http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=Xiaoshui 2026-08-27T17:47:27Z User contributions MediaWiki 1.30.0 https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183151 2014-06-10T03:14:22Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms.As showed in Fig C, Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figureB.png]]<br /> [[File:FF figure5.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> [[File:FF figureC.png]]<br /> [[File:FF figure3.png]]<br /> <br /> <br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183150 2014-06-10T03:13:43Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms.As showed in Fig C, Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> [[File:FF figure1.png]]<br /> [[File:FF figureB.png]]<br /> [[File:FF figure5.png]]<br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> [[File:FF figureC.png]]<br /> [[File:FF figure3.png]]<br /> <br /> <br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183146 2014-06-10T03:12:13Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms.As showed in Fig C, Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> [[File:FF figureB.png]]<br /> [[File:FF figure5.png]]<br /> [[File:FF figureC.png]]<br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> <br /> <br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183143 2014-06-10T03:10:15Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms.As showed in Fig C, Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> [[File:FF figure5.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> [[File:FF figureB.png]]<br /> [[File:FF figureC.png]]<br /> <br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183135 2014-06-10T03:00:59Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> [[File:FF figure5.png]]<br /> [[File:FF figureB.png]]<br /> [[File:FF figureC.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:FF_figureC.png&diff=183134 2014-06-10T03:00:30Z

<p>Xiaoshui: </p> <hr /> <div></div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183133 2014-06-10T03:00:11Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> [[File:FF figure5.png]]<br /> [[File:FF figureB.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:FF_figureB.png&diff=183131 2014-06-10T02:59:36Z

<p>Xiaoshui: </p> <hr /> <div></div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183130 2014-06-10T02:59:18Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> [[File:FF figure5.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:FF_figure5.png&diff=183128 2014-06-10T02:58:23Z

<p>Xiaoshui: </p> <hr /> <div></div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183124 2014-06-10T02:56:21Z

<p>Xiaoshui: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> [[File:FF figure3.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:FF_figure3.png&diff=183122 2014-06-10T02:55:44Z

<p>Xiaoshui: </p> <hr /> <div></div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=183119 2014-06-10T02:55:16Z

<p>Xiaoshui: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> [[File:FF figure1.png]]<br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:FF_figure1.png&diff=183116 2014-06-10T02:53:42Z

<p>Xiaoshui: </p> <hr /> <div></div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0512200&diff=181901 2014-06-09T06:32:57Z

<p>Xiaoshui: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> <br /> <br /> An essential protein in the yeast or Arabidopsis autophagic pathway is Atg8. OsAtg8 conjugation pathway may be conserved in rice and may play important roles in rice autophagy.[1]<br /> <br /> Autophagy occurs at low basal levels in virtually all cells to perform homeostatic functions such as protein and organelle turnover. It is rapidly upregulated when cells need to generate intracellular nutrients and energy, for example, during starvation or high bioenergetic demands. Autophagy is also upregulated when cells are preparing to undergo structural remodeling such as during developmental transitions or to rid themselves of damaging cytoplasmic components, for example, during oxidative stress, infection, or protein aggregate accumulation. Nutritional status, hormonal factors, and other cues like temperature, oxygen concentrations, and cell density are important in the control of autophagy. [2]<br /> <br /> ATG8 is a critical component of the autophagy pathway and it is lipid-modified upon activation of autophagy, leading to its association with autophagosomes（7）.<br /> <br /> ===Expression===<br /> <br /> <br /> OsAtg8 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice.[1]<br /> <br /> ===Evolution===<br /> The formation of the autophagosome is carried out by a set of autophagy-related proteins (Atg), highly conserved from yeast to mammals. The Atg8s play an essential role in autophagosome biogenesis. This family of proteins comprises a single member in yeast and several mammalian homologues.[3]<br /> <br /> A recent genome-wide search revealed significant conservation among autophagy genes (Atgs) in yeast and Arabidopsis, indicating that the molecular basis of autophagy is well conserved in yeast and plants. In Arabidopsis, 25 Atg genes that are homologous to 12 of yeast Atg genes were found [4]. Among them, AtAtg7 and AtAtg9 have been shown to be involved in Arabidopsis autophagy [5], AtAtg8 and AtAtg4 are essential for Arabidopsis autophagy [6].<br /> <br /> ==Labs working on this gene==<br /> Wei Su, Haijie Ma, Chao Liu, Jiaxu Wu<br /> Institute of Genetics, State Key Laboratory of Genetic<br /> Engineering, School of Life Sciences, Fudan University, 220<br /> Handan Road, Shanghai 200433, China<br /> <br /> ==References==<br /> [1]Wei Su ,Haijie Ma ,etc.(2006)Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4.Mol Biol Rep (2006) 33:273–278<br /> <br /> [2]Beth Levine and Guido Kroemer.(2008)Autophagy in the Pathogenesis of Disease.Cell 132, January 11, 2008<br /> <br /> [3]Slobodkin MR1, Elazar Z.(2013)The Atg8 family: multifunctional ubiquitin-like key regulators of autophagy.Essays Biochem. 2013;55:51-64.<br /> <br /> [4]Hanaoka H, Noda T, Shirano Y, Kato T, Hayashi H, Shibata D, Tabata S, Ohsumi Y (2002) Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene. Plant Physiol 129:1181–1193<br /> <br /> [5]Doelling JH, Walker JM, Friedman EM, Thompson AR, Vierstra RD (2002) The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J Biol Chem 277:33105–33114<br /> <br /> [6]Yoshimoto K, Hanaoka H, Sato S, Kato T, Tabata S, Noda T, Ohsumi Y (2004) Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for<br /> plant autophagy. Plant Cell 16:2967–2983<br /> <br /> （7）Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os07g0512200|<br /> Description = Similar to Symbiosis-related like protein|<br /> Version = NM_001066302.1 GI:115472336 GeneID:4343365|<br /> Length = 2701 bp|<br /> Definition = Oryza sativa Japonica Group Os07g0512200, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br /> AP = Chromosome 7:20285683..20288383|<br /> CDS = 20286147..20286241,20286327..20286445,20286846..20286898,20286988..20287043,20288034..20288070&lt;br&gt;|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008400:20285683..20288383<br /> source=RiceChromosome07<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008400:20285683..20288383<br /> source=RiceChromosome07<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggccaggacttccttcaagctcgagcacccactggaaaggaggcaagcagaatctgccaggatccgtgagaagtactcagacagaattccggtgatcgttgagaaggctgacaagaccgatgttccagaaattgacaaaaagaagtaccttgtccctgctgatcttactgttggccagtttgtctatgtggttcggaagaggattaagcttagcccagaaaaggccatctttgtctttgtgaagaacacattgccgccaactgcttctttgatgtctgcaatctacgaagagaacaaggatgaggacggcttcctctacatgacttacagtggcgagaacacattcggctctgcgtaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MARTSFKLEHPLERRQAESARIREKYSDRIPVIVEKADKTDVPE IDKKKYLVPADLTVGQFVYVVRKRIKLSPEKAIFVFVKNTLPPTASLMSAIYEENKDE DGFLYMTYSGENTFGSA&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2143..2237#1939..2057#1486..1538#1341..1396#314..350#aaaccctaccgcgacttccttccttccttccggttgcttccgccgatcgacttctcgccccccaaatcgattcgccccccgcctcgatctatcgattccgcggcagcgccccttcgatcggtgagcctctcgtctcgatcccccaacggagccggccgaattcgcgaggattcgggaggttttccctctgcgttcgtttctgcggatgatttgttttttttttcttttggtggatcggtttgatcgaggggagacgttgaccttgggggtttgtttctgatgatcgattgatgatttgattcgcaggttggagatggccaggacttccttcaagctcgagcacccactgggtttgttgcttcttctctctcgccccattacctctttgccctgtcaatttgttgcgattaggttgcaatctgtgattcgatcgatggtgtggtggtagattgattgcgagtttgtagatgggcgttttataatcggaactagctttgcgtttttgtgtggtatatgatgatctgattgtagattatatatgagtactacttttgtggagactgccttgtgtgtgggattgttttgtcgggcgttgtgtttgttgttggagtatgatttggcccacccaaggattgattttttcttttggttgcgtgtgttgcatattggtcttgagctgttttttagttgcagaagaggactctgtagtttacggtcgcttgtttccagaacaaaagtttaaactctgggatacttgttttattcccagttgcaaaagggtttttcatcatattcggactaacacaatgcttattgtatagatttttgtcggtagttctattactcgtaacacaatgcttattcttcggtagttccattactcgtggcagataacatcaaatgtccaattaagcaaacatatttgttcttgttgatctagtctgttttatgattgaattgtgttcaatgcgcattgttgtttcaataataaactgtttcatgtattgaacttgtttacttcagtcttcaatatatcatgattctcttgattagcagtaccctgtttactggtggttggaacatgctgtactttgtatttatttgattgagccttgaacatatttgctaatctaagaaaagctagcttgtacaagaggttgagatgatattttttcttctatttatctgctttacacttagcacagattacccctaattccattagtgtagcagaaccaactgtgaaaagaaaaaaaaaacattcccgactatgtttatgtcaaccacatgtaatttgcatatagcatcttatgatgtttgtattttgaatgatattgcagaaaggaggcaagcagaatctgccaggatccgtgagaagtactcagacagaattccggtaatatatctctgctgtttactttttcgtttgtgcatatctcctatatgcatctgtcttatcaaaaattctgcgatatgctatttcaggtgatcgttgagaaggctgacaagaccgatgttccagaaattgacaaaaagaagtaagctttcttttccacatctcctttattatgacgggagatgttctatctcatggttgcttatatcagctactaaagctttttttttatgtatgagagggcttccatttttcctctcctttttaacacctgctttagttggaggaagataaaataggagcaacttttctttcacattgggttctatctaactcaatcaggcctaatttcgctttagatgtcctgtattctctggaatttggcttgctatgttctatttgtttggttagtacttagtactctttatttatgttgcttattgacttagaatacccaggcatctgctattaattgaattgaaatcctgaaatattaaccttctcttggatacacacatctttgttttttttttctgatgtaggtaccttgtccctgctgatcttactgttggccagtttgtctatgtggttcggaagaggattaagcttagcccagaaaaggccatctttgtctttgtgaagaacacattgccgccaactggtaaattcattgttcttgatttgtcattgtcatatcacctacccttttggtttccttatattttgcgcatacattctattggcagcttctttgatgtctgcaatctacgaagagaacaaggatgaggacggcttcctctacatgacttacagtggcgagaacacattcggctctgcgtaattcatcaactgttgctgctgctgtaaataaacatggatggccaggtgtcatggtcaacctcctgtgtacatagcatgtccctgtgctggattgcctcaatggtctaatgcgtccttagctttttaagtggttcgtatgctatcgtttgaaagttggaacgacccatagaactgatattattcattctgggttgatgacgtttcttattctaccattatgcatttgcaacgtgttttaagtctgaagtgtgattgggcgtttcaatttcagttatctgttatcattgttaattgcaactgattcaggccaataagaaatcaaggccttcttaatcgtcatatctcgcatggttgcacgcatgattgttttttttttttggtagttgttgttgatgttggagactgcaccgtgttttcttctcgtctcattccatcagttattttcattttatcaatttggtgttt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001066302.1 RefSeq:Os07g0512200]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 7]]<br /> [[Category:Chromosome 7]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181831 2014-06-09T05:45:21Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181830 2014-06-09T05:44:42Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181827 2014-06-09T05:44:01Z

<p>Xiaoshui: /* Annotated Information */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> <br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> <br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> <br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> <br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181826 2014-06-09T05:42:51Z

<p>Xiaoshui: /* Labs working on this gene */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> <br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> <br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181823 2014-06-09T05:42:24Z

<p>Xiaoshui: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> <br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> <br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> <br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> <br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> <br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181822 2014-06-09T05:41:45Z

<p>Xiaoshui: /* Evolution */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181821 2014-06-09T05:41:08Z

<p>Xiaoshui: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> It has found that OsATG8 interacts with OsATG4, which functions as cysteine protease to cleave the C-terminal region of OsATG8(1).<br /> OsAtg4 shows low similarity to yeast and Arabidopsis Atg4, but the Cys-164,Asp-361 and His-361 of OsAtg4 are strictly conserved in all homologues(1), which constitute the conserved geometry observed in the canonical catalytic triad of cysteine protease(2). As shown in Figure B, sequence comparison of OsAtg4 (ABB77259) and its Arabidopsis (BAB88384, 56% identity), yeast (P53867, 26% identity) homologues. Identical residues are shaded in black, similarity residues are shaded in gray. The conserved residues are boxed(1).<br /> As showed in Fig. 5, Atg4 interacts with Atg8 and its mutants, indicating the conserved Gly117 mutation does not affect this interaction. This cleavage reaction may include two-step mechanism involving the recognition of the OsAtg8 core and the subsequent recognition of the OsAtg8 tail by OsAtg4. The tail region of OsAtg8 is crucial for hydrolysis, but it is not indispensable to the interaction between the core region of OsAtg8 and OsAtg4(1).<br /> In addition to Atg8 lipidation, the deconjugation of Atg8 by Atg4 is also<br /> essential for autophagosome formation(3).In addition to ATG8s, When focus on Atg4 homologs, which may function in the C-terminal cleavage of ATG8s required for their modification and in the deconjugation of their modified forms. Two homologs of the ATG4 gene, ATG4a and 4b, were identified in the Arabidopsis genome (4).<br /> <br /> <br /> <br /> ===Expression===<br /> ATG4 proteins had a significant but low level of identity with the yeast Atg4 protein (ATG4a-yeast Atg4, 26%; ATG4b-yeast Atg4, 29%). However, the two ATG4s displayed 71% overall amino acid identity(5).As shown in Figure 1C, the two ATG4s were ubiquitously expressed like ATG8s(5). <br /> As showed in Fig 3, OsAtg8 and OsAtg4 could be detected from mature leaves, young leaves, mature roots, young roots, leaf sheaths, and spikes which indicated they are constitutive expressed gene and maybe have important role in rice(1).<br /> Proteinase ATG4 has several conservative cysteine residues in its structure, and can therefore serve as a redox sensor(6).<br /> <br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> 1. Su W, Ma H, Liu C, et al. Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4[J]. Molecular biology reports, 2006, 33(4): 273-278.<br /> 2. Mariño G, Urı́a J A, Puente X S, et al. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy[J]. Journal of Biological Chemistry, 2003, 278(6): 3671-3678.<br /> 3. Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway[J]. The Journal of cell biology, 2000, 151(2): 263-276.<br /> 4. Hanaoka H, Noda T, Shirano Y, et al. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene[J]. Plant Physiology, 2002, 129(3): 1181-1193.<br /> 5. Yoshimoto K, Hanaoka H, Sato S, et al. Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy[J]. The Plant Cell Online, 2004, 16(11): 2967-2983.<br /> 6. Minibayeva F, Dmitrieva S, Ponomareva A, et al. Oxidative stress-induced autophagy in plants: The role of mitochondria[J]. Plant Physiology and Biochemistry, 2012, 59: 11-19.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181075 2014-06-08T10:33:42Z

<p>Xiaoshui: /* Labs working on this gene */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> （1）Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> （2）Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> （3）Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> （4）Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181074 2014-06-08T10:33:12Z

<p>Xiaoshui: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=181073 2014-06-08T10:32:53Z

<p>Xiaoshui: /* Labs working on this gene */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan<br /> Department of Cell Biology, National Institute for Basic Biology, Myodaijicho, Okazaki 444-8585, Japan<br /> Key Laboratory of Bio-resources &amp; Eco-environment (Ministry of Education), College of Life Science, Sichuan University,Chengdu 610064, China<br /> <br /> ==References==<br /> <br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=180902 2014-06-08T07:52:54Z

<p>Xiaoshui: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> ==References==<br /> <br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=180899 2014-06-08T07:51:00Z

<p>Xiaoshui: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Please input related labs here.<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> ==References==<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0682000&diff=180898 2014-06-08T07:50:43Z

<p>Xiaoshui: /* Labs working on this gene */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> Please input function information here.<br /> <br /> ===Expression===<br /> Please input expression information here.<br /> <br /> ===Evolution===<br /> Please input evolution information here.<br /> <br /> You can also add sub-section(s) at will.<br /> <br /> ==Labs working on this gene==<br /> Please input related labs here.<br /> Institute of Genetics, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University<br /> <br /> ==References==<br /> Please input cited references here.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os04g0682000|<br /> Description = Similar to Autophagy 4a|<br /> Version = NM_001060828.1 GI:115461385 GeneID:4337435|<br /> Length = 3422 bp|<br /> Definition = Oryza sativa Japonica Group Os04g0682000, complete gene.|<br /> Source = Oryza sativa Japonica Group<br /> <br /> ORGANISM Oryza sativa Japonica Group<br /> Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br /> Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br /> clade; Ehrhartoideae; Oryzeae; Oryza.<br /> |<br /> Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br /> AP = Chromosome 4:35216531..35219952|<br /> CDS = 35216815..35217023,35217115..35217185,35217292..35217347,35217776..35217914,35218039..35218424&lt;br&gt;,35218530..35218580,35218665..35218750,35218841..35219279|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008397:35216531..35219952<br /> source=RiceChromosome04<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttag&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MTSLPDRGVSSSSSDPLCEGNIAPCSSSSEQKEDCSLKQSKTSI LSCVFNSPFNIFEAHQDSSANKSPKSSSGSYDWSRVLRRIVCSGSMWRFLGTSKVLTS SDVWFLGKCYKLSSEESSSDSDSESGHATFLEDFSSRIWITYRRGFDAISDSKYTSDV NWGCMVRSSQMLVAQALIFHHLGRSWRRPLEKPYNPEYIGILHMFGDSEACAFSIHNL LQAGNSYGLAAGSWVGPYAMCRAWQTLVRTNREQHEVVDGNESFPMALYVVSGDEDGE RGGAPVVCIDVAAQLCCDFNKGQSTWSPILLLVPLVLGLDKINPRYIPLLKETFTFPQ SLGILGGKPGTSTYIAGVQDDRALYLDPHEVQMAVDIAADNIEADTSSYHCSTVRDLA LDLIDPSLAIGFYCRDKDDFDDFCSRATELVDKANGAPLFTVVQSVQPSKQMYNQDDV LGISGDGNINVEDLDASGETGEEEWQIL&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;2930..3138#2768..2838#2606..2661#2039..2177#1529..1914#1373..1423#1203..1288#674..1112#cgcgattcgccgtctccatctcgtctcccgcttcctccccgcgtccgccacgccaccccccacctcgccgcctcgccgtggctgctcctcccctcccctcccctccccgccgccggtgctccggccttcgctgccgccgtgctttctctatctatcctcttcccccacgcggacgggggtgcggcgattcgggctctccgccggacacgcgtcgcttcggcctcaactgaagagccacgcttcggtctcgactctcgaacccccaaggtattcctctcccccaagccttccttcgccgcaccgcctgcgtggagtaaaactgcagagatccatctggaattgggctgtgttcttttgttggtgatggactctcttagcttgcttgattgggttgtgttcggagttttgttctagtctgtttcacttttgctgtggctaatctaatccgcatatttctttctctgcaatgaatgaataaatgtaataattggcccatccagtttgttgcgttgcagaagattcgtttgatgcgtgctgaagtacaatcgtgaaaggaaggaactgtgccaacaccacctgattggtactcctgtcgttcttggacaggagattgattttgcttcggtaggagacccaattgcggatggaatatgcacacgtgcgttgttaggtaatgacgagcttgcctgataggggtgtatcatcgtcttcatctgatccgttgtgcgagggtaacattgcaccttgttcttctagctcggaacagaaggaggattgtagcctgaaacaatcgaaaacctcgatcctgtcctgcgttttcaattcacctttcaatatctttgaggcgcaccaggattcgtccgcaaacaagtcgccgaaatcgtcctctggatcctatgattggtcgagggtattgaggaggatcgtgtgctctggctcaatgtggcgttttctgggcacctccaaggttctcacttcaagtgatgtgtggttccttggtaaatgttacaagctttcgtcggaggagtcgtctagtgactcagattccgaaagtgggcatgccacatttcttgaggacttctcgtcaaggatatggatcacttatcgcagaggtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcaggctttgatgccatctctgattccaagtatactagtgatgtgaactggggctgcatggtcagaagcagccagatgctggttgctcaggtgcttgtcgactttatttgattgaaataacagcattttttttaccactgcatttgtaaaatgtacttggatggatttttgcaggcattgattttccaccatcttggcagatcttggagaaggcccttggagaaggtgagatacatgactacctgctgatcttaagacaatgaaaattttcttttttcagttgtagtaggtgatgggcctcttttacaatgatcaaatgttcatatgcagccatataacccagaatatatagggatcttacacatgtttggtgattctgaagcttgtgctttctcaattcacaatttacttcaagctggaaatagttatggtctggctgctggatcatgggtgggtccatacgccatgtgtcgggcatggcaaacccttgtccgcaccaatagggagcaacatgaagttgttgatgggaatgaaagtttccctatggctctttatgtggtatccggtgatgaagatggtgaaagaggtggagctccagttgtttgtattgatgttgctgctcagctttgctgtgatttcaacaaaggtcaatcaacttggtcaccgattcttttgctggtccctctggttcttggtcttgacaaaattaatccaaggtaagcagcaagctattaaatctcattctttgtaggcttcatatggtcacccttgaacggttgatgtttctactgatggttgtttctagtattaatcacttcctgccattgcccttactatcaggtacattcctttactaaaggagacgttcacatttcctcagagcttggggattttgggtggaaagcctggaacatcaacctacattgctggggtacaggatgacagggcgctctacctagatccccatgaagttcagatggtaaaactgcattatttacttagcatatatgagcgccaattttatagatgtgtttttctatctgcaatctggtcaataagtaaaactttcatatgtagtaggttgtaatttagaatcttgatttcatcaatgtgataagtaattcatgcctttttaatggtgccctgtcctcccattcacaacaatggcaacacaaaaaaacagcaaagcggtatattagtgttcgcctttgtctattatgcatgcagtcagcgaccgttattatctggctatttttgcagtatccctttttgcttggaatccattttggttagtaaccttgtagaagtagatggattttgtatttatcaatgtaatgactagggagctatttttgtttttcatttttgagctatggtagttacagtggggtgttctctacatctcaggcagttgatattgcagctgataacatagaggcagacacttcttcataccactgcaggtatgttcgcaattgcagttatgatttggtaaatggtacctaatattcgttatccttttaatttttcaataatgaaaaaacttattatctagctgcactttgacagcactgtacgagatttggccctagacctgatagatccgtcattggctattggtttttactgccgtgataaaggtgaactgtgattgtcgaacaaatgtcgcgtcatcattttaagttcactctaatcttggttttcttatttactgtctgcctgcttatgtagatgacttcgatgatttctgttctcgcgccactgagctagtagataaagccaatggagcaccactcttcactgttgtgcagtcggttcaaccgtcaaaacaaatgtacaatcaggacgatgtgttgggcatctcaggggatggcaacatcaatgtcgaggacctcgatgcctcaggtgaaacaggagaggaggaatggcagattctttagtgaaggaacaaaactgacctcatgaggtacagaaaacgttgcgtccaacacgtcggtcgaatgcccttgtttatgtgtgggtgaatagaaatgactcgttgtgttgtctacagaacaagctggcactgtctcgataccccagggggttgggtcttgggagaatcagctttaggtgctaccgatgtaaaaatgtgatcagttcatcgctcattcgttggaaatctccttgtatcatacatgctcttgtggttggctataactcaaaatttattatacgttctgtt&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060828.1 RefSeq:Os04g0682000]|<br /> }}<br /> [[Category:Genes]]<br /> [[Category:Japonica mRNA]]<br /> [[Category:Oryza Sativa Japonica Group]]<br /> [[Category:Japonica Genes]]<br /> [[Category:Japonica Chromosome 4]]<br /> [[Category:Chromosome 4]]</div>

Xiaoshui