologues retain complete paired domains and homeodomains and activate paired-domain (CD19) and homeodomain (P3) reporter targets at indistinguishable levels in the same assay (PMID:18282108); both act as transcriptional activators and both induce ectopic eyes in Drosophila (PMID:9831649). The molecular function is therefore conserved in both copies and is correctly shared across the pair. supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - reference_id: PMID:9831649 supporting_text: >- The coding sequences of the two genes show 82% identity whereas the deduced amino acid sequences are 95% identical with complete conservation of the paired- and homeodomains. - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR017970 review: summary: >- pax6a encodes a paired/homeodomain sequence-specific DNA-binding transcription factor; transcriptional activation by Pax6a has been directly measured in reporter assays. action: ACCEPT reason: >- Both zebrafish Pax6 co-orthologues retain complete paired domains and homeodomains and activate paired-domain (CD19) and homeodomain (P3) reporter targets at indistinguishable levels in the same assay (PMID:18282108); both act as transcriptional activators and both induce ectopic eyes in Drosophila (PMID:9831649). The molecular function is therefore conserved in both copies and is correctly shared across the pair. supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - reference_id: PMID:9831649 supporting_text: >- The coding sequences of the two genes show 82% identity whereas the deduced amino acid sequences are 95% identical with complete conservation of the paired- and homeodomains. - term: id: GO:0003309 label: type B pancreatic cell differentiation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:97488 - MGI:MGI:97490 - PANTHER:PTN002900580 - RGD:3258 - ZFIN:ZDB-GENE-001031-1 review: summary: >- IBA transfer of pancreatic beta-cell differentiation to pax6a. pax6a is not expressed in the developing or adult zebrafish pancreas; this ancestral PAX6 role has been partitioned entirely to pax6b. action: REMOVE reason: >- The PAINT node correctly places endocrine-pancreas function in the vertebrate Pax6 clade, and pax6a retains the molecular function. But there is target-specific evidence that pax6a lost this role at the expression level after the teleost genome duplication: pax6a is not expressed in the embryonic or adult pancreas, is not induced there even when pax6b is mutant (PMID:18282108), and its upstream enhancers A and C are inactive in the pancreas because of divergence in PDX1-binding cis-elements (PMID:18485195). The pancreatic endocrine phenotypes are produced by pax6b loss alone (PMID:20177065). A gene not expressed in the tissue does not take part in the differentiation of its cells, so this IBA is a propagation that the expression partition of the duplicate pair does not support. propagation_review: root_cause: PROPAGATION_BAD failure_modes: - CONTEXT_OR_TISSUE_MISMATCH source_entities: - source_id: PANTHER:PTN002900580 source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: >- Node placement is sound for vertebrate Pax6; after the TGD only the pax6b copy kept pancreatic expression. - source_id: ZFIN:ZDB-GENE-001031-1 source_label: pax6b source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET comment: >- Experimental seed from the paralogue pax6b; pancreas-specific, does not transfer to pax6a. supported_by: - reference_id: PMID:18282108 supporting_text: >- only pax6b is expressed in the pancreas isolated from 6 month old wild type and sri/sri fish, while eyes from the same individuals express both pax6a and pax6b - reference_id: PMID:18282108 supporting_text: >- We also showed that pax6a expression is not induced in the pancreas of the sunrise mutant. - reference_id: PMID:18485195 supporting_text: >- While both zebrafish pax6 genes are expressed in the developing eye and nervous system, only pax6b is expressed in the endocrine cells of the pancreas. - reference_id: PMID:18485195 supporting_text: >- In constrast, regions A and C of the zebrafish pax6a gene are not active in the pancreas, this difference being attributable to sequence divergences within two cis-elements binding the pancreatic homeoprotein PDX1. - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - ARBA:ARBA00029224 - InterPro:IPR001356 - InterPro:IPR001523 - InterPro:IPR043182 - InterPro:IPR043565 review: summary: >- DNA binding is correct but general; pax6a binds specific paired-domain and homeodomain sites in cis-regulatory regions. action: ACCEPT reason: >- Broad electronic term, consistent with the more specific IBA term GO:0000978 on this entry. It is not wrong, and IEA terms broader than the IBA/experimental set are acceptable. supported_by: - reference_id: PMID:9831649 supporting_text: >- The coding sequences of the two genes show 82% identity whereas the deduced amino acid sequences are 95% identical with complete conservation of the paired- and homeodomains. - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - FB:FBgn0000625 - FB:FBgn0001147 - FB:FBgn0001148 - FB:FBgn0003129 - FB:FBgn0003130 - FB:FBgn0005561 - FB:FBgn0036285 - MGI:MGI:97486 - MGI:MGI:97487 - MGI:MGI:97489 - MGI:MGI:97490 - MGI:MGI:97491 - MGI:MGI:97492 - PANTHER:PTN002552508 - RGD:3258 - RGD:620434 - UniProtKB:P23760 - UniProtKB:P26367 - UniProtKB:P55771 - UniProtKB:Q02548 - UniProtKB:Q02962 - UniProtKB:Q06710 - UniProtKB:Q8QGS3 - WB:WBGene00001204 - WB:WBGene00003937 - WB:WBGene00003939 - WB:WBGene00006870 - ZFIN:ZDB-GENE-980526-52 - ZFIN:ZDB-GENE-990415-200 - ZFIN:ZDB-GENE-990415-201 - ZFIN:ZDB-GENE-990415-8 review: summary: Nuclear localization is expected for a sequence-specific transcription factor. action: ACCEPT reason: >- PAX6 family transcription factors act in the nucleus; the IBA and the UniProt subcellular-location mapping agree. pax6a activates target reporters, which requires nuclear activity (PMID:18282108). supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 review: summary: Nuclear localization is expected for a sequence-specific transcription factor. action: ACCEPT reason: >- PAX6 family transcription factors act in the nucleus; the IBA and the UniProt subcellular-location mapping agree. pax6a activates target reporters, which requires nuclear activity (PMID:18282108). supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - term: id: GO:0006355 label: regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in supporting_entities: - InterPro:IPR001523 - InterPro:IPR017970 - InterPro:IPR043565 review: summary: pax6a regulates transcription as a DNA-binding transcription factor. action: ACCEPT reason: >- Correct process for a sequence-specific transcription factor with demonstrated activator activity (PMID:9831649, PMID:18282108). supported_by: - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0000625 - FB:FBgn0003145 - FB:FBgn0005558 - FB:FBgn0005561 - FB:FBgn0019650 - FB:FBgn0036285 - MGI:MGI:97485 - MGI:MGI:97486 - MGI:MGI:97487 - MGI:MGI:97488 - MGI:MGI:97489 - MGI:MGI:97490 - MGI:MGI:97491 - MGI:MGI:97493 - PANTHER:PTN002552508 - RGD:3258 - RGD:620434 - UniProtKB:P23760 - UniProtKB:P26367 - UniProtKB:Q02962 - UniProtKB:Q06710 - WB:WBGene00001204 - WB:WBGene00003938 - WB:WBGene00006870 - ZFIN:ZDB-GENE-001031-1 - ZFIN:ZDB-GENE-990415-200 review: summary: pax6a regulates transcription as a DNA-binding transcription factor. action: ACCEPT reason: >- Correct process for a sequence-specific transcription factor with demonstrated activator activity (PMID:9831649, PMID:18282108). supported_by: - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - term: id: GO:0007420 label: brain development evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0005558 - MGI:MGI:97490 - PANTHER:PTN008693041 - RGD:3258 - ZFIN:ZDB-GENE-001031-1 - ZFIN:ZDB-GENE-990415-200 review: summary: >- pax6a is the major brain-expressed pax6 co-orthologue (telencephalon, diencephalon, hindbrain, spinal cord) and is required for habenular neurogenesis. action: ACCEPT reason: >- The PAINT node places the vertebrate Pax6 role in brain development at an ancestral node; pax6a is inside that clade and, if anything, retains most of the ancestral brain expression and cis-regulatory elements (PMID:18282108). Loss-of-function evidence specific to pax6a exists for the habenula (PMID:27387288). supported_by: - reference_id: PMID:18282108 supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - reference_id: PMID:18282108 supporting_text: >- This may be the situation where several brain-specific elements, with spatiotemporal overlap in expression pattern, have been lost from pax6b. - reference_id: PMID:27387288 supporting_text: >- Here, we show that habenular neurogenesis requires the homeobox transcription factor Pax6a and the redundant action of two proneural bHLH factors, Neurog1 and Neurod4. - term: id: GO:0007423 label: sensory organ development evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0000625 - FB:FBgn0005558 - FB:FBgn0036285 - MGI:MGI:97490 - PANTHER:PTN008693041 - RGD:3258 - RGD:620433 - UniProtKB:A0A1L8GJ29 - UniProtKB:P26367 - WB:WBGene00006870 - ZFIN:ZDB-GENE-001031-1 - ZFIN:ZDB-GENE-081022-10 - ZFIN:ZDB-GENE-990415-200 review: summary: >- pax6a contributes to eye development (retina, lens, anterior segment), a sensory organ. action: ACCEPT reason: >- pax6a is expressed in lens and retina (PMID:18282108) and, together with pax6b, is required for lens and anterior eye segment formation; double mutants lack lens, iris and corneal endothelium (PMID:32555736). General but correct. supported_by: - reference_id: PMID:18282108 supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - reference_id: PMID:32555736 supporting_text: >- In concordance with mouse homozygous pax6 mutant phenotypes, zebrafish pax6a-/-;pax6b-/- double homozygous mutants showed severe defects in distal eye structures, lacking the lens, iris, corneal endothelium and ganglion cell layer of the retina. - term: id: GO:0008284 label: positive regulation of cell population proliferation evidence_type: IMP original_reference_id: PMID:20152834 qualifier: involved_in review: summary: >- Morpholino knockdown of pax6a in the light-damaged adult retina reduced later divisions of Muller glia-derived neuronal progenitors. action: MODIFY reason: >- The IMP is sound, but the proliferating cells are specifically Muller glia-derived neuronal progenitors during photoreceptor regeneration (PMID:20152834); Muller glia and rod precursor proliferation were not Pax6-dependent. A term naming neural precursor proliferation is more accurate than generic cell population proliferation. This is a regeneration context, so non-core. proposed_replacement_terms: - id: GO:2000179 label: positive regulation of neural precursor cell proliferation supported_by: - reference_id: PMID:20152834 supporting_text: >- In contrast, the paralogous Pax6a protein was required for later neuronal progenitor cell divisions, which maximized the number of neuronal progenitors. - reference_id: PMID:20152834 supporting_text: >- This work also defines distinct roles for Pax6a and Pax6b in regulating neuronal progenitor cell proliferation in the adult zebrafish retina - term: id: GO:0009952 label: anterior/posterior pattern specification evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027259 review: summary: >- ARBA-predicted role in anterior/posterior pattern specification; supported by reduced pax6a/pax6b activity anteriorizing the hoxd4a expression border. action: KEEP_AS_NON_CORE reason: >- Knockdown of pax6a and/or pax6b malformed rhombomere boundaries and shifted the hoxd4a border (PMID:17010333), consistent with a conserved Pax6 input to Hoxd4 enhancer activity. A peripheral patterning role, not the core function. supported_by: - reference_id: PMID:17010333 supporting_text: >- Additionally, stage-matched zebrafish embryos having decreased pax6a and/or pax6b activity display malformed rhombomere boundaries and an anteriorized hoxd4a expression border. - term: id: GO:0030154 label: cell differentiation evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027429 review: summary: >- Very general term; pax6a acts in differentiation of several neural and ocular cell types. action: KEEP_AS_NON_CORE reason: >- Not wrong, but uninformative; the specific developmental processes (habenula, retina, lens/anterior segment) are captured by other annotations. supported_by: - reference_id: PMID:27387288 supporting_text: >- Here, we show that habenular neurogenesis requires the homeobox transcription factor Pax6a and the redundant action of two proneural bHLH factors, Neurog1 and Neurod4. - term: id: GO:0030900 label: forebrain development evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:97490 - PANTHER:PTN002900580 - RGD:3258 - ZFIN:ZDB-GENE-001031-1 - ZFIN:ZDB-GENE-990415-200 review: summary: >- pax6a is broadly expressed in the telencephalon and diencephalon and is required for habenular (dorsal diencephalon) neurogenesis. action: ACCEPT reason: >- Supported by the forebrain expression of pax6a (PMID:18282108) and by pax6a-specific loss of habenular neurogenesis markers (PMID:27387288); double knockdown of pax6a and pax6b expands MDO shh expression and disrupts epithalamus formation (PMID:24528677). supported_by: - reference_id: PMID:18282108 supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - reference_id: PMID:27387288 supporting_text: >- Somewhat surprisingly, on the other hand, morpholino knock-down of pax6a alone abrogated the expression of both markers (Fig 2C and 2G); pax6a morphant/pax6bsa86 mutant embryos behaved the same as pax6a morphants alone with respect to these markers (Fig 2D and 2H). - reference_id: PMID:24528677 supporting_text: >- we show that pax6 controls the formation of the epithalamus mostly via the regulation of MDO shh expression in zebrafish. - term: id: GO:0030902 label: hindbrain development evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00088342 review: summary: >- ARBA-predicted role in hindbrain development; pax6a is expressed in hindbrain and knockdown malformed rhombomere boundaries. action: KEEP_AS_NON_CORE reason: >- pax6a is expressed in the hindbrain (PMID:18282108) and reduced pax6a and/or pax6b activity malformed rhombomere boundaries (PMID:17010333). Supported but peripheral. supported_by: - reference_id: PMID:18282108 supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - reference_id: PMID:17010333 supporting_text: >- Additionally, stage-matched zebrafish embryos having decreased pax6a and/or pax6b activity display malformed rhombomere boundaries and an anteriorized hoxd4a expression border. - term: id: GO:0042670 label: retinal cone cell differentiation evidence_type: IMP original_reference_id: PMID:20152834 qualifier: involved_in review: summary: >- Cone photoreceptor regeneration after light damage was reduced after pax6a knockdown, but the reduction was not statistically significant and is secondary to reduced progenitor amplification. action: MARK_AS_OVER_ANNOTATED reason: >- The paper (full text read) reports that the pax6a morphant retina had cone regeneration intermediate between controls and pax6b morphants and that the difference from controls was not statistically significant (PMID:20152834). The effect of Pax6a is on the number of Muller glia-derived neuronal progenitors; fewer cones follow from fewer progenitors. Pax6a function is better captured by the progenitor-proliferation term. supported_by: - reference_id: PMID:20152834 supporting_text: >- the pax6a morphant retina exhibited a level of cone cell regeneration intermediate to the controls and the pax6b morphant and pax6a/pax6b double morphants - reference_id: PMID:20152834 supporting_text: although this value was not statistically significant relative to the controls - reference_id: PMID:20152834 supporting_text: >- The reduced number of INL neuronal progenitor cells in both Pax6 knockdown retinas resulted in a corresponding loss of regenerated cones, but not rods. - term: id: GO:0045944 label: positive regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027996 review: summary: pax6a activates transcription from Pax6 target sites. action: ACCEPT reason: >- Pax6a (Pax6.1) acts as a transcriptional activator in reporter assays (PMID:9831649, PMID:18282108). supported_by: - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - term: id: GO:0048593 label: camera-type eye morphogenesis evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00091222 review: summary: pax6a takes part in camera-type eye morphogenesis together with pax6b. action: ACCEPT reason: >- pax6a is expressed in lens epithelium and retina (PMID:32555736, PMID:18282108); pax6a;pax6b double mutants lack lens, iris and corneal endothelium, and anterior segment defects scale with the number of mutant pax6a/b copies (PMID:32555736). supported_by: - reference_id: PMID:32555736 supporting_text: >- In the WT, the lens epithelium located on the distal end expresses pax6a (E, black arrow) and pax6b (F, black arrow). - reference_id: PMID:32555736 supporting_text: >- In concordance with mouse homozygous pax6 mutant phenotypes, zebrafish pax6a-/-;pax6b-/- double homozygous mutants showed severe defects in distal eye structures, lacking the lens, iris, corneal endothelium and ganglion cell layer of the retina. - reference_id: PMID:32555736 supporting_text: >- Largely, AS phenotypes of pax6a/b single and double mutants supported an overall correlation between the degree of reduced pax6a/b gene copy number and the severity of ASD (Fig 6B–6I), as observed in mouse studies [11][33]. - term: id: GO:0060041 label: retina development in camera-type eye evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:97490 - PANTHER:PTN002900580 - RGD:3258 - RGD:620433 - ZFIN:ZDB-GENE-081022-10 - ZFIN:ZDB-GENE-990415-200 review: summary: >- pax6a is expressed in the developing retina and acts in retinal development, shared with pax6b. action: ACCEPT reason: >- Retinal expression of pax6a is established (PMID:18282108) and double mutants lack the retinal ganglion cell layer (PMID:32555736). The IBA is consistent with the conserved ancestral role. supported_by: - reference_id: PMID:18282108 supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - reference_id: PMID:32555736 supporting_text: >- In concordance with mouse homozygous pax6 mutant phenotypes, zebrafish pax6a-/-;pax6b-/- double homozygous mutants showed severe defects in distal eye structures, lacking the lens, iris, corneal endothelium and ganglion cell layer of the retina. - term: id: GO:0060221 label: retinal rod cell differentiation evidence_type: IMP original_reference_id: PMID:20152834 qualifier: involved_in review: summary: Rod photoreceptor regeneration after light damage did not depend on Pax6a. action: REMOVE reason: >- The cited paper itself shows that reduction of neuronal progenitors after pax6 knockdown reduced regenerated cones but not rods, and that rods regenerate from resident ONL rod precursors whose proliferation is not directly dependent on Pax6 (PMID:20152834). The rod differentiation annotation is contradicted by the full text of its own source. supported_by: - reference_id: PMID:20152834 supporting_text: >- The reduced number of INL neuronal progenitor cells in both Pax6 knockdown retinas resulted in a corresponding loss of regenerated cones, but not rods. - reference_id: PMID:20152834 supporting_text: >- Furthermore, the increased number of PCNA-positive rod precursor cells in both the pax6b and the pax6a morphant retinas clearly shows that rod precursor proliferation is not directly dependent of Pax6. - term: id: GO:0021986 label: habenula development evidence_type: IMP original_reference_id: PMID:27387288 review: summary: pax6a is required for habenular neurogenesis; pax6b is not. action: NEW reason: >- Morpholino knockdown of pax6a abolished expression of the habenular neuron markers cxcr4b and brn3a, whereas pax6b null mutants had normal habenular markers (PMID:27387288). pax6a acts upstream of neurog1/neurod4 in habenular progenitors, so the transcription factor does the regulatory work of this developmental process. ZFIN has made this IMP annotation to pax6a, but on RefSeq-derived UniProt accessions (e.g. A0A8M3AP00), not on the Swiss-Prot entry P26630 reviewed here. supported_by: - reference_id: PMID:27387288 supporting_text: >- Here, we show that habenular neurogenesis requires the homeobox transcription factor Pax6a and the redundant action of two proneural bHLH factors, Neurog1 and Neurod4. - reference_id: PMID:27387288 supporting_text: >- Homozygous pax6bsa86 mutant embryos display cxcr4b and brn3a expression in the habenulae largely indistinguishable from that of wild type siblings (Fig 2A, 2B, 2E and 2F). - reference_id: PMID:27387288 supporting_text: >- Somewhat surprisingly, on the other hand, morpholino knock-down of pax6a alone abrogated the expression of both markers (Fig 2C and 2G); pax6a morphant/pax6bsa86 mutant embryos behaved the same as pax6a morphants alone with respect to these markers (Fig 2D and 2H). - term: id: GO:0021538 label: epithalamus development evidence_type: IGI original_reference_id: PMID:24528677 review: summary: >- Combined pax6a/pax6b knockdown expands MDO shh expression and disrupts epithalamus formation. action: NEW reason: >- Double knockdown of pax6a and pax6b expanded the MDO shh domain and pax6 controls epithalamus formation via shh (PMID:24528677). The same IGI is on pax6b in GOA and is made by ZFIN to pax6a on RefSeq-derived accessions only; it should be shared across the pair. Consistent with the pax6a-specific habenula result (PMID:27387288). supported_by: - reference_id: PMID:24528677 supporting_text: >- Similar to the loss of Pax6 in mice, blockage of the function of both zebrafish homologues pax6a and pax6b by morpholino oligomers led to an expansion of the MDO shh expression domain - reference_id: PMID:24528677 supporting_text: >- we show that pax6 controls the formation of the epithalamus mostly via the regulation of MDO shh expression in zebrafish. - reference_id: PMID:27387288 supporting_text: >- Somewhat surprisingly, on the other hand, morpholino knock-down of pax6a alone abrogated the expression of both markers (Fig 2C and 2G); pax6a morphant/pax6bsa86 mutant embryos behaved the same as pax6a morphants alone with respect to these markers (Fig 2D and 2H). - term: id: GO:0001755 label: neural crest cell migration evidence_type: IGI original_reference_id: PMID:32555736 review: summary: >- pax6a and pax6b together guide two periocular neural crest waves into the anterior eye segment. action: NEW reason: >- Compound pax6a/pax6b mutants misroute neural crest cells in a gene-dose-dependent way (PMID:32555736). The IGI is present on pax6b in GOA and is made by ZFIN to pax6a on RefSeq-derived accessions only; the genetic evidence involves both copies. The effect is partly non-cell-autonomous (lens and guidance cues), so this is a non-core annotation. supported_by: - reference_id: PMID:32555736 supporting_text: >- By analysing zebrafish pax6a/b compound mutants presenting anterior segment dysgenesis, we demonstrate that Pax6a/b guide the two NC populations to distinct proximodistal locations. - reference_id: PMID:32555736 supporting_text: >- Taken together, our data are consistent with a gene number dependent effect of pax6a/b on the migration of the two distinct waves of NC cells. - reference_id: PMID:32555736 supporting_text: >- In double heterozygous mutants, pax6a+/-;pax6b+/-, the 2°NC entry into the distal eye compartment was affected in nearly half of the embryos (39%, Table 1), suggesting that this pax6 gene number provides a borderline dose of Pax6 protein. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000044 title: >- Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:9831649 title: Zebrafish contains two pax6 genes involved in eye development. findings: - statement: Both zebrafish Pax6 proteins are transcriptional activators. supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only; Pax6.1 = pax6a (naming confirmed in PMID:18282108). - id: PMID:17010333 title: >- Stereospecificity and PAX6 function direct Hoxd4 neural enhancer activity along the antero-posterior axis. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; knockdown of pax6a and/or pax6b. - id: PMID:18282108 title: >- Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. findings: - statement: >- Pax6a and Pax6b activate paired-domain and homeodomain reporter targets at equivalent levels. supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different, in contrast to the original observations by Nornes et al [43]. - statement: >- Only pax6b is expressed in the pancreas; pax6a is not induced there in sunrise mutants. supporting_text: >- only pax6b is expressed in the pancreas isolated from 6 month old wild type and sri/sri fish, while eyes from the same individuals express both pax6a and pax6b - statement: pax6a has the broader neural expression domain and lacks pancreatic expression. supporting_text: >- pax6a is expressed in the lens and retina, as well as more widely in the developing telencephalon, diencephalon, hind brain, and spinal cord, although not in developing pancreas [49]. - statement: The pax6a locus retains most ancestral cis-regulatory elements. supporting_text: >- Zebrafish LG25 retains pax6a synteny with wt1a and with the majority of pax6 cis-regulatory elements, but rcn1 and elp4 coding exons have been lost. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text read; key pair paper; tests both copies in the same reporter assay. - id: PMID:18485195 title: >- Expression of zebrafish pax6b in pancreas is regulated by two enhancers containing highly conserved cis-elements bound by PDX1, PBX and PREP factors. findings: - statement: pax6a enhancers A and C are inactive in pancreas owing to PDX1-site divergence. supporting_text: >- In constrast, regions A and C of the zebrafish pax6a gene are not active in the pancreas, this difference being attributable to sequence divergences within two cis-elements binding the pancreatic homeoprotein PDX1. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; explains pax6a absence from pancreas. - id: PMID:20152834 title: >- Pax6a and Pax6b are required at different points in neuronal progenitor cell proliferation during zebrafish photoreceptor regeneration. findings: - statement: >- Pax6a is required for later divisions of regenerating retinal neuronal progenitors. supporting_text: >- In contrast, the paralogous Pax6a protein was required for later neuronal progenitor cell divisions, which maximized the number of neuronal progenitors. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text read; morpholino study of both copies in adult retinal regeneration. - id: PMID:20177065 title: >- The Pax6b homeodomain is dispensable for pancreatic endocrine cell differentiation in zebrafish. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: pax6b-specific pancreas study; context for pax6a absence from pancreas. - id: PMID:23359656 title: >- Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Pax6 family evolution; zebrafish pair from FSGD. - id: PMID:24528677 title: >- Pax6 regulates the formation of the habenular nuclei by controlling the temporospatial expression of Shh in the diencephalon in vertebrates. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Double knockdown only; does not separate the copies. - id: PMID:24951566 title: >- Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene. findings: - statement: pax6a and pax6b arose in the teleost-specific genome duplication. supporting_text: >- By conducting rigorous molecular phylogenetic analyses and considering conserved synteny, we demonstrate that Pax4, -6, and -10 originated in the 2R-WGD, and that the two pax6 genes of teleost fishes (pax6a and pax6b) were duplicated in the TSGD. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Phylogenetic/synteny confirmation of TGD origin. - id: PMID:25692557 title: >- Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: pax6b mutant cornea; mentions pax6a complementation hypothesis. - id: PMID:27387288 title: >- Habenular Neurogenesis in Zebrafish Is Regulated by a Hedgehog, Pax6 Proneural Gene Cascade. findings: - statement: Habenular neurogenesis requires pax6a but not pax6b. supporting_text: >- Somewhat surprisingly, on the other hand, morpholino knock-down of pax6a alone abrogated the expression of both markers (Fig 2C and 2G); pax6a morphant/pax6bsa86 mutant embryos behaved the same as pax6a morphants alone with respect to these markers (Fig 2D and 2H). reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text read; direct comparison pax6a morphant vs pax6b null mutant in habenula. - id: PMID:32555736 title: >- Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves. findings: - statement: >- pax6a/b dosage controls periocular neural crest guidance and anterior segment formation. supporting_text: >- Taken together, our data are consistent with a gene number dependent effect of pax6a/b on the migration of the two distinct waves of NC cells. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text read; CRISPR pax6a allele and pax6a/b compound mutants. - id: PMID:37094695 title: >- Medaka (Oryzias latipes) Olpax6.2 acquires maternal inheritance and germ cells expression, but functionally degenerate in the eye. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Medaka pax6 duplicates; lineage contrast only; abstract only. core_functions: - description: >- Sequence-specific DNA-binding transcription factor (paired domain plus homeodomain) that activates RNA polymerase II target genes; activity equivalent to that of pax6b. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0006357 label: regulation of transcription by RNA polymerase II locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:18282108 supporting_text: >- Activation by the two wild type co-orthologues through the P3 homeodomain target [45] (Figure 1D), or the CD19 paired domain target [46] (Figure 1E), was not significantly different - reference_id: PMID:9831649 supporting_text: >- Both Pax6.1 and Pax6.2 can act as transcriptional activators with Pax6.2 being more efficient than Pax6.1. - description: >- Transcriptional regulator of forebrain development; required (without pax6b) for habenular neurogenesis in the dorsal diencephalon. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0021986 label: habenula development - id: GO:0030900 label: forebrain development locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:27387288 supporting_text: >- Here, we show that habenular neurogenesis requires the homeobox transcription factor Pax6a - description: >- Shared with pax6b in a dose-dependent manner: development of the retina, lens and anterior eye segment. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0060041 label: retina development in camera-type eye - id: GO:0048593 label: camera-type eye morphogenesis locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: PMID:32555736 supporting_text: >- Largely, AS phenotypes of pax6a/b single and double mutants supported an overall correlation between the degree of reduced pax6a/b gene copy number and the severity of ASD suggested_questions: - question: >- ZFIN's experimental annotations for pax6a (e.g. IMP habenula development, IGI neural crest cell migration, IDA transcription factor activity) are attached in GOA to RefSeq-derived TrEMBL accessions (A0A8M3AP00 and others) but not to the Swiss-Prot entry P26630. Should the ZFIN-to-UniProt mapping be fixed so the canonical entry carries them? experts: - ZFIN curators - UniProt - question: >- Does pax6a in the eye carry any function that pax6b cannot supply at equal dose, or is the pair redundant in the eye apart from expression level? suggested_experiments: - hypothesis: >- pax6a and pax6b proteins are interchangeable; the copies differ only in cis-regulation. description: >- Knock the pax6b coding sequence into the pax6a locus (and vice versa) and test rescue of habenular neurogenesis and eye phenotypes in single and double mutants. experiment_type: coding-sequence swap / cross-rescue - hypothesis: >- pax6a mutant phenotypes are mild partly because of maternal transcripts or transcriptional adaptation by pax6b. description: >- Compare maternal-zygotic pax6a mutants carrying a PTC allele with a promoter-deletion (RNA-less) allele, and measure pax6b levels in each. experiment_type: genetic compensation test