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highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c)."}

{"project":"craft-ca-core-ex-dev","denotations":[{"id":"T1715","span":{"begin":9,"end":18},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1716","span":{"begin":19,"end":29},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T1717","span":{"begin":30,"end":34},"obj":"PR_EXT:000012318"},{"id":"T1718","span":{"begin":35,"end":42},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T1719","span":{"begin":97,"end":105},"obj":"SO_EXT:biological_sequence"},{"id":"T1720","span":{"begin":106,"end":118},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1721","span":{"begin":126,"end":136},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T1722","span":{"begin":148,"end":152},"obj":"PR_EXT:000012318"},{"id":"T1723","span":{"begin":153,"end":160},"obj":"CHEBI_PR_EXT:protein"},{"id":"T1724","span":{"begin":184,"end":194},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1725","span":{"begin":195,"end":203},"obj":"SO_EXT:biological_sequence"},{"id":"T1726","span":{"begin":211,"end":215},"obj":"PR_EXT:000012318"},{"id":"T1727","span":{"begin":220,"end":226},"obj":"SO_EXT:0000417"},{"id":"T1728","span":{"begin":228,"end":230},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1729","span":{"begin":258,"end":267},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1730","span":{"begin":268,"end":273},"obj":"SO_EXT:sequence_or_structure_motif"},{"id":"T1731","span":{"begin":293,"end":304},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1732","span":{"begin":331,"end":336},"obj":"SO_EXT:sequence_or_structure_motif"},{"id":"T1733","span":{"begin":357,"end":369},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1734","span":{"begin":400,"end":407},"obj":"NCBITaxon:species"},{"id":"T1735","span":{"begin":416,"end":423},"obj":"NCBITaxon:8296"},{"id":"T1736","span":{"begin":425,"end":444},"obj":"NCBITaxon:8296"},{"id":"T1737","span":{"begin":450,"end":460},"obj":"NCBITaxon:7625"},{"id":"T1738","span":{"begin":462,"end":483},"obj":"NCBITaxon:7656"},{"id":"T1753","span":{"begin":1644,"end":1653},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1754","span":{"begin":1794,"end":1804},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1755","span":{"begin":1805,"end":1812},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T1756","span":{"begin":1879,"end":1890},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1757","span":{"begin":1995,"end":2003},"obj":"CHEBI_EXT:residue"},{"id":"T1758","span":{"begin":2019,"end":2028},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1759","span":{"begin":2161,"end":2171},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T1760","span":{"begin":2172,"end":2179},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T1761","span":{"begin":2202,"end":2213},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T1762","span":{"begin":2217,"end":2221},"obj":"PR_EXT:000012318"},{"id":"T1763","span":{"begin":2236,"end":2245},"obj":"CHEBI_SO_EXT:threonine"},{"id":"T1764","span":{"begin":2257,"end":2267},"obj":"SO_EXT:0000319"},{"id":"T8285","span":{"begin":532,"end":536},"obj":"PR_EXT:000012318"},{"id":"T8286","span":{"begin":537,"end":547},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T8287","span":{"begin":548,"end":555},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T8288","span":{"begin":598,"end":609},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T8289","span":{"begin":613,"end":617},"obj":"PR_EXT:000012318"},{"id":"T8290","span":{"begin":631,"end":638},"obj":"NCBITaxon:species"},{"id":"T8291","span":{"begin":664,"end":672},"obj":"CHEBI_EXT:residue"},{"id":"T8292","span":{"begin":703,"end":716},"obj":"SO_EXT:sequence_substitution_entity_or_process"},{"id":"T8293","span":{"begin":754,"end":767},"obj":"SO_EXT:sequence_substitution_entity_or_process"},{"id":"T8294","span":{"begin":816,"end":825},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T8295","span":{"begin":838,"end":849},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T8296","span":{"begin":900,"end":907},"obj":"CHEBI_SO_EXT:peptide_or_peptide_region"},{"id":"T8297","span":{"begin":920,"end":928},"obj":"CHEBI_EXT:residue"},{"id":"T8298","span":{"begin":946,"end":956},"obj":"CHEBI_SO_EXT:N_terminus_or_N_terminal_region"},{"id":"T1739","span":{"begin":1024,"end":1028},"obj":"PR_EXT:000012318"},{"id":"T1740","span":{"begin":1033,"end":1039},"obj":"SO_EXT:0000417"},{"id":"T1741","span":{"begin":1127,"end":1134},"obj":"CHEBI_PR_EXT:protein"},{"id":"T1742","span":{"begin":1181,"end":1190},"obj":"SO:0000993"},{"id":"T1743","span":{"begin":1239,"end":1245},"obj":"SO_EXT:0000417"},{"id":"T1744","span":{"begin":1313,"end":1323},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T1745","span":{"begin":1392,"end":1401},"obj":"SO_EXT:biological_conservation_process_or_quality"},{"id":"T1746","span":{"begin":1402,"end":1408},"obj":"SO_EXT:0000417"},{"id":"T1747","span":{"begin":1429,"end":1434},"obj":"SO_EXT:sequence_or_structure_motif"},{"id":"T1748","span":{"begin":1458,"end":1463},"obj":"SO_EXT:sequence_or_structure_motif"},{"id":"T1749","span":{"begin":1536,"end":1546},"obj":"CHEBI_SO_EXT:C_terminus_or_C_terminal_region"},{"id":"T1750","span":{"begin":1547,"end":1553},"obj":"SO_EXT:0000417"},{"id":"T1751","span":{"begin":1582,"end":1587},"obj":"SO_EXT:sequence_or_structure_motif"},{"id":"T1752","span":{"begin":1598,"end":1608},"obj":"SO_EXT:0000319"}],"text":"A highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c)."}

{"project":"craft-ca-core-dev","denotations":[{"id":"T1697","span":{"begin":30,"end":34},"obj":"PR:000012318"},{"id":"T1698","span":{"begin":148,"end":152},"obj":"PR:000012318"},{"id":"T1699","span":{"begin":211,"end":215},"obj":"PR:000012318"},{"id":"T1700","span":{"begin":220,"end":226},"obj":"SO:0000417"},{"id":"T1701","span":{"begin":400,"end":407},"obj":"NCBITaxon:species"},{"id":"T1702","span":{"begin":416,"end":423},"obj":"NCBITaxon:8296"},{"id":"T1703","span":{"begin":425,"end":444},"obj":"NCBITaxon:8296"},{"id":"T1704","span":{"begin":450,"end":460},"obj":"NCBITaxon:7625"},{"id":"T1705","span":{"begin":462,"end":483},"obj":"NCBITaxon:7656"},{"id":"T1706","span":{"begin":1024,"end":1028},"obj":"PR:000012318"},{"id":"T1707","span":{"begin":1033,"end":1039},"obj":"SO:0000417"},{"id":"T1708","span":{"begin":1181,"end":1190},"obj":"SO:0000993"},{"id":"T1709","span":{"begin":1239,"end":1245},"obj":"SO:0000417"},{"id":"T1710","span":{"begin":1402,"end":1408},"obj":"SO:0000417"},{"id":"T1711","span":{"begin":1547,"end":1553},"obj":"SO:0000417"},{"id":"T1712","span":{"begin":1598,"end":1608},"obj":"SO:0000319"},{"id":"T1713","span":{"begin":2217,"end":2221},"obj":"PR:000012318"},{"id":"T1714","span":{"begin":2257,"end":2267},"obj":"SO:0000319"},{"id":"T8282","span":{"begin":532,"end":536},"obj":"PR:000012318"},{"id":"T8283","span":{"begin":613,"end":617},"obj":"PR:000012318"},{"id":"T8284","span":{"begin":631,"end":638},"obj":"NCBITaxon:species"}],"text":"A highly conserved C-terminal PAX6 peptide\nWe and others [31-33] noted that there is significant sequence conservation at the C-terminal end of the PAX6 protein. BLAST analysis of the amino acid sequence of the PAX6 PST domain (aa 278–422) revealed a highly conserved motif within the last 28 amino acids (beginning at the 'GLISP' motif, Figure 1a). Strong conservation was seen in distantly related species such as axolotl (Ambystoma mexicanum) and sea urchin (Paracentrotus lividus) (Figure 1a).\nFigure 1 Characterisation of the PAX6 C-terminal peptide. (a) CLUSTAL alignment of the terminal 42 amino acids of PAX6 from diverse species. (*) indicates invariant residues, (:) indicates highly similar substitutions and (.) indicates moderately similar substitutions. (b) Secondary structure analysis of the highly conserved terminal 28 amino acids predicts a single beta sheet (arrow) in the SVPVQ peptide. (c) When 4 residues are added in the N-terminal direction, 2 beta sheets are now predicted. We subjected the whole PAX6 PST domain to secondary structure analysis using JPRED, a program that uses a number of different protein structure prediction algorithms to generate a consensus secondary structure (Figure 1) [25,26]. The PST domain was largely devoid of predicted secondary structure except for the C-terminal region, which contained two predicted beta sheets within the highly conserved domain, one in the 'GLISP' motif and one in the 'SPVPQ' motif (identical to the pattern shown in Figure 1c). Initially we defined the C-terminal domain as running from the 'GLISP' motif up to the stop codon, since this region was most highly conserved and contained strongly predicted secondary structure elements. However when we performed secondary structure prediction analysis on this 28 amino acid peptide, the first beta sheet was lost (Figure 1b). Addition of another 4 amino acids (TTST) immediately before 'GLISP' caused recovery of the first beta sheet (Figure 1c). Although these 4 residues are not highly conserved (Figure 1a), they appear to be important for seeding the first beta sheet and therefore for secondary structure. Thus we define the C-terminal peptide as being the final 32 amino acids of PAX6, running from threonine 391 to the stop codon (top line of Figure 1c)."}