http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=Xysj2012RiceWiki - User contributions [en]2026-05-26T06:35:51ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=RiceWiki:Participants&diff=278146RiceWiki:Participants2018-01-16T04:04:10Z<p>Xysj2012: </p>
<hr />
<div>==RiceWiki Team (ricewiki@big.ac.cn)==<br />
* Zhang Zhang: Beijing Institute of Genomics, Chinese Academy of Sciences (PI)<br />
<br />
* Jian Sang: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Li Man: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Guangyi Niu: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Zhennan Wang: Institute of Zoology，Chinese Academy of Sciences<br />
<br />
* Xiaonan Liu: School of Future Technology, Chinese Academy of Sciences<br />
<br />
* Lina Ma: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Hao Wu: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Dawei Huang: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Dong Zou: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Ang Li: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Siqi Liu: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Ling-Ling Chen: Huazhong Agricultural University<br />
<br />
* Songnian Hu: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Jun Yu: Beijing Institute of Genomics, Chinese Academy of Sciences<br />
<br />
* Ye Zhang: Huazhong Agricultural University<br />
<br />
<br />
<br />
==Advisory Board==<br />
* Lihuang Zhu: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences<br />
* Xiangfeng Wang: University of Arizona<br />
* Zheng Wang: Yale University<br />
* Hang He: Peking University<br />
* Donghui Li: TAIR, Stanford University<br />
* Xiaodong Wang: WormBase, California Institute of Technology<br />
<br />
==Contributors==<br />
See [[Special:ListUsers|contributor list]] for details.</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0323700&diff=278145Os08g03237002018-01-16T02:37:27Z<p>Xysj2012: /* Evolution */</p>
<hr />
<div>The rice ''OsCCC1'' is a member of the cation-Cl- cotransporter (CCC) family and plays a significant role in K+ and Cl－ homeostasis and rice plant development.<ref name="ref1" /><br />
<br />
==Annotated Information==<br />
===Function===<br />
* ''Xiang-Qiang Kong et al.'' have cloned an Oryza sativa cDNA encoding for a member of the cation–Cl- cotransporter (CCC) family. Plant CCC proteins are highly conserved and that they have greater sequence similarity to the sub-family of animal K+ –Cl- cotransporters than to other cation–Cl- cotransporters. In plants CCCs are involved in the homeostasis of Cl-.<ref name="ref1" /><ref name="ref2" /><br><br />
* ''OsCCC1'' was primarily involved in K+ homeostasis and Cl- homeostasis, it might be an K+ -Cl- cotransporter. It is a compact phylogenetic cluster with highly conserved genes that shows the highest similarity to animal KCCs. ''OsCCC1'' plays a significant role in ion homeostasis and rice development under saline conditions. The analysis of ''OsCCC1'' RNAi lines designed by ''Xiang-Qiang Kong et al.'' strongly suggests its involvement in pivotal developmental processes.<ref name="ref1" /><br />
<br />
===Mutation===<br />
* WT plants VS. Transgenic plants<ref name="ref1" />:<br><br />
[[File: OsCCC1 wt.png|right|thumb|400px|'''Figure 1.'''''WT plants VS. Transgenic plants (from reference <ref name="ref1" />).'']]<br />
*Southern blot analysis of genomic DNA from the RNAi plants confirmed that ''OsCCC1'' was integrated into the genome of the transgenic plants and that more than half of the transgenic lines contained two or more copies of the gene. (Figure 1A)<br />
*Real-time PCR analysis to examine the expression levels of ''OsCCC1''in the T3 plants of the transgenic lines revealed that the expression level of ''OsCCC1'' in RNAi transgenic lines Ri 3-4 and Ri 7-2 had decreased to 30 and 39%, respectively. (Figure 1B) <br />
*The effect of NaCl and KCl on the germination of ''OsCCC1'' RNAi seeds was also tested.There was no difference in seed germination between the WT and RNAi seedlings under normal conditions under normal conditions. In the presence of 150 mM NaCl, the germination of both WT and ''OsCCC1'' RNAi seeds was inhibited slightly, but there was no obvious difference between the WT and RNAi seedlings. In the presence of KCl, the germination of ''OsCCC1''RNAi seeds was inhibited significantly and WT seeds inhibited to a lesser extent. When the seeds were subjected to the 50 mM NaCl + 100 mM KCl treatment, approximately 96% of WT seeds germinated compared with only 83% of the seeds of the RNAi plants. Under 150 mM KCl treatment, 82% of the WT seeds germinated compared with only 41% seeds of the RNAi plants.(Figure 1C) Thus, during germination, gene silencing of ''OsCCC1'' in rice decreased the tolerance to KCl but not to NaCl.<br />
*The progeny of T3 homozygous kanamycin-tolerant plants (T4 generation) of lines Ri 3-4 and Ri 7-2 and WT seedlings were cultivated under salt stress (NaCl and KCl)or non-salt-stress conditions. In contrast to WT plants, the transgenic plants of line Ri 7-2 displayed progressive chlorosis, reduced leaf size, and a general growth inhibition under KCl conditions. These inhibitory effects increased progressively with increasing KCl concentrations. (Figure 1D)<br />
*Similar phenomena occurred in the progeny of line Ri 3-4. These seedlings were harvested and their fresh and dry weight measured. Under normal conditions, the fresh and dry weight of ''OsCCC1'' RNAi lines was lower than those of WT seedlings. The KCl and NaCl treatments significantly decreased the fresh weight and dry weight of both WT and RNAi seedlings; however, compared to normal conditions, the fresh and dry weight of RNAi seedlings decreased more obviously than those of the WT under NaCl and KCl conditions, especially under KCl conditions.Of the three stress treatments, the RNAi lines showed the greatest decrease in shoot and root fresh and dry weight compared to the WT under the 150 mM KCl treatment. (Figure 1E–H)<br />
<br />
===Expression===<br />
Expression Pattern of ''OsCCC1''<ref name="ref1"/>:<br><br />
[[File:OsCCC1 ExpressionPattern.png|right|thumb|300px|'''Figure 2.''' ''Expression analyses of ''OsCCC1''(from reference <ref name="ref1"/>).'']]<br />
*The ''OsCCC1'' transcript levels in the leaves and roots were slightly upregulated by NaCl treatment, but distinctly upregulated by KCl treatment,suggesting that ''OsCCC1''was mainly involved in KCl rather than NaCl transport (Figure 2e, f).<br />
*A real-time PCR analysis of ''OsCCC1'' expression levels in different tissues revealed that ''OsCCC1'' mRNA was more abundant in the leaves and roots, especially in leaf and root tips, than in the stem.(Figure 2g).<br><br />
*''OsCCC1'' cDNA was obtained by PCR amplification with gene-specific primers (forward primer:5'-ATGGAGAACGGGGAGATCGAG-3'; reverse primer:5'-AAAGCTGTGAATAAAGTGGCTGAGT-3').<br />
<br />
===Subcellular localization===<br />
The full-length gene of OsCCC1 fused with C-terminal GFP (OsCCC1::GFP) was used to examine the exact subcellular localization of the OsCCC1 protein in plant<br />
cells.Two experiments designed by ''Xiang-Qiang Kong et al.'',the results confirmed that ''OsCCC1'' localizes to the plasma membrane of plant cells. <ref name="ref1" /><br />
<br />
===Evolution===<br />
*Orthologue CCC genes: A complete open reading frame (ORF) was found in the At CCC cDNA sequence, and its comparison with the genomic sequence allowed us to determine the intron/exon structure of the At CCC gene. TBLASTN searches identified orthologue CCC genes in other plant genomes. Two CCC genes were identified in rice (Oryza sativa, japonica), ''OsCCC1'' and ''OsCCC2'', and one more in Medicago truncatula, ''MtCCC''.Interestingly, these plant CCC genes contained 12 introns located in the same position, indicating that the exon/intron structure was perfectly conserved.<ref name="ref2" /><br />
Plant and animal CCCs were highly conserved in the C-termini and the central hydrophobic core, particularly within the putative Tm domains and the predicted intracellular loops.<ref name="ref2" /><br />
<br />
===Knowledge Extension===<br />
*Regarding the ions involved in the symport mechanism, CCCs are divided into three groups: K+ : Cl－cotransporters, known as the KCC group; Na+ : Cl－cotransporters, NCC group; and Na+ :K+ :Cl－ cotransporters, NKCC group. Ion transport studies have demonstrated that the members of all three groups shared an absolute requirement for both Cl－ and at least one cation (Na+ and/or K+), and that the three cotransport processes are electrically silent or electroneutral. <ref name="ref2" /> <ref name="ref3" /><br />
*When grown with unmodified soil, ''ccc'' mutants were observed to produce seed that over-accumulate Ca and S, and underaccumulate Na and K. CCC encodes the only known cation chloride co-transporter in ''A. thaliana.'' Promoter-GUS and public expression profiling analyses suggest that CCC is expressed throughout the plant, including roots, shoots, seeds and pollen.<ref name="ref3" /><br />
<br />
==Labs working on this gene==<br />
*Kay Lab of Plant Stress Research, School of Life Science, Shandong Normal University, 250014 Jinan, Shandong Province, People’s Republic of China<br />
*Cotton Research Center, Shandong Academy of Agricultural Sciences, 250100 Jinan, Shandong Province, People’s Republic of China<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Kong X Q, Gao X H, Sun W, et al. Cloning and functional characterization of a cation–chloride cotransporter gene OsCCC1[J]. Plant molecular biology, 2011, 75(6): 567-578.<br />
</ref><br />
* <ref name="ref2"><br />
Colmenero‐Flores J M, Martínez G, Gamba G, et al. Identification and functional characterization of cation–chloride cotransporters in plants[J]. The Plant Journal, 2007, 50(2): 278-292.<br />
</ref><br />
* <ref name="ref3"><br />
McDowell S C, Akmakjian G, Sladek C, et al. Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions[J]. PloS one, 2013, 8(5): e63014.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0323700&diff=278144Os08g03237002018-01-16T02:37:06Z<p>Xysj2012: </p>
<hr />
<div>The rice ''OsCCC1'' is a member of the cation-Cl- cotransporter (CCC) family and plays a significant role in K+ and Cl－ homeostasis and rice plant development.<ref name="ref1" /><br />
<br />
==Annotated Information==<br />
===Function===<br />
* ''Xiang-Qiang Kong et al.'' have cloned an Oryza sativa cDNA encoding for a member of the cation–Cl- cotransporter (CCC) family. Plant CCC proteins are highly conserved and that they have greater sequence similarity to the sub-family of animal K+ –Cl- cotransporters than to other cation–Cl- cotransporters. In plants CCCs are involved in the homeostasis of Cl-.<ref name="ref1" /><ref name="ref2" /><br><br />
* ''OsCCC1'' was primarily involved in K+ homeostasis and Cl- homeostasis, it might be an K+ -Cl- cotransporter. It is a compact phylogenetic cluster with highly conserved genes that shows the highest similarity to animal KCCs. ''OsCCC1'' plays a significant role in ion homeostasis and rice development under saline conditions. The analysis of ''OsCCC1'' RNAi lines designed by ''Xiang-Qiang Kong et al.'' strongly suggests its involvement in pivotal developmental processes.<ref name="ref1" /><br />
<br />
===Mutation===<br />
* WT plants VS. Transgenic plants<ref name="ref1" />:<br><br />
[[File: OsCCC1 wt.png|right|thumb|400px|'''Figure 1.'''''WT plants VS. Transgenic plants (from reference <ref name="ref1" />).'']]<br />
*Southern blot analysis of genomic DNA from the RNAi plants confirmed that ''OsCCC1'' was integrated into the genome of the transgenic plants and that more than half of the transgenic lines contained two or more copies of the gene. (Figure 1A)<br />
*Real-time PCR analysis to examine the expression levels of ''OsCCC1''in the T3 plants of the transgenic lines revealed that the expression level of ''OsCCC1'' in RNAi transgenic lines Ri 3-4 and Ri 7-2 had decreased to 30 and 39%, respectively. (Figure 1B) <br />
*The effect of NaCl and KCl on the germination of ''OsCCC1'' RNAi seeds was also tested.There was no difference in seed germination between the WT and RNAi seedlings under normal conditions under normal conditions. In the presence of 150 mM NaCl, the germination of both WT and ''OsCCC1'' RNAi seeds was inhibited slightly, but there was no obvious difference between the WT and RNAi seedlings. In the presence of KCl, the germination of ''OsCCC1''RNAi seeds was inhibited significantly and WT seeds inhibited to a lesser extent. When the seeds were subjected to the 50 mM NaCl + 100 mM KCl treatment, approximately 96% of WT seeds germinated compared with only 83% of the seeds of the RNAi plants. Under 150 mM KCl treatment, 82% of the WT seeds germinated compared with only 41% seeds of the RNAi plants.(Figure 1C) Thus, during germination, gene silencing of ''OsCCC1'' in rice decreased the tolerance to KCl but not to NaCl.<br />
*The progeny of T3 homozygous kanamycin-tolerant plants (T4 generation) of lines Ri 3-4 and Ri 7-2 and WT seedlings were cultivated under salt stress (NaCl and KCl)or non-salt-stress conditions. In contrast to WT plants, the transgenic plants of line Ri 7-2 displayed progressive chlorosis, reduced leaf size, and a general growth inhibition under KCl conditions. These inhibitory effects increased progressively with increasing KCl concentrations. (Figure 1D)<br />
*Similar phenomena occurred in the progeny of line Ri 3-4. These seedlings were harvested and their fresh and dry weight measured. Under normal conditions, the fresh and dry weight of ''OsCCC1'' RNAi lines was lower than those of WT seedlings. The KCl and NaCl treatments significantly decreased the fresh weight and dry weight of both WT and RNAi seedlings; however, compared to normal conditions, the fresh and dry weight of RNAi seedlings decreased more obviously than those of the WT under NaCl and KCl conditions, especially under KCl conditions.Of the three stress treatments, the RNAi lines showed the greatest decrease in shoot and root fresh and dry weight compared to the WT under the 150 mM KCl treatment. (Figure 1E–H)<br />
<br />
===Expression===<br />
Expression Pattern of ''OsCCC1''<ref name="ref1"/>:<br><br />
[[File:OsCCC1 ExpressionPattern.png|right|thumb|300px|'''Figure 2.''' ''Expression analyses of ''OsCCC1''(from reference <ref name="ref1"/>).'']]<br />
*The ''OsCCC1'' transcript levels in the leaves and roots were slightly upregulated by NaCl treatment, but distinctly upregulated by KCl treatment,suggesting that ''OsCCC1''was mainly involved in KCl rather than NaCl transport (Figure 2e, f).<br />
*A real-time PCR analysis of ''OsCCC1'' expression levels in different tissues revealed that ''OsCCC1'' mRNA was more abundant in the leaves and roots, especially in leaf and root tips, than in the stem.(Figure 2g).<br><br />
*''OsCCC1'' cDNA was obtained by PCR amplification with gene-specific primers (forward primer:5'-ATGGAGAACGGGGAGATCGAG-3'; reverse primer:5'-AAAGCTGTGAATAAAGTGGCTGAGT-3').<br />
<br />
===Subcellular localization===<br />
The full-length gene of OsCCC1 fused with C-terminal GFP (OsCCC1::GFP) was used to examine the exact subcellular localization of the OsCCC1 protein in plant<br />
cells.Two experiments designed by ''Xiang-Qiang Kong et al.'',the results confirmed that ''OsCCC1'' localizes to the plasma membrane of plant cells. <ref name="ref1" /><br />
<br />
===Evolution===<br />
*Orthologue CCC genes:<br />
A complete open reading frame (ORF) was found in the At CCC cDNA sequence, and its comparison with the genomic sequence allowed us to determine the intron/exon structure of the At CCC gene. TBLASTN searches identified orthologue CCC genes in other plant genomes. Two CCC genes were identified in rice (Oryza sativa, japonica), ''OsCCC1'' and ''OsCCC2'', and one more in Medicago truncatula, ''MtCCC''.Interestingly, these plant CCC genes contained 12 introns located in the same position, indicating that the exon/intron structure was perfectly conserved.<ref name="ref2" /><br />
Plant and animal CCCs were highly conserved in the C-termini and the central hydrophobic core, particularly within the putative Tm domains and the predicted intracellular loops.<ref name="ref2" /><br />
<br />
===Knowledge Extension===<br />
*Regarding the ions involved in the symport mechanism, CCCs are divided into three groups: K+ : Cl－cotransporters, known as the KCC group; Na+ : Cl－cotransporters, NCC group; and Na+ :K+ :Cl－ cotransporters, NKCC group. Ion transport studies have demonstrated that the members of all three groups shared an absolute requirement for both Cl－ and at least one cation (Na+ and/or K+), and that the three cotransport processes are electrically silent or electroneutral. <ref name="ref2" /> <ref name="ref3" /><br />
*When grown with unmodified soil, ''ccc'' mutants were observed to produce seed that over-accumulate Ca and S, and underaccumulate Na and K. CCC encodes the only known cation chloride co-transporter in ''A. thaliana.'' Promoter-GUS and public expression profiling analyses suggest that CCC is expressed throughout the plant, including roots, shoots, seeds and pollen.<ref name="ref3" /><br />
<br />
==Labs working on this gene==<br />
*Kay Lab of Plant Stress Research, School of Life Science, Shandong Normal University, 250014 Jinan, Shandong Province, People’s Republic of China<br />
*Cotton Research Center, Shandong Academy of Agricultural Sciences, 250100 Jinan, Shandong Province, People’s Republic of China<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Kong X Q, Gao X H, Sun W, et al. Cloning and functional characterization of a cation–chloride cotransporter gene OsCCC1[J]. Plant molecular biology, 2011, 75(6): 567-578.<br />
</ref><br />
* <ref name="ref2"><br />
Colmenero‐Flores J M, Martínez G, Gamba G, et al. Identification and functional characterization of cation–chloride cotransporters in plants[J]. The Plant Journal, 2007, 50(2): 278-292.<br />
</ref><br />
* <ref name="ref3"><br />
McDowell S C, Akmakjian G, Sladek C, et al. Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions[J]. PloS one, 2013, 8(5): e63014.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278143Os05g01250002018-01-16T02:35:52Z<p>Xysj2012: /* Function */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref1" /><ref name="ref2" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence<ref name="ref3" /><ref name="ref4" />.<br />
<br />
'''GO assignment(s)''': GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
* In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs.<br />
* Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). <br />
* The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
* Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental <br />
* Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278142Os05g01250002018-01-16T02:35:16Z<p>Xysj2012: /* Annotated Information */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref1" /><ref name="ref2" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence<ref name="ref3" /><ref name="ref4" />.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
* In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs.<br />
* Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). <br />
* The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
* Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental <br />
* Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278141Os05g01250002018-01-16T02:34:56Z<p>Xysj2012: /* Function */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
* In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs.<br />
* Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). <br />
* The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
* Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental <br />
* Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278140Os05g01250002018-01-16T02:34:42Z<p>Xysj2012: /* Subcellular localization */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
* In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs.<br />
* Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). <br />
* The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
* Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental <br />
* Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278139Os05g01250002018-01-16T02:34:17Z<p>Xysj2012: /* Labs working on this gene */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
* Division of Applied Life Science (BK21 program), Plant Molecular Biology and Biotechnology Research Center and Environmental <br />
* Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278138Os05g01250002018-01-16T02:31:52Z<p>Xysj2012: /* Evolution */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein.]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278137Os05g01250002018-01-16T02:31:28Z<p>Xysj2012: /* Expression */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
* In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
===Subcellular localization===<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein with its orthologs in other plant species. .]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278136Os05g01250002018-01-16T02:30:40Z<p>Xysj2012: /* Evolution */</p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|right|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein with its orthologs in other plant species. .]]<br />
<br />
* Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). <br />
* A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. <br />
* Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278135Os05g01250002018-01-16T02:29:58Z<p>Xysj2012: </p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /> <ref name="ref2" />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|left|thumb|200px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein with its orthologs in other plant species. .]]<br />
<br />
Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278134Os05g01250002018-01-16T02:28:57Z<p>Xysj2012: </p>
<hr />
<div><br><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /><ref name="ref2 />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|left|thumb|300px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein with its orthologs in other plant species. .]]<br />
<br />
Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0125000&diff=278133Os05g01250002018-01-16T02:28:37Z<p>Xysj2012: </p>
<hr />
<div><br />
==Annotated Information==<br />
===Function===<br />
* Sumoylation is a post-translational regulatory process in diverse cellular processes in eukaryotes, involving conjugation/deconjugation of small ubiquitin-like modifier (SUMO) proteins to other proteins thus modifying their function. The PIAS [protein inhibitor of activated signal transducers and activators of transcription (STAT)] and SAP (scaffold attachment factor A/B/acinus/PIAS)/MIZ (SIZ) proteins exhibit SUMO E3-ligase activity that facilitates the conjugation of SUMO proteins to target substrates. Here, we report the isolation and molecular characterization of Oryza sativa SIZ1 (OsSIZ1) and SIZ2 (OsSIZ2), rice homologs of Arabidopsis SIZ1. The rice SIZ proteins are localized to the nucleus and showed sumoylation activities in a tobacco system. Our analysis showed increased amounts of SUMO conjugates associated with environmental stresses such as high and low temperature, NaCl and abscisic acid (ABA) in rice plants. The expression of OsSIZ1 and OsSIZ2 in siz1-2 Arabidopsis plants partially complemented the morphological mutant phenotype and enhanced levels of SUMO conjugates under heat shock conditions. In addition, ABA-hypersensitivity of siz1-2 seed germination was partially suppressed by OsSIZ1 and OsSIZ2. The results suggest that rice SIZ1 and SIZ2 are able to functionally complement Arabidopsis SIZ1 in the SUMO conjugation pathway. Their effects on the Arabidopsis mutant suggest a function for these genes related to stress responses and stress adaptation<ref name="ref1" /><ref name="ref2 />.<br />
<br />
* OsSIZ1 Regulates the Vegetative Growth and Reproductive Development in Rice.Two homologous genes from rice (Oryza sativa) were isolated and designated as OsSIZ1 and OsSIZ2 based on amino acid sequence homology to AtSIZ1 and their phylogenetic relationship. The function in the vegetative growth and reproductive development in rice was investigated using OsSIZ1 mutants containing a T-DNA insertion. The results showed that the mutant Ossiz1 exhibited the significant changes in several growth and developmental parameters, including primary root length, adventitious root number, plant height, leaf and panicle length, flower formation, and seed-setting rate compared with wild type. Taking together these results indicate that OsSIZ1 plays an important role in regulating growth and development in rice <ref name="ref3" /><ref name="ref4" />.<br />
<br />
* Rice SIZ1, a SUMO E3 ligase, controls spikelet fertility through regulation of anther dehiscence.Genetic results revealed the co-segregation of single T-DNA insertional recessive mutation with the observed phenotypes in siz1. In addition to showing reduced plant height, tiller number and seed set percentage, both the siz1 mutant and SIZ1-RNAi transgenic plants showed obvious defects in anther dehiscence, but not pollen viability. The anther indehiscence in siz1 was probably a result of defects in endothecium development before anthesis. Interestingly, rice orthologs of AtIRX and ZmMADS2, which are essential for endothecium development during anther dehiscence, were significantly down-regulated in siz1. Compared with the wild-type, the sumoylation profile of high-molecular-weight proteins in mature spikelets was reduced significantly in siz1 and the SIZ1-RNAi line with notably reduced SIZ1 expression. The nuclear localization signal located in the SIZ1 C-terminus was sufficient for its nuclear targeting in bombarded onion epidermis.The results suggest the functional role of SIZ1, a SUMO E3 ligase, in regulating rice anther dehiscence.<br />
<br />
Heterologous expression of OsSIZ1, a rice SUMO E3 ligase, enhances broad abiotic stress tolerance in transgenic creeping bentgrass.<br />
<br />
GO assignment(s): GO:0009901, GO:0009737, GO:0009651, GO:0009408, GO:0009409, GO:0016925<br />
<br />
===Expression===<br />
[[File:Untitled.png|right|thumb|300px|'''Figure 1.''' Nucleus-localized SIZ1 in bombarded onion epidermal cells. .]]<br />
<br />
In rice, SIZ1 was universally present in all examined tissues and all developmental stages (data not shown). Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms.<br />
<br />
In Arabidopsis, AtSIZ1 protein is primarily localized in the nucleus, and PHR1, a MYB transcriptional activator, is its direct target in response to phosphate deficiency .Therefore, the subcellular localization is important to reveal the potential functions of rice SIZs. Recently, Park et al. (2010) showed the nuclear localization of OsSIZ1 and OsSIZ2 in rice protoplasts. To verify whether NLS in the SIZ1 C-terminus is responsible for its nuclear targeting, the NLS-containing C-terminal SIZ1 was fused to the N-terminus of eGFP for particle bombardment-mediated transient assay in onion epidermis (Fig. 1). The mRFP-tagged Ethylene Response Factor 4 (P35S::ERF4-mRFP:T35S), a known transcription factor, was used as a positive nuclear localization marker. Cells expressing the SIZ1–CT–eGFP fusion construct showed co-localization of GFP signals with ERF4 specifically in the nuclei (Fig. 3b). Our subcellular localization study suggested that the NLS-containing C-terminus of SIZ1 was sufficient for its nuclear targeting.<br />
<br />
===Evolution===<br />
[[File:NPH 3538 sm FigS1-3.jpg|left|thumb|300px|'''Figure 2.''' Schematic diagram of SIZ protein domains, amino acid comparison of SIZ1 protein with its orthologs in other plant species. .]]<br />
<br />
Similar to most of the characterized and annotated SIZ/PIAS (SAP and MIZ/Protein Inhibitor of Activated STAT) SUMO E3 ligases from all organisms, rice SIZ1 also contains SAP, PINIT, SP-RING, a SUMO binding motif (hhhSXSaaa), a C-terminal nuclear localization signal (NLS) and the plant-specific PHD domain (plant homeodomain with C4HC3-type Zn-finger) (Fig. 2a,b). PINIT (Pro-Ile-Asn-Ile-Thr) and SP-RING, containing a zinc-finger (C2HC3), are essential for SUMO E3 ligase activity, and SAP (scaffold attachment factors SAF-A/B, Acinus, PIAS, a helix–extended loop–helix) forms a helix–extended loop–helix structure probably involved in DNA binding (Aravind & Koonin, 2000). Amino acid comparison revealed that all plant SIZs possess all consensus domains (Fig. 2b). A BlastP search analysis with SIZ1 amino acid sequences used as a query was employed to generate a rooted phylogenetic tree to illustrate the relationship of rice SIZs to their plant orthologs. As shown in Fig. S2c, rice SIZ1 and SIZ2 are positioned in different clades, and AtSIZ1 is closer to rice SIZ1 than to SIZ2. Sequence similarity analysis also confirmed that rice SIZ1 is closely related to AtSIZ1 (Fig. 2d). The amino acid sequences of SIZ1 and SIZ2 showed high similarity to sorghum loci Sb09g002225 and Sb08g000380, with 65.0% and 57.1% identity, respectively (data not shown). This is probably because both rice and sorghum originate from the grass family and have high synteny for sharing similar panicle architecture.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Hyeong Cheol Park, Hun Kim, Sung Cheol Koo, Hee Jin Park, Mi Sun Cheong, Hyewon Hong, Dongwon Baek, Woo Sik Chung, Doh Hoon Kim, Ray A. Bressan, Sang Yeol Lee, Hans J. Bohnert, Dae-Jin Yun.Plant, Cell & Environment, 2010, 33(11): 1923-1934<br />
</ref><br />
* <ref name="ref2"><br />
Huadun Wang, Kousar Makeen, Yan Yan, Yue Cao, Shubin Sun, Guohua Xu.Plant Molecular Biology Reporter, 2011, 29(2): 411-417 DOI: 10.1007/s11105-010-0232-y<br />
</ref><br />
* <ref name="ref3"><br />
Saminathan Thangasamy, Cian-Ling Guo, Ming-Hsiang Chuang, Ming-Hsing Lai, Jychian Chen, Guang-Yuh Jauh.New Phytologist, 2011, 189(3): 869-882 DOI: 10.1111/j.1469-8137.2010.03538.x <br />
</ref><br />
* <ref name="ref4"><br />
Zhigang Li, Qian Hu, Man Zhou, Joshua Vandenbrink, Dayong Li, Nick Menchyk, Shane Reighard, Ayla Norris, Haibo Liu, Dongfa Sun, Hong Luo Plant Biotechnology Journal, 2013, 11(4): 432-445 DOI: 10.1111/pbi.12030<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=278132Os01g01971002018-01-16T02:25:40Z<p>Xysj2012: /* References */</p>
<hr />
<div><br />
==Annotated Information==<br />
<br />
* This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
<br />
===Expression===<br />
* RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:Sjb1.png|right|thumb|250px|]]<br />
<br />
=== Mutantion ===<br />
[[File:Sjb2.png|right|thumb|150px|]][[File:Figure3.png|right|thumb|150px|]]<br />
* ''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
<br />
===Evolution===<br />
<br />
* We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
* Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
* In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
<br />
*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
<br />
*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
<br />
*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
<br />
*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
<br />
*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
<br />
*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
<br />
*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]<br />
<br />
==Structured Information==</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0197100&diff=278131Os01g01971002018-01-16T02:25:11Z<p>Xysj2012: </p>
<hr />
<div><br />
==Annotated Information==<br />
<br />
* This gene is a rice dwarf mutant, ebisu dwarf (d2), which first was described asebisu dwarf in an article published in 1925. The D2 gene encodes a P450 protein that is classified in the CYP90D group that is highly similar to other BR biosynthesis P450 proteins, such as CPD/CYP90A, DWF4/CYP90B, and DWARF/CYP85. ebisu dwarf (dwarf2 or d2) is a good example of dwarf mutant, although its dwarfism is slightly stronger than the desirable level. In fact, the erect leaves of d2 allow this cultivar to be planted more densely than the original cultivar, which has bent leaves; consequently, a greater volume of crop products can be harvested in the same cultivation area.This dwarf mutant has unusual phenotypic characteristics, such as its erect leaves and the specific inhibition of second internode elongation. Thus, elucidation of the molecular mechanism of the relationship between dwarfism and erect leaves in d2 mutants is important for further molecular breeding for architectural modification.<br />
<br />
===Expression===<br />
* RNAs extracted from the leaf blade and elongating stem produced the strongest bands derived from the D2 mRNA. Bands of intermediate intensity were amplified with RNAs from the shoot apical region and leaf sheath, whereas RNAs from the root, flower, rachis, and elongated stem produced only faint bands. The preferential expression of D2 in the leaf and elongating stem corresponded to the abnormal phenotype of the leaf structure and shortened stem. There also examined the expression pattern of the D2 homologous gene (CYP90D3). The expression level of CYP90D3 was much less than that of D2/CYP90D2, and the PCR product of CYP90D3 was barely detected in any organs under conditions identical to those used for D2/CYP90D2 (25 cycles). However, when the number of cycles was increased to 37, strong bands were observed in the root and faint bands were seen in the stem, leaf sheath, and flower<ref name="ref1" />.<br />
[[File:Sjb1.png|right|thumb|250px|]]<br />
<br />
=== Mutantion ===<br />
[[File:Sjb2.png|right|thumb|150px|]][[File:Figure3.png|right|thumb|150px|]]<br />
* ''ebisu dwarf'' (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants.Sequence analysis of CYP90D2/D2 from the three lines revealed that d2-3 had a single nucleotide substitution at the junction of exon 5 and intron 5 (G to C), d2-4 had a single nucleotide sub- stitution (G to T) in exon 2 that induced an amino acid residue change (from Gly to Cys), whereas d2-6 had a 40-bp deletion in exon 4 (Figure 2).The plant heights of the d2-3, d2-4, and d2-6 mutants were about 30 cm, whereas that of Nipponbare, the wild-type that gave rise to d2-3, d2-4, and d2-6, was about 90 cm (Figure 3)<ref name="ref2" />.<br />
<br />
===Evolution===<br />
<br />
* We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway<ref name="ref1" />.<br />
<br />
=== Knowledge Extension ===<br />
[[File:SLs signal patyway.jpg|right|thumb|150px|''A proposed model of Strigolactone(SL) signalling patyway <ref name="李家洋nature12870" />).'']]<br />
* Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching<ref name="李家洋nature12870" />. SL signaling requires the hormone-dependent interaction of DWARF14 (D14) which is regulated by the interaction of OsMADS57 with OsTB1<ref name="NATURE rice-1" />.<br />
* In this study<ref name="李家洋nature12870" />, they have identified theD53gene that encodes a substrate of the SCF(D3) ubiquitination complex, and revealed that D53 functions as a repressor ofSL signalling. These results allow to establish a model of SL signalling that is centred around a D14–D3–D53 signalling axis . In the presence of SLs, perception of SL by D14 and the SCF(D3) complex leads to ubiquitination of D53 and its subsequent degradation by the ubiquitin proteasome system, which in turn releases the repression of downstream target genes . In the d53 plant, the mutated D53 protein is resistant to ubiquitination and degradation, leading to the accumulation of d53, which blocks SL signalling and results in dwarf and high tillering phenotypes. The signalling paradigm of SLs is still emerging as SLs are a relatively new class of plant hormone for which many knowledge gaps still exist. Identification of D53 as a repressor of SL signalling adds a critical piece of information that helps to paint the whole picture of the SL signalling pathways. <br />
Moreover, the work has also provided an important paradigm for understanding signalling pathways of other plant hormones, for example, karrikins, a class of plant growth regulators found in the smoke of burning plants. Karrikin signalling involves MAX2 and KAI2, a D14-like α / β-hydrolase. It is probable that a similar protein to D53 could serve as the repressor of karrikin signalling. Indeed, multiple D53-like proteins are found in rice and inArabidopsis. We propose that these proteins could serve as repressors of signalling by karrikin and other plant hormones, in a similar way to D53 in SL signalling.<ref name="李家洋nature12870" /><br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
*BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
<br />
*Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan<br />
<br />
*RIKEN (The Institute of Physical and Chemical Research), Wako-shi, Saitama 351-0198, Japan<br />
<br />
*Department of Chemistry, Joetsu University of Education, Joetsu-shi, Niigata 943-8512, Japan<br />
<br />
*Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan<br />
<br />
*State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China<br />
<br />
*National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China<br />
<br />
*Department of Life Science, Chung-Ang University, Seoul, Korea<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Zhi Hong;Miyako Ueguchi-Tanaka;Kazuto Umemura;Sakurako Uozu;Shozo Fujioka;Suguru Takatsuto;Shigeo Yoshida;Motoyuki Ashikari;Hidemi Kitano and Makoto Matsuok. A Rice Brassinosteroid-Deficient Mutant, ebisu dwarf (d2), Is Caused by a Loss of Function of a New Member of Cytochrome P450.The Plant Cell, 2003, 15(12):2900-2910</ref><br />
<ref name="ref2"> Sakamoto, Tomoaki; Morinaka, Yoichi; Kitano, Hidemi; Fujioka, Shozo.New Alleles of Rice ebisu dwarf (d2) Mutant Show Both Brassinosteroid-Deficient and -Insensitive Phenotypes,American Journal of Plant Sciences . Dec2012, Vol. 3 Issue 12, p1699-1707. 9p.</ref><br />
<ref name="李家洋nature12870"> Jiang L, Liu X, Xiong G, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature 2013.</ref><br />
<ref name="NATURE rice-1">Guo S, Xu Y, Liu H, et al. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14[J]. Nature communications 2013; 4: 1566.</ref><br />
</references><br />
<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0856700&diff=278130Os03g08567002018-01-16T02:07:46Z<p>Xysj2012: </p>
<hr />
<div>* The rice '''''Os03g0856700''''' was first reported as '''''OsGA20ox1''''' in 2004 by the researchers from Japan <ref name="ref1" />. <br><br><br />
<br />
==Annotated Information==<br />
===Function===<br />
'''''OsGA20ox1''''', encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice. Gibberellin (GA) 20-oxidase (GA20ox) is a key enzyme that normally catalyzes the penultimate steps in GA biosynthesis<ref name="ref1" />.<br />
===Mutation===<br />
*Figure 1 shows the gross morphology of the wild type and mutant plants. A mutant, B142, tagged with a T-DNA containing three CaMV 35S promoters showed a tall, GA-overproduction phenotype.The integrated T-DNAs, which contain three CaMV 35S promoters, are located upstream of the OsGA20ox1 open reading frame (ORF) in the B142 mutant genome. The final stature of the B142 mutant reflects internode overgrowth and is approximately twice that of its wild-type parent<ref name="ref1" />.<br />
*Figure 2 shows a typical phenotype of a rice GA deficient mutant at the young seedling stage. The GA-related mutants showed dwarfism without the induction of additionally aberrantmorphology. The final plant height of GA-deficient mutants ranged widely between \5% and 90% of the wild-type plants. The leaf blades of the mutant plants became dark green, shorter, and wider than those of the wild-type plants<ref name="ref2" />.<br />
[[File:Fig.1 OsGA20ox1.jpg|right|thumb|200px|Fig.1 B142 Mutant VS. WT.(From reference <ref name="ref1" />).'']]<br />
<br />
===Expression===<br />
Semiquantitative reverse transcription (RT)-PCR analysis revealed that ''OsGA20ox1'' were expressed at different levels in various organs of wild-type rice(Fig. 3)<ref name="ref2" />. ''OsGA20ox1'' were simultaneously expressed in all vegetative organs of rice, and all ''OsGA20ox'' genes were expressed in the reproductive organs. This overlap expression pattern, accompanied with the feedback up-regulation of other GA biosynthetic enzymes by the homeostatic system<ref name="ref3" />, compensate the defect in OsGA20ox2 function in shoot elongation, and consequently the defect in ''OsGA20ox2/SD1'' induces suitable semidwarfism of the rice height for useful breeding.<br />
<br />
===Evolution===<br />
Figure 4 shows that phylogenetic analysis of 2ODDs (GA20ox, GA3ox, and GA2ox) revealed that the GA20ox proteins from dicot plants shared higher amino acid identity each other (49%–80% identities) and formed a single group. ''OsGA20ox2'' showed higher similarity (61% identity) to ''OsGA20ox4'' than the other OsGA20ox proteins, and ''OsGA20ox2'' and ''OsGA20ox4'' formed one subgroup (36%–48% identities with dicot proteins), whereas ''OsGA20ox1'' and ''OsGA20ox3'' were separately located from the ''OsGA20ox2/OsGA20ox4'' subgroup (39%–54% and 39%–49% identities with dicot proteins, respectively)<ref name="ref2" />.<br />
<br />
===Knowledge Extension===<br />
The GAs form a large family of tetracyclic diterpenoid phytohormones that are involved in the regulation of various growth and developmental processes in higher plants. Bioactive GAs, such as GA1 and GA4,are synthesized from trans-geranylgeranyl diphosphate (GGDP) as shown in Figure 5<ref name="ref4" />.<br />
<br />
==Labs working on this gene==<br />
* Laboratory of Bio-control, Graduate School of Natural Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan<br />
* Department of Genetics and Physiology, National Institute of Floricultural Science, 2-1, Fujimoto, Tsukuba, Ibaraki 305-8519, Japan;<br />
* Faculty of Agriculture, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan;<br />
* Department of Rice Research, National Agricultural Research Center (NARC), 1-2-1, Inada, Jo-etsu, Niigata 943-0193, Japan<br />
* Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188–0002, Japan <br />
* Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464–8601, Japan <br />
* BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305–0074, Japan<br />
* Molecular Genetics Department, National Institute of Agrobiological Sciences,Tsukuba, Ibaraki 305–8602, Japan.<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Oikawa T, Koshioka M, Kojima K, et al. A role of OsGA20ox1, encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice[J]. Plant molecular biology, 2004, 55(5): 687-700.PMID 15604710</ref><br />
<ref name="ref2">Sakamoto T, Miura K, Itoh H, et al. An overview of gibberellin metabolism enzyme genes and their related mutants in rice[J]. Plant Physiology, 2004, 134(4): 1642-1653.PMID 15075394</ref><br />
<ref name="ref3">Hedden P, Phillips A L. Gibberellin metabolism: new insights revealed by the genes[J]. Trends in plant science, 2000, 5(12): 523-530.PMID 11120474</ref><br />
<ref name="ref4">Hedden P, Kamiya Y. GIBBERELLIN BIOSYNTHESIS: Enzymes, Genes and Their Regulation[J]. Annu. Rev. Plant Physiol. Plant Mol. Biol, 1997, 48: 431-60.PMID 15012270</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0856700&diff=278129Os03g08567002018-01-16T02:07:15Z<p>Xysj2012: </p>
<hr />
<div>* The rice '''''Os03g0856700''''' was first reported as '''''OsGA20ox1''''' in 2004 by the researchers from Japan <ref name="ref1" />. <br><br><br />
<br />
==Annotated Information==<br />
===Function===<br />
'''''OsGA20ox1''''', encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice. Gibberellin (GA) 20-oxidase (GA20ox) is a key enzyme that normally catalyzes the penultimate steps in GA biosynthesis<ref name="ref1" />.<br />
===Mutation===<br />
*Figure 1 shows the gross morphology of the wild type and mutant plants. A mutant, B142, tagged with a T-DNA containing three CaMV 35S promoters showed a tall, GA-overproduction phenotype.The integrated T-DNAs, which contain three CaMV 35S promoters, are located upstream of the OsGA20ox1 open reading frame (ORF) in the B142 mutant genome. The final stature of the B142 mutant reflects internode overgrowth and is approximately twice that of its wild-type parent<ref name="ref1" />.<br />
*Figure 2 shows a typical phenotype of a rice GA deficient mutant at the young seedling stage. The GA-related mutants showed dwarfism without the induction of additionally aberrantmorphology. The final plant height of GA-deficient mutants ranged widely between \5% and 90% of the wild-type plants. The leaf blades of the mutant plants became dark green, shorter, and wider than those of the wild-type plants<ref name="ref2" />.<br />
[[File:Fig.1 OsGA20ox1.jpg|right|thumb|250px|Fig.1 B142 Mutant VS. WT.(From reference <ref name="ref1" />).'']]<br />
[[File:Fig.2 OsGA20ox1.jpg|right|thumb|250px|Fig.2 Typical phenotype of GA-deficient rice dwarfmutants.(From reference <ref name="ref2" />).'']]<br />
<br />
===Expression===<br />
Semiquantitative reverse transcription (RT)-PCR analysis revealed that ''OsGA20ox1'' were expressed at different levels in various organs of wild-type rice(Fig. 3)<ref name="ref2" />. ''OsGA20ox1'' were simultaneously expressed in all vegetative organs of rice, and all ''OsGA20ox'' genes were expressed in the reproductive organs. This overlap expression pattern, accompanied with the feedback up-regulation of other GA biosynthetic enzymes by the homeostatic system<ref name="ref3" />, compensate the defect in OsGA20ox2 function in shoot elongation, and consequently the defect in ''OsGA20ox2/SD1'' induces suitable semidwarfism of the rice height for useful breeding.<br />
<br />
===Evolution===<br />
Figure 4 shows that phylogenetic analysis of 2ODDs (GA20ox, GA3ox, and GA2ox) revealed that the GA20ox proteins from dicot plants shared higher amino acid identity each other (49%–80% identities) and formed a single group. ''OsGA20ox2'' showed higher similarity (61% identity) to ''OsGA20ox4'' than the other OsGA20ox proteins, and ''OsGA20ox2'' and ''OsGA20ox4'' formed one subgroup (36%–48% identities with dicot proteins), whereas ''OsGA20ox1'' and ''OsGA20ox3'' were separately located from the ''OsGA20ox2/OsGA20ox4'' subgroup (39%–54% and 39%–49% identities with dicot proteins, respectively)<ref name="ref2" />.<br />
<br />
===Knowledge Extension===<br />
The GAs form a large family of tetracyclic diterpenoid phytohormones that are involved in the regulation of various growth and developmental processes in higher plants. Bioactive GAs, such as GA1 and GA4,are synthesized from trans-geranylgeranyl diphosphate (GGDP) as shown in Figure 5<ref name="ref4" />.<br />
<br />
==Labs working on this gene==<br />
* Laboratory of Bio-control, Graduate School of Natural Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan<br />
* Department of Genetics and Physiology, National Institute of Floricultural Science, 2-1, Fujimoto, Tsukuba, Ibaraki 305-8519, Japan;<br />
* Faculty of Agriculture, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan;<br />
* Department of Rice Research, National Agricultural Research Center (NARC), 1-2-1, Inada, Jo-etsu, Niigata 943-0193, Japan<br />
* Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188–0002, Japan <br />
* Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464–8601, Japan <br />
* BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305–0074, Japan<br />
* Molecular Genetics Department, National Institute of Agrobiological Sciences,Tsukuba, Ibaraki 305–8602, Japan.<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Oikawa T, Koshioka M, Kojima K, et al. A role of OsGA20ox1, encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice[J]. Plant molecular biology, 2004, 55(5): 687-700.PMID 15604710</ref><br />
<ref name="ref2">Sakamoto T, Miura K, Itoh H, et al. An overview of gibberellin metabolism enzyme genes and their related mutants in rice[J]. Plant Physiology, 2004, 134(4): 1642-1653.PMID 15075394</ref><br />
<ref name="ref3">Hedden P, Phillips A L. Gibberellin metabolism: new insights revealed by the genes[J]. Trends in plant science, 2000, 5(12): 523-530.PMID 11120474</ref><br />
<ref name="ref4">Hedden P, Kamiya Y. GIBBERELLIN BIOSYNTHESIS: Enzymes, Genes and Their Regulation[J]. Annu. Rev. Plant Physiol. Plant Mol. Biol, 1997, 48: 431-60.PMID 15012270</ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 3]]<br />
[[Category:Chromosome 3]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278128Main Page2017-09-22T09:27:44Z<p>Xysj2012: </p>
<hr />
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<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 13th to 17th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''May 20th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/dpd The Workshop on DNA Methylation and Precision Medicine] will be held in Beijing China from June 08th to 10th.<br />
* '''Nov 05th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from December 05th to 08th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278127Main Page2017-09-19T16:31:07Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 13th to 17th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''May 20th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/dpd The Workshop on DNA Methylation and Precision Medicine] will be held in Beijing China from June 08th to 10th.<br />
* '''Nov 05th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from December 05th to 08th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278126Main Page2017-09-15T15:10:03Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
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<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
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<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''May 20th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/dpd The Workshop on DNA Methylation and Precision Medicine] will be held in Beijing China from June 08th to 10th.<br />
* '''Nov 05th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from December 05th to 08th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278125Main Page2017-09-15T15:08:54Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2016''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''May 20th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/dpd The Workshop on DNA Methylation and Precision Medicine] will be held in Beijing China from June 08th to 10th.<br />
* '''Nov 05th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278124Main Page2017-09-15T15:06:41Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://www.ibc2017.cn/ The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''Nov 05th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf The 2016 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278123Main Page2017-09-15T15:00:35Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] will be held in Beijing China from October 23th to 29th.<br />
* '''Jun 07th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The XIX International Botanical Congress in 2017] will be held in Shenzhen China from July 10th to 13th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
<br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278122Main Page2017-09-15T14:51:17Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
{|style="border:none; background-color:transparent; width:100%;" <br />
|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
<html><br />
<div style="width: 527px; height: 300px; padding-bottom: 30px;text-align:center"><br />
<script src="http://cdn.tagul.com/embed/tc86pr9cqqh1"></script><br />
<!-- Please don't remove attribution to Tagul.com --><br />
<a href="http://tagul.com/">Created with Tagul.com</a><br />
</div><br />
</html><br />
</center><br />
|}<br />
<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Sep 04th, 2017''': The Upcoming Conference Note: [http://bigd.big.ac.cn/conference/bdf2017 The 2017 Big Data Forum for Life and Health Sciences] in China will be held in Beijing China from October 10th to 13th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
* '''Jan 31th, 2016''': The staffs of BIG Data Center presented a keynote lecture at [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php the KAUST Research Conference in Saudi Arabia]. <br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Curated_Genes&diff=278117Curated Genes2017-06-30T03:48:40Z<p>Xysj2012: Blanked the page</p>
<hr />
<div></div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278116Main Page2017-06-30T03:47:18Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[Special:CuratedGenes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
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<center><br />
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|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Jun 24th, 2016''': The Upcoming Conference Note: [http://pgc.hzau.edu.cn/ The 17th Conference of Plant Genomics] in China will be held in Fuzhou China from August 19th to 22th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
* '''Jan 31th, 2016''': The staffs of BIG Data Center presented a keynote lecture at [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php the KAUST Research Conference in Saudi Arabia]. <br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
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<htmlet nocache="yes">earth</htmlet><br />
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|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=278115Main Page2017-06-30T03:45:54Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[RiceWiki:Curated Genes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[Special:CuratedGenes|'''1000 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
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|-style="background:transcript; color:black;" valign="top"<br />
<center><br />
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<br />
<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Jun 24th, 2016''': The Upcoming Conference Note: [http://pgc.hzau.edu.cn/ The 17th Conference of Plant Genomics] in China will be held in Fuzhou China from August 19th to 22th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
* '''Jan 31th, 2016''': The staffs of BIG Data Center presented a keynote lecture at [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php the KAUST Research Conference in Saudi Arabia]. <br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
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|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
</div><br />
|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os11g0102100&diff=278073Os11g01021002017-05-22T13:09:13Z<p>Xysj2012: </p>
<hr />
<div>The rice '''''Os11g0102100''''' was reported as '''''OsWOX''''' in 2007 <ref name="ref1" /> by researchers from China. <br />
==Annotated Information==<br />
[[File:118-Os11g0102100.png|right|thumb|427px|'''Figure 3.''' ''Nuclear localization of OsWOX.<ref name="ref1" />.'']]<br />
===Gene Symbol===<br />
*'''''Os11g0102100''''' '''''<=>''''' '''''OsWOX，WOX'''''<br />
===Function===<br />
* '''''WOX3''''' acted as a transcriptional repressor of '''''YAB3'''''. <br />
* A regulatory network involving '''''YAB3''''', '''''WOX3''''', and '''''KNOX''''' genes required for rice leaf development.<br />
===Evolution===<br />
* The rice '''''WOX3''''' is highly conserved with maize narrow sheath1 (NS1) and NS2 and Arabidopsis PRESSED FLOWER (PRS)<br />
<br />
===Subcellular localization===<br />
* '''''WOX3''''' protein was also targeted into the nucleus of transiently transfected onion cells.<br />
<br />
==Labs working on this gene==<br />
* National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China<br />
* Institut de Biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France<br />
<br />
== References ==<br />
<references><br />
* <ref name="ref1"><br />
Dai M, Hu Y, Zhao Y, Liu H, Zhou DX. A WUSCHEL-LIKE HOMEOBOX gene represses a <br />
YABBY gene expression required for rice leaf development. Plant Physiol. 2007<br />
May;144(1):380-90. Epub 2007 Mar 9. PubMed PMID: 17351053; PubMed Central PMCID: <br />
PMC1913789.<br />
<br />
</ref><br />
</references><br />
== Structured Information ==</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0143400&diff=278072Os08g01434002017-05-22T13:00:27Z<p>Xysj2012: /* Phenotypic analysis */</p>
<hr />
<div>The rice '''''Os08g0143400''''' was reported as '''''Hd18''''' in 2016 <ref name="ref1" /> by researchers from Japan. <br />
<br />
==Annotated Information==<br />
===Gene Symbol===<br />
*'''''Os08g0143400''''' '''''<=>''''' '''''Hd18'''''<br />
===Function===<br />
*Hd18 acts as an accelerator in the rice-flowering pathway under both short- and long-day conditions by elevating transcription levels of Ehd1<br />
<br />
===Phenotypic analysis===<br />
*The Hayamasari Hd18 allele and knockdown of Hd18 gene expression delayed the flowering time of rice plants regardless of the day-length condition. <br />
<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
*National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Shibaya T, Hori K, Ogiso-Tanaka E, Yamanouchi U, Shu K, Kitazawa N, Shomura A, Ando T, Ebana K, Wu J, Yamazaki T, Yano M. Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice. Plant Cell Physiol. 2016 Sep;57(9):1828-38. doi:10.1093/pcp/pcw105. Epub 2016 Jun 18. PubMed PMID: 27318280.<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os10g0544200&diff=276930Os10g05442002017-03-22T00:51:05Z<p>Xysj2012: </p>
<hr />
<div>The rice '''Os10g0544200''' was reported as '''''OsbHLH004''''' in 2006 <ref name="ref1" /> by researchers from the China. It is a member of bHLH transcription factor gene family.<br />
<br />
==Annotated Information==<br />
===Gene Symbol===<br />
*'''''Os10g0544200''''' '''''<=>''''' '''''OsbHLH004'''''<br />
<br />
===Function===<br />
* The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes.<br />
* rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs.<br />
* bHLHs represent key regulatory components in transcriptional networks controlling a number of biological processes.<br />
* Plant bHLHs have been reported to function in light signaling, hormone signaling, wound and drought stress responses, symbiotic ammonium transport, shoot branching, root, fruit and flower development, et al. <ref name="ref1" /> <ref name="ref2" /> <ref name="ref3" /><br />
<br />
===Expression===<br />
* Similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.<br />
<br />
===Evolution===<br />
* The studies of researchers indicate that the ancient bHLH gene family has likely expanded considerably during flowering plant evolution to include many relatively young members, allowing both the conservation and divergence of gene function.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
* Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, 200240<br />
* School of Life Science, Shanghai University, Shanghai, People’s Republic of China, 200444<br />
* School of Life Science, Xiamen University, Xiamen, People’s Republic of China, 361005<br />
* Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China, 200032<br />
* Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J,<br />
Ma H, Wang J, Zhang D. Genome-wide analysis of basic/helix-loop-helix<br />
transcription factor family in rice and Arabidopsis. Plant Physiol. 2006<br />
Aug;141(4):1167-84. PubMed PMID: 16896230; PubMed Central PMCID: PMC1533929.<br />
</ref><br />
* <ref name="ref2"><br />
Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF,<br />
Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary<br />
analysis of the bHLH family of transcription factors in Arabidopsis, poplar,<br />
rice, moss, and algae. Plant Physiol. 2010 Jul;153(3):1398-412. doi:<br />
10.1104/pp.110.153593. PubMed PMID: 20472752; PubMed Central PMCID: PMC2899937.<br />
</ref><br />
* <ref name="ref3"><br />
Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative<br />
analysis of MYB and bHLH plant transcription factors. Plant J. 2011<br />
Apr;66(1):94-116. doi: 10.1111/j.1365-313X.2010.04459.x. Review. PubMed PMID:<br />
21443626.<br />
<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 10]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os10g0544200&diff=276929Os10g05442002017-03-22T00:50:46Z<p>Xysj2012: /* Function */</p>
<hr />
<div>The rice '''Os10g0544200''' was reported as '''''OsbHLH004''''' in 2006 <ref name="ref1" /> by researchers from the China. It is a member of bHLH transcription factor gene family.<br />
<br />
==Annotated Information==<br />
===Gene Symbol===<br />
*'''''Os10g0544200''''' '''''<=>''''' '''''OsbHLH004'''''<br />
<br />
===Function===<br />
* The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes.<br />
* rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs.<br />
* bHLHs represent key regulatory components in transcriptional networks controlling a number of biological processes.<br />
* Plant bHLHs have been reported to function in light signaling, hormone signaling, wound and drought stress responses, symbiotic ammonium transport, shoot branching, root, fruit and flower development, et al.<br />
<br />
===Expression===<br />
* Similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.<br />
<br />
===Evolution===<br />
* The studies of researchers indicate that the ancient bHLH gene family has likely expanded considerably during flowering plant evolution to include many relatively young members, allowing both the conservation and divergence of gene function.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
* Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, 200240<br />
* School of Life Science, Shanghai University, Shanghai, People’s Republic of China, 200444<br />
* School of Life Science, Xiamen University, Xiamen, People’s Republic of China, 361005<br />
* Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China, 200032<br />
* Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J,<br />
Ma H, Wang J, Zhang D. Genome-wide analysis of basic/helix-loop-helix<br />
transcription factor family in rice and Arabidopsis. Plant Physiol. 2006<br />
Aug;141(4):1167-84. PubMed PMID: 16896230; PubMed Central PMCID: PMC1533929.<br />
</ref><br />
* <ref name="ref2"><br />
Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF,<br />
Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary<br />
analysis of the bHLH family of transcription factors in Arabidopsis, poplar,<br />
rice, moss, and algae. Plant Physiol. 2010 Jul;153(3):1398-412. doi:<br />
10.1104/pp.110.153593. PubMed PMID: 20472752; PubMed Central PMCID: PMC2899937.<br />
</ref><br />
* <ref name="ref3"><br />
Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative<br />
analysis of MYB and bHLH plant transcription factors. Plant J. 2011<br />
Apr;66(1):94-116. doi: 10.1111/j.1365-313X.2010.04459.x. Review. PubMed PMID:<br />
21443626.<br />
<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 10]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os10g0544200&diff=276928Os10g05442002017-03-22T00:50:33Z<p>Xysj2012: </p>
<hr />
<div>The rice '''Os10g0544200''' was reported as '''''OsbHLH004''''' in 2006 <ref name="ref1" /> by researchers from the China. It is a member of bHLH transcription factor gene family.<br />
<br />
==Annotated Information==<br />
===Gene Symbol===<br />
*'''''Os10g0544200''''' '''''<=>''''' '''''OsbHLH004'''''<br />
<br />
===Function===<br />
* The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes.<br />
* rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs.<br />
* bHLHs represent key regulatory components in transcriptional networks controlling a number of biological processes.<br />
* Plant bHLHs have been reported to function in light signaling, hormone signaling, wound and drought stress responses, symbiotic ammonium trans-<br />
port, shoot branching, root, fruit and flower development, et al.<br />
===Expression===<br />
* Similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.<br />
<br />
===Evolution===<br />
* The studies of researchers indicate that the ancient bHLH gene family has likely expanded considerably during flowering plant evolution to include many relatively young members, allowing both the conservation and divergence of gene function.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
* Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, 200240<br />
* School of Life Science, Shanghai University, Shanghai, People’s Republic of China, 200444<br />
* School of Life Science, Xiamen University, Xiamen, People’s Republic of China, 361005<br />
* Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China, 200032<br />
* Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J,<br />
Ma H, Wang J, Zhang D. Genome-wide analysis of basic/helix-loop-helix<br />
transcription factor family in rice and Arabidopsis. Plant Physiol. 2006<br />
Aug;141(4):1167-84. PubMed PMID: 16896230; PubMed Central PMCID: PMC1533929.<br />
</ref><br />
* <ref name="ref2"><br />
Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García JF,<br />
Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary<br />
analysis of the bHLH family of transcription factors in Arabidopsis, poplar,<br />
rice, moss, and algae. Plant Physiol. 2010 Jul;153(3):1398-412. doi:<br />
10.1104/pp.110.153593. PubMed PMID: 20472752; PubMed Central PMCID: PMC2899937.<br />
</ref><br />
* <ref name="ref3"><br />
Feller A, Machemer K, Braun EL, Grotewold E. Evolutionary and comparative<br />
analysis of MYB and bHLH plant transcription factors. Plant J. 2011<br />
Apr;66(1):94-116. doi: 10.1111/j.1365-313X.2010.04459.x. Review. PubMed PMID:<br />
21443626.<br />
<br />
</ref><br />
</references><br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 10]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os10g0544200&diff=276927Os10g05442002017-03-22T00:39:18Z<p>Xysj2012: </p>
<hr />
<div>The rice '''Os10g0544200''' was reported as '''''OsbHLH004''''' in 2006 <ref name="ref1" /> by researchers from the China. It is a member of bHLH transcription factor gene family.<br />
<br />
==Annotated Information==<br />
===Function===<br />
* The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes.<br />
* rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs.<br />
<br />
===Expression===<br />
* Similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.<br />
<br />
===Evolution===<br />
* The studies of researchers indicate that the ancient bHLH gene family has likely expanded considerably during flowering plant evolution to include many relatively young members, allowing both the conservation and divergence of gene function.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
* Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Key Laboratory of Microbial Metabolism, Ministry of Education, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, 200240<br />
* School of Life Science, Shanghai University, Shanghai, People’s Republic of China, 200444<br />
* School of Life Science, Xiamen University, Xiamen, People’s Republic of China, 361005<br />
* Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China, 200032<br />
* Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802<br />
<br />
==References==<br />
Please input cited references here.<br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 10]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0129200&diff=276926Os01g01292002017-03-22T00:30:23Z<p>Xysj2012: </p>
<hr />
<div>The rice '''Os01g0129200''' was reported as '''''ZOS1-02''''' in 2007 <ref name="ref1" /> by researchers from the India. It is a member of C2H2 transcription factor gene family.<br />
<br />
==Annotated Information==<br />
===Gene Symbol===<br />
*'''''Os01g0129200''''' '''''<=>''''' '''''ZOS1-02'''''<br />
<br />
===Function===<br />
* The Cys 2/His 2 zinc-finger proteins (ZFPs) constitute one of the largest transcription factor class regulatory protein families in eukaryotes. <ref name="ref1" /> <ref name="ref2" /><br />
* The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. <br />
* Plant Q-type C2H2 zinc finger transcription factors play an important role in plant tolerance to various environmental stresses such as drought, cold, osmotic stress, wounding and mechanical loading. <br />
* The ZFPs not only interact with DNA or chromatin but their interactions with RNA and other proteins are also well documented in lower as well as higher eukaryotes.<br />
<br />
==Labs working on this gene==<br />
* Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India<br />
* Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India<br />
* Plant Disease Resistance Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602 Ibaraki, Japan<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Xu H, Watanabe KA, Zhang L, Shen QJ. WRKY transcription factor genes in wild<br />
rice Oryza nivara. DNA Res. 2016 Aug;23(4):311-23. doi: 10.1093/dnares/dsw025.<br />
PubMed PMID: 27345721; PubMed Central PMCID: PMC4991837.<br />
</ref><br />
* <ref name="ref2"><br />
Englbrecht CC, Schoof H, Böhm S. Conservation, diversification and expansion<br />
of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics.<br />
2004 Jul 5;5(1):39. PubMed PMID: 15236668; PubMed Central PMCID: PMC481060.<br />
</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 01]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os01g0733200&diff=276923Os01g07332002017-03-21T13:40:50Z<p>Xysj2012: /* References */</p>
<hr />
<div>The rice ''OsHsfC1b'' gene is well known as the "heat shock transcription factor gene" and regulates salt tolerance and development in Oryza sativa ssp. japonica.<br />
==Annotated Information==<br />
===Function===<br />
OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice<ref name="ref1" />.The role of class C HSFs in stress response is currently unknown;however, expression patterns of class C HSF genes from rice suggest, in addition to a role in the heat shock response, a participation in non-thermal stress responses such as salt,drought and oxidative stress.In particular, OsHsfC1b and OsHsf2b are highly responsive to salt and drought stress<ref name="ref2" />.<br />
<br />
Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions<ref name="ref1" />.In contrast to class A HSFs, OsHsfC1b acts as a positive regulator of growth under standard growth conditions. We therefore propose that class C HSFs play an opposite role to class A members in plant growth control.<br />
<br />
===Expression===<br />
Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H2O2<ref name="ref1" />.OsHsfC1b was significantly induced in roots after 30 min treatment with salt, mannitol and ABA. In addition, OsHsfC1b was also significantly upregulated in leaves after 30 min of salt treatment. After 3 h,the expression level of OsHsfC1b in roots was significantly increased by salt and ABA, but not by mannitol. Again,salt stress resulted in an upregulation of expression in leaves. H2O2 had no effect on OsHsfC1b transcript level.<br />
<br />
OsHsfC1b is localized in the nucleus in the absence of stress,which indicates that a stress-dependent modification is not required for nuclear accumulation.<br />
<br />
===Evolution===<br />
To determine the phylogenetic relationship among the OsHsfs, neighbor-joining phylogenetic trees were constructed using the amino acid sequences of DBD, the HR-A/B region, and the linker between them <ref name="ref3" />. As expected, the classes A, B and C Hsfs formed three individual clusters. Furthermore, the class A Hsfs were divided into two sub-clusters. In a previous study, the N-terminal part and C-terminal part of DBD and HR-A/B regions were used separately to draw phylogenetic trees. Although most proteins fixed their positions in the different phylogenetic trees, a few Hsfs changed theirpositions (Nover et al., 2001). Similar phenomenon was also observed on the OsHsfs (data not shown). A more convinced relationship of the Hsfs was revealed by combining the DBD, HR-A/B, and the flexible linker between DBD and HR-A/B.<br />
[[File:tileshop.jpg]]<br />
=== Knowledge Extension ===<br />
A typical Hsf protein contains a modular structure with an N-terminal DNA-binding domain (DBD), an adjacent bipartite oligomerization domain composed of heptads repeat of hydrophobic amino acid residues (HR-A/B), a nuclear localization signal (NLS) essential for nuclear uptake of the protein, a nuclear export signal (NES),and in many cases a less conserved C-terminal activation domain (CTAD) rich in aromatic, hydrophobic and acidic amino acids (AHA) that have been reported<br />
to be crucial for activation function<ref name="ref4" />.Based on the conservative DBD and the HR-A/B regions, 21 putative Hsfs from the Arabidopsis,23 from rice, and 18 from tomato have been identified through the genome-wide analysis. Plant Hsf gene family is divided into three classes, HsfA, HsfB, and HsfC, according to<br />
their protein structures<ref name="ref4" />.HsfA and HsfC have insertions of 21 and 7 amino acids, between the hydrophobic regions HR-A and HR-B,respectively. HsfB and HsfC are also characterized bylack of AHA motifs in their C-terminal regions(CTRs).<br />
<br />
==Labs working on this gene==<br />
Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany<br />
<br />
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany<br />
<br />
CIRAD, UMR AGAP, Avenue Agropolis, 34398 Montpellier, Cedex 5, France<br />
<br />
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China<br />
<br />
National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China<br />
<br />
State Key Lab of Rice Biology, China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou 30016, China<br />
<br />
Graduate School of the Chinese Academy of Sciences, Beijing 100039, China<br />
<br />
Biocenter of the Goethe University, Frankfurt/Main, Germany<br />
==References==<br />
<references><br />
<ref name="ref1">Romy Schmidt, Jos H.M. Schippers, Annelie Welker, Delphine Mieulet, Emmanuel Guiderdoni and Bernd Mueller-Roeber,et al.（2009）Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. japonica.AoB PLANTS 011:1-17.</ref><br />
<ref name="ref2">Wenhuo Hua, Guocheng Hua, Bin Han et al.(2009)Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice.Journal of Zhejiang University SCIENCE B 10:291-300.</ref><br />
<ref name="ref3">Chuang WANG, Qian ZHANG, Hui-xia SHOU et al.(2009)Identification and expression analysis of OsHsfs in rice.Plant Science 176:583–590.</ref><br />
<ref name="ref4">Nover, L., Bharti, K., Doring, P., Mishra, S.K., Ganguli, A.,Scharf, K.D. et al.(2001)Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need?Cell Stress Chaperones 6:177-89.</ref><br />
</references><br />
<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 1]]<br />
[[Category:Chromosome 1]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0174700&diff=276922Os08g01747002017-03-21T13:39:03Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
The gene Os08g0174700 encode a somatic embryogenesis（SERK-family）receptor-like protein kinase 1(OsSERK1).Functionally, OsSERK1 is the closest homolog of AtBAK1 in<br />
rice. Therefore, we named it as OsBAK1( BRI1-Associated receptor Kinase 1)<ref name="ref1" />. The expression of OsBAK1changed important agricultural traits of rice such as plant height, leaf erectness, grain morphologic features, and disease resistance responses. A new rice variety with erect-leaf and normal reproduction can be generated simply by suppressing the expression level of OsBAK1<ref name="ref1" />.<br />
Reduceing levels of OsBAK1 and decreasing sensitivity to BL will lead to semidwarfism in overall growth and result in abnormal growth patterns(Fig.1)[[File:The unnormal growth condition of OsBAK1.jpg|left|thumb|200px|'' Fig.1The_unnormal_growth_condition_of_OsBAK1.(The outer appearance of OsBAK1RNAi line leaves (right) showing constitutive sickness compared with those of control plants (left) grown for two weeks. (from reference <ref name="ref2" />).'']], especially in leaf development(Fig.8)[[File:Defective_leaf_development_of__OsBAK1_RNAi_plants.jpg|right|thumb|200px|'' Fig.8 Defective_leaf_development_of__OsBAK1_RNAi_plants.(A) Surface of leaves of an OsBAK1RNAi plants (right) and control plant (left) grown for four weeks.Pictures in the lower panel show higher magnification of the boxed region.White bars indicate 300 µm. (B) Internal structures of leaves of an OsBAK1RNAi #5 plant (right) and a wild-type plant (left) grown for five weeks. Leaves containing veins were transversely sectioned by hand and observed under a compound microscope. Bulliform cells shown in wild-type plants are marked with arrow heads. Bar indicates 500 µm.(from reference <ref name="ref2" />).'']]. OsBAK1RNAi transgenic rice plants are defective in the development of bulliform cells in the leaf epidermal layer and increase expression level of pathogenesis related gene and enhance susceptibility to a rice blast-causing fungal pathogen, Magnaporthe oryzae (Fig.2)[[File:Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.jpg|left|thumb|200px|''Fig.2 Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.(Extent of OsBAK1RNAi line (right) infection with Magnaporthe oryzae compared to wild-type plant (left) grown for 7 weeks. Enlarged leaf features of them are shown in the lower panel.)(from reference <ref name="ref2" />).'']]. OsBAK1, play versatile roles in rice growth and development<ref name="ref2" />.<br />
<br />
===Expression===<br />
<br />
1.Expression of OsSERK1 and in various organs of rice<br />
Using a set of OsSERK1 primers (K-1; 5’AT(CT)AT(ATC)CATCG(AT)GATGTCAA3’ and K6-2; 5’CCATCTTGGGGCGTTCTGTG3’, where nucleotides in parentheses are a mixture). Actin (RAc-1; 5’AACTGGGATGATATGGAGAA3’, RAc-2; 5’CCTCCAATCCAGACACTGTA3’) was used as an internal control. The result showed that OsSERK1 was expressed in all organs and calli examined with different levels.Expression of OsSERK1 was relatively strong in a 1 DAP flower which contained a very early embryo, a leaf blade and a shoot apex<ref name="ref3" />. A callus on a regeneration medium with both cytokinin and auxin did not show significant change of the level of the OsSERK1expression in comparison to a callus on a callus-inducing medium(Fig.3 ).[[File:Expression of OsSERK1 and in various organs of rice.jpg|right|thumb|200px|''Fig.3 Expression of OsSERK1 and in various organs of rice(Poly(A)+RNAs isolated from the indicated organs were reversetranscribed and used as templates of the PCR. RT-PCR products were detected by Southern blot (OsSERK1) or ethidium bromide staining (actin). + and–indicate whether reverse transcriptase was add). (from reference <ref name="ref3" />).'']]<br />
2.OsSERK genes were expressed in various organs but with some tissue specificity<br />
The OsSERK1 promoter showed reporter gene activities in some specific tissues in a germinating seed, leaf and root, but not in a developing embryo<ref name="ref3" />. This promoter activity suggests that OsSERK1 may have roles in non-embryonic tissues rather than in the embryo<ref name="ref3" />.OsSERK1 might also be involved in signaling of or response to phytohormones in these tissues(Fig.4 ).<br />
3.Rice SERKs are involved in BR signalling<br />
Overexpress the OsSERK1 rice gene in a weak BRI1 mutant,bri1-5.The transgenic Arabidopsis lines ectopically expressing OsSERK1 partially rescued the defective phenotypes of bri1-5(Fig.9).Compared to bri1-5, transgenic plants expressing OsSERK1 showed larger statures, longer petioles and earlier flowering phenotypes<ref name="ref1" />.The expression of CPD has been widely used as a molecular marker to detect the effectiveness of the BR signalling pathway <ref name="ref5" />. BRI1 mutants usually show higher CPD expression levels than that of wild-type plants. Compared to bri1-5, the transgenic lines expressing OsSERKs showed significantly decreased expression of CPD (Fig.10).These results indicated that OsSERKs, like AtBAK1, can partially rescue bri1-5 mutant phenotypes.Functionally, OsSERK1 is the closest homolog of AtBAK1 in rice. Therefore, we named it as OsBAK1<ref name="ref1" />.<br />
4.The subcellular localization of OsBAK1 protein<br />
The OsBAK1 protein in onion epidermis cells is located at plasma membrane<ref name="ref1" /> (Fig.5)<br />
5.OsBAK1 interacts with OsBRI1 in vivo<br />
Full length OsBAK1,the extracellular domain (OsBAK1-ECD), the intracellular domain (OsBAK1-ICD), and a truncated intracellular domain (OsBAK1-ICDD)(Fig.11)<br />
===Evolution===<br />
Phylogenetic analysis and suppression of a weak Arabidopsis mutant bri1-5 indicated that OsBAK1 (Os08g0174700) is the closest relative of Arabidopsis BAK1(AtBAK1). Genetic, physiological, and biochemical analyses all suggest that the function of OsBAK1 is conserved with AtBAK1<ref name="ref3" />(Fig.6).<br />
Phylogenetic analysis of SERK proteins in Arabidopsis and rice.<br />
In order to search for AtBAK1 orthologs among the rice genes that were reported to be as OsSERKs or OsSERLs in the public database using the amino acid sequence of AtBAK1 as a query. It was difficult to determine which gene was an exact AtBAK1 ortholog, because many similar genes were identified<ref name="ref2" />. OsSERKs and OsBISERK1 cluster together, closer to each other than to any other AtSERKs based on amino acid sequence homology <ref name="ref4" />(Fig.7).<br />
===References===<br />
Please input cited references here.<br />
<references> <br />
<ref name="ref1">Dan Li; Lei Wang; Min Wang; Yun-Yuan Xu; Wei Luo; Ya-Ju Liu; Zhi-Hong Xu; Jia Li; Kang Chong Engineering OsBAK1 gene as a molecular tool to improve rice architecture for high yield Plant Biotechnology Journal, 2009, 7(8): 791-806.</ref><br />
<ref name="ref2">Hye Sun Park;Hee Young Ryu;Beg Hab Kim;Sun Young Kim;In Sun Yoon;Kyoung Hee Nam A subset of OsSERK genes, including OsBAK1, affects normal growth and leaf development of rice Molecules and Cells, 2011, 32(6): 561-569.</ref><br />
<ref name="ref3">Yukihiro Ito; Kazuhiko Takaya; Nori Kurata Expression of SERK family receptor-like protein kinase genes in rice Biochimica et Biophysica Acta, 2005, 1730(3): 253-258.</ref><br />
<ref name="ref4">Guindon, S., and Gascuel, O.A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Syst. Biol. 2003,52, 696-704. </ref><br />
<ref name="ref5"> Albrecht, C., Russinova, E., Kemmerling, B., Kwaaitaal, M. and de Vries, S.C. (2008) Arabidopsis somatic embryogenesis receptor kinase proteins serve brassinosteroid dependent and independent signaling pathways. Plant Physiology, 148, 611–619. </ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0174700&diff=276921Os08g01747002017-03-21T13:38:38Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
The gene Os08g0174700 encode a somatic embryogenesis（SERK-family）receptor-like protein kinase 1(OsSERK1).Functionally, OsSERK1 is the closest homolog of AtBAK1 in<br />
rice. Therefore, we named it as OsBAK1( BRI1-Associated receptor Kinase 1)<ref name="ref1" />. The expression of OsBAK1changed important agricultural traits of rice such as plant height, leaf erectness, grain morphologic features, and disease resistance responses. A new rice variety with erect-leaf and normal reproduction can be generated simply by suppressing the expression level of OsBAK1<ref name="ref1" />.<br />
Reduceing levels of OsBAK1 and decreasing sensitivity to BL will lead to semidwarfism in overall growth and result in abnormal growth patterns(Fig.1)[[File:The unnormal growth condition of OsBAK1.jpg|left|thumb|200px|'' Fig.1The_unnormal_growth_condition_of_OsBAK1.(The outer appearance of OsBAK1RNAi line leaves (right) showing constitutive sickness compared with those of control plants (left) grown for two weeks. (from reference <ref name="ref2" />).'']], especially in leaf development(Fig.8)[[File:Defective_leaf_development_of__OsBAK1_RNAi_plants.jpg|right|thumb|200px|'' Fig.8 Defective_leaf_development_of__OsBAK1_RNAi_plants.(A) Surface of leaves of an OsBAK1RNAi plants (right) and control plant (left) grown for four weeks.Pictures in the lower panel show higher magnification of the boxed region.White bars indicate 300 µm. (B) Internal structures of leaves of an OsBAK1RNAi #5 plant (right) and a wild-type plant (left) grown for five weeks. Leaves containing veins were transversely sectioned by hand and observed under a compound microscope. Bulliform cells shown in wild-type plants are marked with arrow heads. Bar indicates 500 µm.(from reference <ref name="ref2" />).'']]. OsBAK1RNAi transgenic rice plants are defective in the development of bulliform cells in the leaf epidermal layer and increase expression level of pathogenesis related gene and enhance susceptibility to a rice blast-causing fungal pathogen, Magnaporthe oryzae (Fig.2)[[File:Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.jpg|left|thumb|200px|''Fig.2 Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.(Extent of OsBAK1RNAi line (right) infection with Magnaporthe oryzae compared to wild-type plant (left) grown for 7 weeks. Enlarged leaf features of them are shown in the lower panel.)(from reference <ref name="ref2" />).'']]. OsBAK1, play versatile roles in rice growth and development<ref name="ref2" />.<br />
<br />
===Expression===<br />
<br />
1.Expression of OsSERK1 and in various organs of rice<br />
Using a set of OsSERK1 primers (K-1; 5’AT(CT)AT(ATC)CATCG(AT)GATGTCAA3’ and K6-2; 5’CCATCTTGGGGCGTTCTGTG3’, where nucleotides in parentheses are a mixture). Actin (RAc-1; 5’AACTGGGATGATATGGAGAA3’, RAc-2; 5’CCTCCAATCCAGACACTGTA3’) was used as an internal control. The result showed that OsSERK1 was expressed in all organs and calli examined with different levels.Expression of OsSERK1 was relatively strong in a 1 DAP flower which contained a very early embryo, a leaf blade and a shoot apex<ref name="ref3" />. A callus on a regeneration medium with both cytokinin and auxin did not show significant change of the level of the OsSERK1expression in comparison to a callus on a callus-inducing medium(Fig.3 ).[[File:Expression of OsSERK1 and in various organs of rice.jpg|right|thumb|200px|''Fig.3 Expression of OsSERK1 and in various organs of rice(Poly(A)+RNAs isolated from the indicated organs were reversetranscribed and used as templates of the PCR. RT-PCR products were detected by Southern blot (OsSERK1) or ethidium bromide staining (actin). + and–indicate whether reverse transcriptase was add). (from reference <ref name="ref3" />).'']]<br />
2.OsSERK genes were expressed in various organs but with some tissue specificity<br />
The OsSERK1 promoter showed reporter gene activities in some specific tissues in a germinating seed, leaf and root, but not in a developing embryo<ref name="ref3" />. This promoter activity suggests that OsSERK1 may have roles in non-embryonic tissues rather than in the embryo<ref name="ref3" />.OsSERK1 might also be involved in signaling of or response to phytohormones in these tissues(Fig.4 ).[[File:Tissue-specific GUS activities in the OsSERK1-GUS rice plants.jpg |left|thumb|200px|''Fig.4 Tissue-specific_GUS_activities_in_the_OsSERK1-GUS_rice_plants((A) 1-day imbibed embryo of plant #7. (B) Lamina joint of plant #7. (C) Growing lateral roots of plant #7. (D) Developing embryo (10 DAP) of plant #7. (E) 1-day imbibed embryo of plant #23. (F) Lamina joint of plant #23. (G) Growing lateral roots of plant).(from reference <ref name="ref3" />).'']]<br />
3.Rice SERKs are involved in BR signalling<br />
Overexpress the OsSERK1 rice gene in a weak BRI1 mutant,bri1-5.The transgenic Arabidopsis lines ectopically expressing OsSERK1 partially rescued the defective phenotypes of bri1-5(Fig.9).Compared to bri1-5, transgenic plants expressing OsSERK1 showed larger statures, longer petioles and earlier flowering phenotypes<ref name="ref1" />.The expression of CPD has been widely used as a molecular marker to detect the effectiveness of the BR signalling pathway <ref name="ref5" />. BRI1 mutants usually show higher CPD expression levels than that of wild-type plants. Compared to bri1-5, the transgenic lines expressing OsSERKs showed significantly decreased expression of CPD (Fig.10).These results indicated that OsSERKs, like AtBAK1, can partially rescue bri1-5 mutant phenotypes.Functionally, OsSERK1 is the closest homolog of AtBAK1 in rice. Therefore, we named it as OsBAK1<ref name="ref1" />.<br />
4.The subcellular localization of OsBAK1 protein<br />
The OsBAK1 protein in onion epidermis cells is located at plasma membrane<ref name="ref1" /> (Fig.5)<br />
5.OsBAK1 interacts with OsBRI1 in vivo<br />
Full length OsBAK1,the extracellular domain (OsBAK1-ECD), the intracellular domain (OsBAK1-ICD), and a truncated intracellular domain (OsBAK1-ICDD)(Fig.11)<br />
===Evolution===<br />
Phylogenetic analysis and suppression of a weak Arabidopsis mutant bri1-5 indicated that OsBAK1 (Os08g0174700) is the closest relative of Arabidopsis BAK1(AtBAK1). Genetic, physiological, and biochemical analyses all suggest that the function of OsBAK1 is conserved with AtBAK1<ref name="ref3" />(Fig.6).<br />
Phylogenetic analysis of SERK proteins in Arabidopsis and rice.<br />
In order to search for AtBAK1 orthologs among the rice genes that were reported to be as OsSERKs or OsSERLs in the public database using the amino acid sequence of AtBAK1 as a query. It was difficult to determine which gene was an exact AtBAK1 ortholog, because many similar genes were identified<ref name="ref2" />. OsSERKs and OsBISERK1 cluster together, closer to each other than to any other AtSERKs based on amino acid sequence homology <ref name="ref4" />(Fig.7).<br />
===References===<br />
Please input cited references here.<br />
<references> <br />
<ref name="ref1">Dan Li; Lei Wang; Min Wang; Yun-Yuan Xu; Wei Luo; Ya-Ju Liu; Zhi-Hong Xu; Jia Li; Kang Chong Engineering OsBAK1 gene as a molecular tool to improve rice architecture for high yield Plant Biotechnology Journal, 2009, 7(8): 791-806.</ref><br />
<ref name="ref2">Hye Sun Park;Hee Young Ryu;Beg Hab Kim;Sun Young Kim;In Sun Yoon;Kyoung Hee Nam A subset of OsSERK genes, including OsBAK1, affects normal growth and leaf development of rice Molecules and Cells, 2011, 32(6): 561-569.</ref><br />
<ref name="ref3">Yukihiro Ito; Kazuhiko Takaya; Nori Kurata Expression of SERK family receptor-like protein kinase genes in rice Biochimica et Biophysica Acta, 2005, 1730(3): 253-258.</ref><br />
<ref name="ref4">Guindon, S., and Gascuel, O.A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Syst. Biol. 2003,52, 696-704. </ref><br />
<ref name="ref5"> Albrecht, C., Russinova, E., Kemmerling, B., Kwaaitaal, M. and de Vries, S.C. (2008) Arabidopsis somatic embryogenesis receptor kinase proteins serve brassinosteroid dependent and independent signaling pathways. Plant Physiology, 148, 611–619. </ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0174700&diff=276920Os08g01747002017-03-21T13:36:49Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
The gene Os08g0174700 encode a somatic embryogenesis（SERK-family）receptor-like protein kinase 1(OsSERK1).Functionally, OsSERK1 is the closest homolog of AtBAK1 in<br />
rice. Therefore, we named it as OsBAK1( BRI1-Associated receptor Kinase 1)<ref name="ref1" />. The expression of OsBAK1changed important agricultural traits of rice such as plant height, leaf erectness, grain morphologic features, and disease resistance responses. A new rice variety with erect-leaf and normal reproduction can be generated simply by suppressing the expression level of OsBAK1<ref name="ref1" />.<br />
Reduceing levels of OsBAK1 and decreasing sensitivity to BL will lead to semidwarfism in overall growth and result in abnormal growth patterns(Fig.1)[[File:The unnormal growth condition of OsBAK1.jpg|left|thumb|200px|'' Fig.1The_unnormal_growth_condition_of_OsBAK1.(The outer appearance of OsBAK1RNAi line leaves (right) showing constitutive sickness compared with those of control plants (left) grown for two weeks. (from reference <ref name="ref2" />).'']], especially in leaf development(Fig.8)[[File:Defective_leaf_development_of__OsBAK1_RNAi_plants.jpg|right|thumb|200px|'' Fig.8 Defective_leaf_development_of__OsBAK1_RNAi_plants.(A) Surface of leaves of an OsBAK1RNAi plants (right) and control plant (left) grown for four weeks.Pictures in the lower panel show higher magnification of the boxed region.White bars indicate 300 µm. (B) Internal structures of leaves of an OsBAK1RNAi #5 plant (right) and a wild-type plant (left) grown for five weeks. Leaves containing veins were transversely sectioned by hand and observed under a compound microscope. Bulliform cells shown in wild-type plants are marked with arrow heads. Bar indicates 500 µm.(from reference <ref name="ref2" />).'']]. OsBAK1RNAi transgenic rice plants are defective in the development of bulliform cells in the leaf epidermal layer and increase expression level of pathogenesis related gene and enhance susceptibility to a rice blast-causing fungal pathogen, Magnaporthe oryzae (Fig.2)[[File:Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.jpg|left|thumb|200px|''Fig.2 Higher susceptibility to biotic stress of leaves of OsBAK1RNAi plants.(Extent of OsBAK1RNAi line (right) infection with Magnaporthe oryzae compared to wild-type plant (left) grown for 7 weeks. Enlarged leaf features of them are shown in the lower panel.)(from reference <ref name="ref2" />).'']]. OsBAK1, play versatile roles in rice growth and development<ref name="ref2" />.<br />
<br />
===Expression===<br />
<br />
1.Expression of OsSERK1 and in various organs of rice<br />
Using a set of OsSERK1 primers (K-1; 5’AT(CT)AT(ATC)CATCG(AT)GATGTCAA3’ and K6-2; 5’CCATCTTGGGGCGTTCTGTG3’, where nucleotides in parentheses are a mixture). Actin (RAc-1; 5’AACTGGGATGATATGGAGAA3’, RAc-2; 5’CCTCCAATCCAGACACTGTA3’) was used as an internal control. The result showed that OsSERK1 was expressed in all organs and calli examined with different levels.Expression of OsSERK1 was relatively strong in a 1 DAP flower which contained a very early embryo, a leaf blade and a shoot apex<ref name="ref3" />. A callus on a regeneration medium with both cytokinin and auxin did not show significant change of the level of the OsSERK1expression in comparison to a callus on a callus-inducing medium(Fig.3 ).[[File:Expression of OsSERK1 and in various organs of rice.jpg|right|thumb|200px|''Fig.3 Expression of OsSERK1 and in various organs of rice(Poly(A)+RNAs isolated from the indicated organs were reversetranscribed and used as templates of the PCR. RT-PCR products were detected by Southern blot (OsSERK1) or ethidium bromide staining (actin). + and–indicate whether reverse transcriptase was add). (from reference <ref name="ref3" />).'']]<br />
2.OsSERK genes were expressed in various organs but with some tissue specificity<br />
The OsSERK1 promoter showed reporter gene activities in some specific tissues in a germinating seed, leaf and root, but not in a developing embryo<ref name="ref3" />. This promoter activity suggests that OsSERK1 may have roles in non-embryonic tissues rather than in the embryo<ref name="ref3" />.OsSERK1 might also be involved in signaling of or response to phytohormones in these tissues(Fig.4 ).[[File:Tissue-specific GUS activities in the OsSERK1-GUS rice plants.jpg |left|thumb|200px|''Fig.4 Tissue-specific_GUS_activities_in_the_OsSERK1-GUS_rice_plants((A) 1-day imbibed embryo of plant #7. (B) Lamina joint of plant #7. (C) Growing lateral roots of plant #7. (D) Developing embryo (10 DAP) of plant #7. (E) 1-day imbibed embryo of plant #23. (F) Lamina joint of plant #23. (G) Growing lateral roots of plant).(from reference <ref name="ref3" />).'']]<br />
3.Rice SERKs are involved in BR signalling<br />
Overexpress the OsSERK1 rice gene in a weak BRI1 mutant,bri1-5.The transgenic Arabidopsis lines ectopically expressing OsSERK1 partially rescued the defective phenotypes of bri1-5(Fig.9).[[File:OsBAK1_rescue_partially_the_Arabidopsis_mutant_bri1-5.jpg |left|thumb|200px|''Fig.9 OsBAK1_rescue_partially_the_Arabidopsis_mutant_bri1-5.( (a) Phenotypes of bri1-5 and transgenic bri1-5,expressing OsSERK1 is shown, which were grown in soil for 3 weeks. (b) The phenotypesof longer petioles and larger leaves in transgenic Arabidopsis (a) are shown. ).(from reference <ref name="ref1" />).'']]Compared to bri1-5, transgenic plants expressing OsSERK1 showed larger statures, longer petioles and earlier flowering phenotypes<ref name="ref1" />.The expression of CPD has been widely used as a molecular marker to detect the effectiveness of the BR signalling pathway <ref name="ref5" />. BRI1 mutants usually show higher CPD expression levels than that of wild-type plants. Compared to bri1-5, the transgenic lines expressing OsSERKs showed significantly decreased expression of CPD (Fig.10).[[File:Real-time_PCR_analysed_theexpression_of_CPD_gene_in_transgenic_plants,_bri1-5_itself_and_wild-type_Ws-2.jpg |right|thumb|200px|''Fig.10 Real-time_PCR_analysed_theexpression_of_CPD_gene_in_transgenic_plants,_bri1-5_itself_and_wild-type_Ws-2.(from reference <ref name="ref1" />).'']]These results indicated that OsSERKs, like AtBAK1, can partially rescue bri1-5 mutant phenotypes.Functionally, OsSERK1 is the closest homolog of AtBAK1 in rice. Therefore, we named it as OsBAK1<ref name="ref1" />.<br />
4.The subcellular localization of OsBAK1 protein<br />
The OsBAK1 protein in onion epidermis cells is located at plasma membrane<ref name="ref1" /> (Fig.5)<br />
5.OsBAK1 interacts with OsBRI1 in vivo<br />
Full length OsBAK1,the extracellular domain (OsBAK1-ECD), the intracellular domain (OsBAK1-ICD), and a truncated intracellular domain (OsBAK1-ICDD)(Fig.11)<br />
===Evolution===<br />
Phylogenetic analysis and suppression of a weak Arabidopsis mutant bri1-5 indicated that OsBAK1 (Os08g0174700) is the closest relative of Arabidopsis BAK1(AtBAK1). Genetic, physiological, and biochemical analyses all suggest that the function of OsBAK1 is conserved with AtBAK1<ref name="ref3" />(Fig.6).[[File:A_phylogenetic_tree_of_the_SERK_family_protein_kinases_drawn_on_the_basis_of_predicted_entire_amino_acid_sequences.jpg|left|thumb|200px|''Fig.6 A_phylogenetic_tree_of_the_SERK_family_protein_kinases_drawn_on_the_basis_of_predicted_entire_amino_acid_sequences.(from reference <ref name="ref3"/>).'']]<br />
Phylogenetic analysis of SERK proteins in Arabidopsis and rice.<br />
In order to search for AtBAK1 orthologs among the rice genes that were reported to be as OsSERKs or OsSERLs in the public database using the amino acid sequence of AtBAK1 as a query. It was difficult to determine which gene was an exact AtBAK1 ortholog, because many similar genes were identified<ref name="ref2" />. OsSERKs and OsBISERK1 cluster together, closer to each other than to any other AtSERKs based on amino acid sequence homology <ref name="ref4" />(Fig.7).[[File:Phylogenetic_analysis_of_SERK_proteins_in_Arabidopsis_and_rice.jpg|left|thumb|200px|''Fig.7 Phylogenetic_analysis_of_SERK_proteins_in_Arabidopsis_and_rice.(Amino acid sequences encoded by AtSERK1 (At1g71830),AtSERK2 (At1g34210), AtBAK1/AtSERK3 (At4g33430),AtSERK4/ BAK7/BKK1 (At2g13790), AtSERK5(At 2g13800) in Arabidopsis and OsSERK2(Os04g0457800),OsSERK3 (Os06g0225300), OsSERK4(Os02g0283800) in rice (Oryza) (from reference <ref name="ref4" />).'']]<br />
<br />
===References===<br />
Please input cited references here.<br />
<references> <br />
<ref name="ref1">Dan Li; Lei Wang; Min Wang; Yun-Yuan Xu; Wei Luo; Ya-Ju Liu; Zhi-Hong Xu; Jia Li; Kang Chong Engineering OsBAK1 gene as a molecular tool to improve rice architecture for high yield Plant Biotechnology Journal, 2009, 7(8): 791-806.</ref><br />
<ref name="ref2">Hye Sun Park;Hee Young Ryu;Beg Hab Kim;Sun Young Kim;In Sun Yoon;Kyoung Hee Nam A subset of OsSERK genes, including OsBAK1, affects normal growth and leaf development of rice Molecules and Cells, 2011, 32(6): 561-569.</ref><br />
<ref name="ref3">Yukihiro Ito; Kazuhiko Takaya; Nori Kurata Expression of SERK family receptor-like protein kinase genes in rice Biochimica et Biophysica Acta, 2005, 1730(3): 253-258.</ref><br />
<ref name="ref4">Guindon, S., and Gascuel, O.A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.Syst. Biol. 2003,52, 696-704. </ref><br />
<ref name="ref5"> Albrecht, C., Russinova, E., Kemmerling, B., Kwaaitaal, M. and de Vries, S.C. (2008) Arabidopsis somatic embryogenesis receptor kinase proteins serve brassinosteroid dependent and independent signaling pathways. Plant Physiology, 148, 611–619. </ref><br />
</references><br />
<br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0522000&diff=276919Os09g05220002017-03-21T09:23:13Z<p>Xysj2012: /* References */</p>
<hr />
<div>OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The OsDREB proteins probably bind to the sequence and activate expression of these genes in rice. These rice genes are expected to be upregulated by overexpression of the OsDREB proteins.The structures of DREB1-type ERF/AP2 domains in monocots are closely related to each other as compared with that in the dicots. OsDREB1A is potentially useful for producing transgenic monocots that are tolerant to drought, high-salt, and/or cold stresses<ref name="ref1" />. OsDREB1A specifically binds DRE-related core binding motif, GCCGAC more preferentially than to ACCGAC unlike AtDREB1A, which shows efficient binding to both ACCGAC and GCCGAC<ref name="ref1" />. The responsiveness of OsDREB1A to NaCl and wounding stresses, in addition to its sensitivity to cold stress, imply that its role in the transduction of abiotic stress signals in rice is more similar to DREB1C rather than DREB1A in Arabidopsis. On the other hand, OsDREB1C was constitutively expressed in rice plants, which has a unique expression profile(Fig.1) <ref name="ref1" />.[[File:picture1 RNA-gel blot analysis of the OsDREB transcripts under various stress conditions.jpg|right|thumb|150px|''picture1. RNA-gel blot analysis of the OsDREB transcripts under various stress conditions. (from reference <ref name="ref1" />).'']]<br />
<br />
===Expression===<br />
Expression of OsDREB1A and OsDREB1B was induced by cold, whereas expression of OsDREB2A was induced by dehydration and high-salt stresses, and transgenic Arabidopsis that over-express OsDREB1A were tolerant to drought, high salt and cold stresses. Over-expression of transcription factor OsDREB1B could improve not only freezing tolerance but heat tolerance as well of Arabidopsis, which might lay a strong foundation for exploiting the freezing and heat tolerance of rice and other species<ref name="ref2" />. DREB/CBF genes have been induced in response to cold-, drought-, and high salt-stresses, but the expression of DREB1A and DREB1B genes have been observed only under cold stress<ref name="ref1" /><ref name="ref3" />.<br />
To investigate the response of rice DREB1s in abiotic stresses, we compared the expression of all these genes in rice variety IR64 under three types of stress (drought, salt, and cold) using microarray data from RiceGE (Fig. 2). [[File:picture2 Expression of rice DREB1s under drought, salt, and cold stresses in rice seedlings from the SALK RiceGE database.jpg|right|thumb|150px|''picture2. Expression of rice DREB1s under drought, salt, and cold stresses in rice seedlings from the SALK RiceGE database. (from reference <ref name="ref4" />).'']] Two genes in the paralogous regions of chromosomes 2/4 (Os02g45450, Os04g45380), and those in the cluster of chromosome 9(Os09g35010/Os09g35030) were massively and rapidly induced only by cold stress (4uC for 3 h). Os01g73770 and Os06g03670 were induced by all three abiotic stresses; moreover, the expression levels of Os01g73770 in response to salt stress and that of Os06g03670 in response to drought stress were much higher than those seen in response to other stresses. The other genes (Os06g06970, Os08g43200, Os08g43210, and Os09g35020) were not responsive to any of the stresses (data not shown) <ref name="ref4" />.<br />
<br />
===Evolution===<br />
Plants have evolved several mechanisms in order to cope with adverse environmental conditions. The transcription factors(TFs) belonging to the DREB1/CBF subfamily have been described as major regulators of the plant responses to different abiotic stresses. OsDREB1B is not only induced by low temperatures, but also by drought and mechanical stress<ref name="ref5" />.<br />
<br />
=== Transcription level===<br />
The gene expression of OsDREB1B (Os09g35010) was analysed in plants subjected to several abiotic stress conditions, using semi-quantitative reverse-transcription (RT) PCR. For this, 2-week-old rice seedlings were subjected to cold (5 and 10 ¬C), salt (200 mM NaCl), drought, and ABA (100 lM) treatments for up to 24 h (Fig. 3A and Supplementary Fig. S3). [[File:picture3 Transcriptional profile of OsDREB1B in rice seedlings subjected to different stress treatments.jpg|right|thumb|150px|''picture3. Transcriptional profile of OsDREB1B in rice seedlings subjected to different stress treatments. (from reference <ref name="ref5" />).'']] The results confirmed that OsDREB1B is highly regulated by cold, as previously described<ref name="ref1" />. In addition, it was observed that this regulation is temperature dependent and shows a similar pattern in both shoots and roots (Fig. 3A). When rice seedlings were subjected to 10 ¬C, the OsDREB1B transcript level was rapidly induced (10 min), reached a peak at 1–2 h, and then started to decrease, returning to basal levels afterwards. At 5 ¬C, however, the induction of OsDREB1B only started after 40 min of cold and remained high until the end of the assay. Rice seedlings treated with ABA or subjected to high salinity showed a similar gene expression pattern for OsDREB1B in both shoots and roots. The transcript level of OsDREB1B was rapidly (10 min) upregulated after the onset of stress and followed by a downregulation after 20–40 min. This pattern was also observed in shoots under drought stress, whereas in roots the transcript level of OsDREB1B was kept high at least during 24 h after drought treatment. This suggests that OsDREB1B may play an important role in the plant response to drought, particularly at root level. In the case of NaCl and ABA treatments, there was also a transient upregulation of OsDREB1B after 5–10 h of NaCl treatment in shoots and 1–2 h of ABA treatment in roots. However, given that these changes also appear in the mock control, they are likely to be not specific to NaCl and ABA treatments.<br />
Under mock treatment, a circadian regulation of OsDREB1B could be observed, with the transcript level reaching a peak at 2–5 h after the start of the assay (6–9 h after dawn), decreasing afterwards. In addition, under the same treatment, OsDREB1B showed a transient increase of gene expression at 10 and 20 min. Since, in this case, the only change in conditions was the transfer of the plants to new growth medium, it was hypothesized if this upregulation could be due to a response to mechanical stress. Therefore, another assay was performed, in the same conditions as above, but where the plants were damaged and transferred to new medium. In this case, the OsDREB1B transcript level was highly induced in response to mechanical damage for at least 20 minutes, returning to basal levels afterwards (Fig. 3B). This may also explain the transient upregulation that was observed in the salt, drought, and ABA treatments around 10 and 20 min after the start of stress (Fig. 1A and Supplementary Fig. S1). Nevertheless, the transient induction observed in the salt and drought treatments seems to be more significant than the one seen in the mock treatment<ref name="ref5" />.<br />
<br />
==Labs working on this gene==<br />
* Japan International Research Center for Agricultural Sciences (JIRCAS)<br />
* Ministry of Agriculture, Forestry and Fisheries, Japan<br />
* RIKEN Tsukuba Institute<br />
* the Youth Fund of Shanghai Academy of Agricultural Sciences<br />
* the Shanghai Key Basic Research Project<br />
* Council of Scientific and Industrial Research (CSIR)<br />
* National Bureau of Plant Genetic Resources (NBPGR)<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Joseph G. Dubouzet, Yoh Sakuma, Yusuke Ito, et al. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. The Plant Journal 33(4): 751-763.<br />
</ref><br />
* <ref name="ref2"><br />
Qiu-lin Qin, Jin-ge Liu, Zhen Zhang, et al. (2007) Isolation, optimization, and functional analysis of the cDNA encoding transcription factor OsDREB1B in Oryza Sativa L. Molecular Breeding 19(4): 329-340.<br />
</ref><br />
* <ref name="ref3"><br />
Ito Y, Katsura K, Maruyama K, et al. (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol 47:141–153.<br />
</ref><br />
* <ref name="ref4"><br />
Donghai Mao;Caiyan Chen. (2012) Colinearity and Similar Expression Pattern of Rice DREB1s Reveal Their Functional Conservation in the Cold-Responsive Pathway. PLoS ONE 7(10): e47275<br />
</ref><br />
* <ref name="ref5"><br />
Duarte D. Figueiredo;Pedro M. Barros;André M. Cordeiro, et al. (2012) Seven zinc-finger transcription factors are novel regulators of the stress responsive gene OsDREB1B. Journal of Experimental Botany 63(10): 3643-3656.<br />
</ref><br />
</references><br />
<br><br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0522000&diff=276918Os09g05220002017-03-21T09:22:57Z<p>Xysj2012: /* References */</p>
<hr />
<div>OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression.<br />
<br />
==Annotated Information==<br />
===Function===<br />
The OsDREB proteins probably bind to the sequence and activate expression of these genes in rice. These rice genes are expected to be upregulated by overexpression of the OsDREB proteins.The structures of DREB1-type ERF/AP2 domains in monocots are closely related to each other as compared with that in the dicots. OsDREB1A is potentially useful for producing transgenic monocots that are tolerant to drought, high-salt, and/or cold stresses<ref name="ref1" />. OsDREB1A specifically binds DRE-related core binding motif, GCCGAC more preferentially than to ACCGAC unlike AtDREB1A, which shows efficient binding to both ACCGAC and GCCGAC<ref name="ref1" />. The responsiveness of OsDREB1A to NaCl and wounding stresses, in addition to its sensitivity to cold stress, imply that its role in the transduction of abiotic stress signals in rice is more similar to DREB1C rather than DREB1A in Arabidopsis. On the other hand, OsDREB1C was constitutively expressed in rice plants, which has a unique expression profile(Fig.1) <ref name="ref1" />.[[File:picture1 RNA-gel blot analysis of the OsDREB transcripts under various stress conditions.jpg|right|thumb|150px|''picture1. RNA-gel blot analysis of the OsDREB transcripts under various stress conditions. (from reference <ref name="ref1" />).'']]<br />
<br />
===Expression===<br />
Expression of OsDREB1A and OsDREB1B was induced by cold, whereas expression of OsDREB2A was induced by dehydration and high-salt stresses, and transgenic Arabidopsis that over-express OsDREB1A were tolerant to drought, high salt and cold stresses. Over-expression of transcription factor OsDREB1B could improve not only freezing tolerance but heat tolerance as well of Arabidopsis, which might lay a strong foundation for exploiting the freezing and heat tolerance of rice and other species<ref name="ref2" />. DREB/CBF genes have been induced in response to cold-, drought-, and high salt-stresses, but the expression of DREB1A and DREB1B genes have been observed only under cold stress<ref name="ref1" /><ref name="ref3" />.<br />
To investigate the response of rice DREB1s in abiotic stresses, we compared the expression of all these genes in rice variety IR64 under three types of stress (drought, salt, and cold) using microarray data from RiceGE (Fig. 2). [[File:picture2 Expression of rice DREB1s under drought, salt, and cold stresses in rice seedlings from the SALK RiceGE database.jpg|right|thumb|150px|''picture2. Expression of rice DREB1s under drought, salt, and cold stresses in rice seedlings from the SALK RiceGE database. (from reference <ref name="ref4" />).'']] Two genes in the paralogous regions of chromosomes 2/4 (Os02g45450, Os04g45380), and those in the cluster of chromosome 9(Os09g35010/Os09g35030) were massively and rapidly induced only by cold stress (4uC for 3 h). Os01g73770 and Os06g03670 were induced by all three abiotic stresses; moreover, the expression levels of Os01g73770 in response to salt stress and that of Os06g03670 in response to drought stress were much higher than those seen in response to other stresses. The other genes (Os06g06970, Os08g43200, Os08g43210, and Os09g35020) were not responsive to any of the stresses (data not shown) <ref name="ref4" />.<br />
<br />
===Evolution===<br />
Plants have evolved several mechanisms in order to cope with adverse environmental conditions. The transcription factors(TFs) belonging to the DREB1/CBF subfamily have been described as major regulators of the plant responses to different abiotic stresses. OsDREB1B is not only induced by low temperatures, but also by drought and mechanical stress<ref name="ref5" />.<br />
<br />
=== Transcription level===<br />
The gene expression of OsDREB1B (Os09g35010) was analysed in plants subjected to several abiotic stress conditions, using semi-quantitative reverse-transcription (RT) PCR. For this, 2-week-old rice seedlings were subjected to cold (5 and 10 ¬C), salt (200 mM NaCl), drought, and ABA (100 lM) treatments for up to 24 h (Fig. 3A and Supplementary Fig. S3). [[File:picture3 Transcriptional profile of OsDREB1B in rice seedlings subjected to different stress treatments.jpg|right|thumb|150px|''picture3. Transcriptional profile of OsDREB1B in rice seedlings subjected to different stress treatments. (from reference <ref name="ref5" />).'']] The results confirmed that OsDREB1B is highly regulated by cold, as previously described<ref name="ref1" />. In addition, it was observed that this regulation is temperature dependent and shows a similar pattern in both shoots and roots (Fig. 3A). When rice seedlings were subjected to 10 ¬C, the OsDREB1B transcript level was rapidly induced (10 min), reached a peak at 1–2 h, and then started to decrease, returning to basal levels afterwards. At 5 ¬C, however, the induction of OsDREB1B only started after 40 min of cold and remained high until the end of the assay. Rice seedlings treated with ABA or subjected to high salinity showed a similar gene expression pattern for OsDREB1B in both shoots and roots. The transcript level of OsDREB1B was rapidly (10 min) upregulated after the onset of stress and followed by a downregulation after 20–40 min. This pattern was also observed in shoots under drought stress, whereas in roots the transcript level of OsDREB1B was kept high at least during 24 h after drought treatment. This suggests that OsDREB1B may play an important role in the plant response to drought, particularly at root level. In the case of NaCl and ABA treatments, there was also a transient upregulation of OsDREB1B after 5–10 h of NaCl treatment in shoots and 1–2 h of ABA treatment in roots. However, given that these changes also appear in the mock control, they are likely to be not specific to NaCl and ABA treatments.<br />
Under mock treatment, a circadian regulation of OsDREB1B could be observed, with the transcript level reaching a peak at 2–5 h after the start of the assay (6–9 h after dawn), decreasing afterwards. In addition, under the same treatment, OsDREB1B showed a transient increase of gene expression at 10 and 20 min. Since, in this case, the only change in conditions was the transfer of the plants to new growth medium, it was hypothesized if this upregulation could be due to a response to mechanical stress. Therefore, another assay was performed, in the same conditions as above, but where the plants were damaged and transferred to new medium. In this case, the OsDREB1B transcript level was highly induced in response to mechanical damage for at least 20 minutes, returning to basal levels afterwards (Fig. 3B). This may also explain the transient upregulation that was observed in the salt, drought, and ABA treatments around 10 and 20 min after the start of stress (Fig. 1A and Supplementary Fig. S1). Nevertheless, the transient induction observed in the salt and drought treatments seems to be more significant than the one seen in the mock treatment<ref name="ref5" />.<br />
<br />
==Labs working on this gene==<br />
* Japan International Research Center for Agricultural Sciences (JIRCAS)<br />
* Ministry of Agriculture, Forestry and Fisheries, Japan<br />
* RIKEN Tsukuba Institute<br />
* the Youth Fund of Shanghai Academy of Agricultural Sciences<br />
* the Shanghai Key Basic Research Project<br />
* Council of Scientific and Industrial Research (CSIR)<br />
* National Bureau of Plant Genetic Resources (NBPGR)<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Joseph G. Dubouzet, Yoh Sakuma, Yusuke Ito, et al. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. The Plant Journal 33(4): 751-763.<br />
</ref><br />
* <ref name="ref2"><br />
Qiu-lin Qin, Jin-ge Liu, Zhen Zhang, et al. (2007) Isolation, optimization, and functional analysis of the cDNA encoding transcription factor OsDREB1B in Oryza Sativa L. Molecular Breeding 19(4): 329-340.<br />
</ref><br />
* <ref name="ref3"><br />
Ito Y, Katsura K, Maruyama K, et al. (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol 47:141–153.<br />
</ref><br />
* <ref name="ref4"><br />
Donghai Mao;Caiyan Chen. (2012) Colinearity and Similar Expression Pattern of Rice DREB1s Reveal Their Functional Conservation in the Cold-Responsive Pathway. PLoS ONE 7(10): e47275<br />
</ref><br />
* <ref name="ref5"><br />
Duarte D. Figueiredo;Pedro M. Barros;André M. Cordeiro, et al. (2012) Seven zinc-finger transcription factors are novel regulators of the stress responsive gene OsDREB1B. Journal of Experimental Botany 63(10): 3643-3656.<br />
</ref><br />
</references><br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os12g0641400&diff=276917Os12g06414002017-03-21T08:53:20Z<p>Xysj2012: /* References */</p>
<hr />
<div>Gene Os12g0641400,namely '''OsSUT2''',means sucrose transporter.<br />
<br />
[mailto:wangzhennan@ioz.ac.cn email me]<br />
==Annotated Information==<br />
===Function===<br />
* '''OsSUT2''' (Os12g0641400) The ossut2 mutant exhibited a growth retardation phenotype with a significant reduction in tiller number, plant height, 1,000-grain weight, and root dry weight compared with the controls, the wild type, and complemented transgenic lines. Analysis of primary carbon metabolites revealed that ossut2 accumulated more Suc, glucose, and fructose in the leaves than the controls. Further sugar export analysis of detached leaves indicated that ossut2 had a significantly decreased sugar export ability compared with the controls. These results suggest that OsSUT2 is involved in Suc transport across the tonoplast from the vacuole lumen to the cytosol in rice, playing an essential role in sugar export from the source leaves to sink organs.<ref name="ref 1"/><br><br><br />
* The OsSUT2 cDNA (accession no. HQ875341) encodes a protein of 501 amino acids in length. According to membrane protein topology prediction using Hidden Markov Models in TMMOD software <ref name="ref 4"/>, the OsSUT2 protein contains 12 transmembrane domains.<ref name="ref 1"/><br />
* Results of Suc transport assays in yeast were consistent with a H + -Sucsymport mechanism, suggesting that OsSUT2 functions in Suc uptake from the vacuole.<ref name="ref 2"/>.<br><br><br />
* OsSUT2 is involved in Suc transport across the tonoplast from the vacuole lumen to the cytosol in rice, playing an essential role in sugar export from the source leaves to sink organs.<ref name="ref 3"/>.<br><br><br />
<br />
===Expression Pattern===<br />
* In embryos of germinating seeds, the expression of OsSUT2 gradually increased during the early germinating stage. The developmental regulations of OsSUT2 in germinating embryos could be mediated by sugars transported from endosperms. OsSUT2 expression was up-regulated by glucose through a hexokinase-independent pathway.<ref name="ref 1"/><br><br><br />
* Based on OsSUT2 promoter::GUS expression in germinating seeds of transgenic rice, OsSUT2 was signifi-cantly expressed in the embryos and aleurone layers. In embryos, strong GUS expression was detected in the scutellum and vascular bundle tissues. Developmental stage- and sugar-dependent OsSUT2 expression was suggested to be controlled by transcriptional regulation of the promoter region.<ref name="ref 1"/><br><br> <br />
* Expression of OsSUT2-green fluorescent protein in rice revealed that OsSUT2 localizes to the tonoplast. Analysis of the OsSUT2 promoter::b-glucuronidase transgenic rice indicated that this gene is highly expressed in leaf mesophyll cells, emerging lateral roots, pedicels of fertilized spikelets, and cross cell layers of seed coats.(Figure 1)<ref name="ref 2"/><br><br><br />
[[File:Sut-4.png|right|thumb|300px|'''Figure 1.''' Changes in OsSUT2 expression in embryos during seed germination. The data are presented as mean±SD.<ref name="ref 1"/>'']]<br />
* Carbohydrate transport from endosperms and embryos to coleoptiles, shoots, and roots is an important process for supplying developing tissues with a carbon source during seed germination and seedling establishment. The levels of OsSUT2 mRNA gradually increased from 1 to 5 DAI.(Figure 1.)<ref name="ref 1"/><br><br><br />
<br />
===Evolution===<br />
* Based on a previous phylogenetic analysis of the SUT gene family by Braun and Slewinski, OsSUT2 was grouped with Arabidopsis. AtSUT4 is also classified with StSUT4 and LeSUT4 in the same group. The amino acid identities between OsSUT2 and StSUT4, LeSUT4, and AtSUT4 are 66%, 66%, and 64%.<ref name="ref 1"/><br />
* In the plant SUT protein family, OsSUT1, 3, 4 and 5 are clustered together with members of the dicot-SUT2 group, forming the Type-II subfamily. Within this subfamily OsSUT1 and the orthologues from other cereal species form the cereal (monocot) -SUT1 group, sharing at least 80% identity to one another. OsSUT3 and OsSUT5 are mapped separately in the Type-II subfamily. OsSUT4 seems to be the rice orthologue of the dicot-SUT2 proteins, sharing 58–63% identity and the common features of an extended N-terminal and central loop. OsSUT2, together with HvSUT2, is closely related to dicot-SUT4 group, forming the Type-III subfamily.(Figure 2)<ref name="ref 2"/><br />
[[File:Sut-5.png|center|thumb|300px|'''Figure 2.''' An un-rooted dendrogram of plant SUTs, based on deduced amino acid sequences. The CLUSTALW program was used to show the relationship between the members of the OsSUT gene family (bold) and other plant SUTs.<ref name="ref 1"/>'']]<br />
<br />
===Subcellular localization===<br />
* OsSUT2 encodes a putative sucrose transporter containing 12 transmembrane domains in rice plants. Subcellular localization of the OsSUT2::GFP fusion protein indicated that OsSUT2 is a cell membrane protein(Figure 3,4).<ref name="ref 1" /><br>[[File:Sut-1.png|left|thumb|300px|'''Figure 3.''' Alignment of amino acid sequences from potato SUT4 (StSUT4; Genbank accession AF237780), tomato SUT4 (LeSUT4; AF176950), Arabidopsis SUT4 (AtSUT4; AY072092), and rice OsSUT2 (HQ875341). TM transmembrane domain. <ref name="ref 1" />.'']]<br />
[[File:Sut-2.png|center|thumb|320px|'''Figure 4.''' Comparison of SUT protein structures. The inside and outside membrane regions and transmembrane domains of OsSUT2, StSUT4, AtSUT4, LeSUT4, AtSUT2 (AK226970), and LeSUT2 (AF166498) were predicted using TMMOD software. <ref name="ref 1" />.'']]<br />
<br />
* The expression of OsSUT2-GFP fusion protein was observed in the aleurone layer cells of barley seeds. Fluorescence imaging showed that the fusion protein was localized on the plasma membrane.(Figure 5)<ref name="ref 1"/><br />
[[File:Sut-3.png|right|thumb|320px|'''Figure 5.''' Subcellular localization of OsSUT2 by transient expression of OsSUT2-GFP fusion proteins in barley aleurone layer cells. a Bright field image. b GFP fluorescence image. c Merged field and fluorescence image. <ref name="ref 1" />.'']]<br />
<br />
* OsSUT2 contains 12 transmembrane domains and was localized on plasma membrane. Amino acid alignment showed that the number of amino acids in the central inside loops are similar among OsSUT2 and other SUTs in group 4. The length of the OsSUT2 central loop is shorter than that of SUTs belonging to group 2, i.e., AtSUT2 and LeSUT2. LeSUT2 is considered to function as a putative sucrose sensor.<ref name="ref 1"/><br />
<br />
===Knowledge Extension===<br />
* SUT proteins are important carriers for transporting sucrose across the plasma membrane or vacuolar membranes. Arabidopsis SUT protein has also been found on the chloroplast membrane. Rice OsSUT2 is classified in the same group with Arabidopsis AtSUT4, tomato LeSUT4, potato StSUT4, Lotus japonicus LjSUT4, and barley HvSUT2. Some of the above-mentioned SUTs, including AtSUT4, StSUT4, and LjSUT4, have been identified as low-affinity/high-capacity transporters.<br />
<br />
==Labs working on this gene==<br />
*Naohiro Aoki, Graham N. Scofield, Paul R. Whitfeld:CSIRO Plant Industry, Canberra, ACT, 2601 Australia<br><br />
*Tatsuro Hirose: Department of Rice Research, National Agricultural Research Center, Joetsu, Niigata, 943-0193 Japan<br><br />
*Naohiro Aoki, Tatsuro Hirose: These authors have contributed equally to this work and should be considered as joint first authors<br><br />
*Robert T. Furbank: Corresponding author: Email, robert.furbank@csiro.au; Fax, +61-2-6246-5000<br><br />
*Joon-Seob Eom, Jung-Il Cho: Graduate School of Biotechnology and Plant Metabolism Research Center<br><br />
*Sang-Won Lee, Youngchul Yoo, Gynheung An: Department of Plant Molecular Systems Biotechnology<br><br />
*Joon-Seob Eom, Jung-Il Cho, Sang-Won Lee, Youngchul Yoo, Gynheung An: Crop Biotech Institute<br><br />
*Anke Reinders, John M. Ward: Kyung Hee University, Yongin 446–701, Korea; Department of Plant Biology, University of Minnesota, St.Paul, Minnesota 55108–1095<br><br />
*Pham Quoc Tuan， Sang-Bong Choi： Division of Bioscience and Bioinformatics, Myongji University, Yongin 449–728, Korea<br><br />
* Geul Bang, Youn-Il Park: Department of Biological Science and Analytical Science and Technology, Chungnam National University, Daejeon 305–764, Korea<br><br />
*W. Siao : J.-Y. Chen : H.-H. Hsiao : P. Chung : S.-J. Wang: Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd.<br><br />
<br />
==References==<br />
<references><br />
* <ref name="ref 1"><br />
Siao W, Chen J Y, Hsiao H H, et al. Characterization of OsSUT2 expression and regulation in germinating embryos of rice seeds[J]. Rice, 2011, 4(2): 39-49.<br />
</ref><br />
* <ref name="ref 2"><br />
Eom J S, Cho J I, Reinders A, et al. Impaired function of the tonoplast-localized sucrose transporter in rice, OsSUT2, limits the transport of vacuolar reserve sucrose and affects plant growth[J]. Plant Physiology, 2011, 157(1): 109-119.<br />
</ref><br />
* <ref name="ref 3"><br />
Aoki N, Hirose T, Scofield G N, et al. The sucrose transporter gene family in rice[J]. Plant and Cell Physiology, 2003, 44(3): 223-232.<br />
</ref><br />
* <ref name="ref 4"><br />
Kahsay R Y, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes[J]. Bioinformatics, 2005, 21(9): 1853-1858.<br />
</ref><br />
</references><br />
<br />
<br><br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 12]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os12g0641400&diff=276916Os12g06414002017-03-21T08:53:12Z<p>Xysj2012: /* References */</p>
<hr />
<div>Gene Os12g0641400,namely '''OsSUT2''',means sucrose transporter.<br />
<br />
[mailto:wangzhennan@ioz.ac.cn email me]<br />
==Annotated Information==<br />
===Function===<br />
* '''OsSUT2''' (Os12g0641400) The ossut2 mutant exhibited a growth retardation phenotype with a significant reduction in tiller number, plant height, 1,000-grain weight, and root dry weight compared with the controls, the wild type, and complemented transgenic lines. Analysis of primary carbon metabolites revealed that ossut2 accumulated more Suc, glucose, and fructose in the leaves than the controls. Further sugar export analysis of detached leaves indicated that ossut2 had a significantly decreased sugar export ability compared with the controls. These results suggest that OsSUT2 is involved in Suc transport across the tonoplast from the vacuole lumen to the cytosol in rice, playing an essential role in sugar export from the source leaves to sink organs.<ref name="ref 1"/><br><br><br />
* The OsSUT2 cDNA (accession no. HQ875341) encodes a protein of 501 amino acids in length. According to membrane protein topology prediction using Hidden Markov Models in TMMOD software <ref name="ref 4"/>, the OsSUT2 protein contains 12 transmembrane domains.<ref name="ref 1"/><br />
* Results of Suc transport assays in yeast were consistent with a H + -Sucsymport mechanism, suggesting that OsSUT2 functions in Suc uptake from the vacuole.<ref name="ref 2"/>.<br><br><br />
* OsSUT2 is involved in Suc transport across the tonoplast from the vacuole lumen to the cytosol in rice, playing an essential role in sugar export from the source leaves to sink organs.<ref name="ref 3"/>.<br><br><br />
<br />
===Expression Pattern===<br />
* In embryos of germinating seeds, the expression of OsSUT2 gradually increased during the early germinating stage. The developmental regulations of OsSUT2 in germinating embryos could be mediated by sugars transported from endosperms. OsSUT2 expression was up-regulated by glucose through a hexokinase-independent pathway.<ref name="ref 1"/><br><br><br />
* Based on OsSUT2 promoter::GUS expression in germinating seeds of transgenic rice, OsSUT2 was signifi-cantly expressed in the embryos and aleurone layers. In embryos, strong GUS expression was detected in the scutellum and vascular bundle tissues. Developmental stage- and sugar-dependent OsSUT2 expression was suggested to be controlled by transcriptional regulation of the promoter region.<ref name="ref 1"/><br><br> <br />
* Expression of OsSUT2-green fluorescent protein in rice revealed that OsSUT2 localizes to the tonoplast. Analysis of the OsSUT2 promoter::b-glucuronidase transgenic rice indicated that this gene is highly expressed in leaf mesophyll cells, emerging lateral roots, pedicels of fertilized spikelets, and cross cell layers of seed coats.(Figure 1)<ref name="ref 2"/><br><br><br />
[[File:Sut-4.png|right|thumb|300px|'''Figure 1.''' Changes in OsSUT2 expression in embryos during seed germination. The data are presented as mean±SD.<ref name="ref 1"/>'']]<br />
* Carbohydrate transport from endosperms and embryos to coleoptiles, shoots, and roots is an important process for supplying developing tissues with a carbon source during seed germination and seedling establishment. The levels of OsSUT2 mRNA gradually increased from 1 to 5 DAI.(Figure 1.)<ref name="ref 1"/><br><br><br />
<br />
===Evolution===<br />
* Based on a previous phylogenetic analysis of the SUT gene family by Braun and Slewinski, OsSUT2 was grouped with Arabidopsis. AtSUT4 is also classified with StSUT4 and LeSUT4 in the same group. The amino acid identities between OsSUT2 and StSUT4, LeSUT4, and AtSUT4 are 66%, 66%, and 64%.<ref name="ref 1"/><br />
* In the plant SUT protein family, OsSUT1, 3, 4 and 5 are clustered together with members of the dicot-SUT2 group, forming the Type-II subfamily. Within this subfamily OsSUT1 and the orthologues from other cereal species form the cereal (monocot) -SUT1 group, sharing at least 80% identity to one another. OsSUT3 and OsSUT5 are mapped separately in the Type-II subfamily. OsSUT4 seems to be the rice orthologue of the dicot-SUT2 proteins, sharing 58–63% identity and the common features of an extended N-terminal and central loop. OsSUT2, together with HvSUT2, is closely related to dicot-SUT4 group, forming the Type-III subfamily.(Figure 2)<ref name="ref 2"/><br />
[[File:Sut-5.png|center|thumb|300px|'''Figure 2.''' An un-rooted dendrogram of plant SUTs, based on deduced amino acid sequences. The CLUSTALW program was used to show the relationship between the members of the OsSUT gene family (bold) and other plant SUTs.<ref name="ref 1"/>'']]<br />
<br />
===Subcellular localization===<br />
* OsSUT2 encodes a putative sucrose transporter containing 12 transmembrane domains in rice plants. Subcellular localization of the OsSUT2::GFP fusion protein indicated that OsSUT2 is a cell membrane protein(Figure 3,4).<ref name="ref 1" /><br>[[File:Sut-1.png|left|thumb|300px|'''Figure 3.''' Alignment of amino acid sequences from potato SUT4 (StSUT4; Genbank accession AF237780), tomato SUT4 (LeSUT4; AF176950), Arabidopsis SUT4 (AtSUT4; AY072092), and rice OsSUT2 (HQ875341). TM transmembrane domain. <ref name="ref 1" />.'']]<br />
[[File:Sut-2.png|center|thumb|320px|'''Figure 4.''' Comparison of SUT protein structures. The inside and outside membrane regions and transmembrane domains of OsSUT2, StSUT4, AtSUT4, LeSUT4, AtSUT2 (AK226970), and LeSUT2 (AF166498) were predicted using TMMOD software. <ref name="ref 1" />.'']]<br />
<br />
* The expression of OsSUT2-GFP fusion protein was observed in the aleurone layer cells of barley seeds. Fluorescence imaging showed that the fusion protein was localized on the plasma membrane.(Figure 5)<ref name="ref 1"/><br />
[[File:Sut-3.png|right|thumb|320px|'''Figure 5.''' Subcellular localization of OsSUT2 by transient expression of OsSUT2-GFP fusion proteins in barley aleurone layer cells. a Bright field image. b GFP fluorescence image. c Merged field and fluorescence image. <ref name="ref 1" />.'']]<br />
<br />
* OsSUT2 contains 12 transmembrane domains and was localized on plasma membrane. Amino acid alignment showed that the number of amino acids in the central inside loops are similar among OsSUT2 and other SUTs in group 4. The length of the OsSUT2 central loop is shorter than that of SUTs belonging to group 2, i.e., AtSUT2 and LeSUT2. LeSUT2 is considered to function as a putative sucrose sensor.<ref name="ref 1"/><br />
<br />
===Knowledge Extension===<br />
* SUT proteins are important carriers for transporting sucrose across the plasma membrane or vacuolar membranes. Arabidopsis SUT protein has also been found on the chloroplast membrane. Rice OsSUT2 is classified in the same group with Arabidopsis AtSUT4, tomato LeSUT4, potato StSUT4, Lotus japonicus LjSUT4, and barley HvSUT2. Some of the above-mentioned SUTs, including AtSUT4, StSUT4, and LjSUT4, have been identified as low-affinity/high-capacity transporters.<br />
<br />
==Labs working on this gene==<br />
*Naohiro Aoki, Graham N. Scofield, Paul R. Whitfeld:CSIRO Plant Industry, Canberra, ACT, 2601 Australia<br><br />
*Tatsuro Hirose: Department of Rice Research, National Agricultural Research Center, Joetsu, Niigata, 943-0193 Japan<br><br />
*Naohiro Aoki, Tatsuro Hirose: These authors have contributed equally to this work and should be considered as joint first authors<br><br />
*Robert T. Furbank: Corresponding author: Email, robert.furbank@csiro.au; Fax, +61-2-6246-5000<br><br />
*Joon-Seob Eom, Jung-Il Cho: Graduate School of Biotechnology and Plant Metabolism Research Center<br><br />
*Sang-Won Lee, Youngchul Yoo, Gynheung An: Department of Plant Molecular Systems Biotechnology<br><br />
*Joon-Seob Eom, Jung-Il Cho, Sang-Won Lee, Youngchul Yoo, Gynheung An: Crop Biotech Institute<br><br />
*Anke Reinders, John M. Ward: Kyung Hee University, Yongin 446–701, Korea; Department of Plant Biology, University of Minnesota, St.Paul, Minnesota 55108–1095<br><br />
*Pham Quoc Tuan， Sang-Bong Choi： Division of Bioscience and Bioinformatics, Myongji University, Yongin 449–728, Korea<br><br />
* Geul Bang, Youn-Il Park: Department of Biological Science and Analytical Science and Technology, Chungnam National University, Daejeon 305–764, Korea<br><br />
*W. Siao : J.-Y. Chen : H.-H. Hsiao : P. Chung : S.-J. Wang: Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Rd.<br><br />
<br />
==References==<br />
<references><br />
* <ref name="ref 1"><br />
Siao W, Chen J Y, Hsiao H H, et al. Characterization of OsSUT2 expression and regulation in germinating embryos of rice seeds[J]. Rice, 2011, 4(2): 39-49.<br />
</ref><br />
* <ref name="ref 2"><br />
Eom J S, Cho J I, Reinders A, et al. Impaired function of the tonoplast-localized sucrose transporter in rice, OsSUT2, limits the transport of vacuolar reserve sucrose and affects plant growth[J]. Plant Physiology, 2011, 157(1): 109-119.<br />
</ref><br />
* <ref name="ref 3"><br />
Aoki N, Hirose T, Scofield G N, et al. The sucrose transporter gene family in rice[J]. Plant and Cell Physiology, 2003, 44(3): 223-232.<br />
</ref><br />
* <ref name="ref 4"><br />
Kahsay R Y, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes[J]. Bioinformatics, 2005, 21(9): 1853-1858.<br />
</ref><br />
</references><br />
<br />
<br><br><br />
[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 12]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0580500&diff=276915Os05g05805002017-03-21T08:42:38Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
'''''Rad21/Rec8''''' is an important component and key regulator of cohesins. '''''OsRAD21-4''''', a '''''RAD21'''''-like gene from rice Zhonghua 10 (Oryza sativa L. ssp.japonica), is a single-copy gene in the rice genome and essential for efficient meiosis.<br />
<br />
===Function===<br />
'''''OsRad21-4''''' is composed of 20 exons and 19 introns.<ref name="ref1" /> It encodes a relatively hydrophilic protein and contains the entire Pfam04825 and Pfam04824 domains (spanning amino acids 1–115 and 554–608, respectively) (Figure 2A), of which Pfam04825 is highly conserved in all known members and Pfam04824 present in most of the '''''Rad21/Rec8''''' family.<ref name="ref1" /><ref name="ref2" /> The two domain regions are spaced by a long linker sequence (amino acids 116-553).<ref name="ref1" /> This linker sequence contains a potential nuclear targeting motif at positions 272–279 (KRKKRRKD), 2 separase recognition sites at 411–421 (ADDIEKLRGNT) and 420–430 (NTSGEYGRDYD) and a PEST motif at 511– 534 (RLSDVGPTPDLLEEIEPTQTPYEK) (Figure 2A)<ref name="ref1" />. These motifs are proposed to be implicated in function regulation in cohesion establishment and disassociation.<ref name="ref1" /><ref name="ref3" /> The deficiency of '''''OsRad21-4''''' at the mRNA and protein is correlated with pollen cell sterility phenotype.(Figure6)<ref name="ref1" /> '''''OsRad21-4''''' was essential to meiosis. (Figure7, Figure8)<ref name="ref1" /> In addtion, '''''OsRad21-4''''' is responsible for the pairing of some homologous chromosomes.(Figure9, Figure10)<ref name="ref1" /><br />
<br />
===Expression===<br />
'''''OsRad21-4''''' is present in the rice genome as a single-copy gene.<ref name="ref1" /> The mRNA and protein of '''''OsRad21-4''''' were expressed preferentially in young flowers where the pollen mother cells (PMCs) were in pre-meiotic stages.<ref name="ref1" /> '''''OsRAD21-4''''' cDNA cloned here is 2133 bp long and has a 5' UTR of 54 bp, a 3' UTR of 255 bp and an ORF of 1824 bp encoding a deduced polypeptide of 608 amino acids (OsRad21-4).<ref name="ref1" /> OsRad21-4 has a calculated molecular mass of 68.5 kDa and an isoelectric point (pI) of 5.45.<ref name="ref1" /> The protein is a nucleus-localizing protein.(Figure 2B)<ref name="ref1" />[[File:F23.png|200px|thumb|left|Figure2(B)]] As shown in Figure 3A, '''''OsRad21-4''''' was expressed preferentially in flowers, weakly in leaves and barely in buds and roots.<ref name="ref1" /> Furthermore, '''''OsRad21-4''''' was expressed dominantly just before the premeiotic stage of PMCs.(Figure 3C)<ref name="ref1" /> This gene should function in premeiotic and meiotic PMCs, which is consistent with this notion that meiotic cohesion is established at the pre-meiotic S phase. (Figur 4)<ref name="ref4" /><br />
<br />
===Evolution===<br />
'''''OsRad21-4''''' is a rice orthologue of yeast Rec8.(Figure2(C))<ref name="ref1" /> In rice, '''''OsRad21-4''''' is required for homologous pairing and segregation.<ref name="ref1" /> It might be responsible mainly for sister chromatid-arm cohesion and to a lesser extent or not at all for centromere cohesion.<ref name="ref1" /> In addition, '''''OsRad21-4''''' is required for chromosome condensation.<ref name="ref1" /> Besides, Zhang et al suggest possible link between Rec8 proteins and chromosome fragmentation in higher eukaryotes.<ref name="ref1" /> Furthermore, appearance of micronuclei and/or undetached dinuclei-containing spores and unequal cell division at anaphase I and II in the deficient plants were similar to those reported in mutants of genes related to other early events of meiosis prophase I<ref name="ref5" />, suggesting possible interaction of early events of prophase I.<br />
<br />
==Labs working on this gene==<br />
1.Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Research Center of Molecular & Developmental Biology, Institute of Botany, Chinese academy of Sciences, Beijing 100093,China<br />
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2.Graduate School of the Chinese Academy of Sciences, Beijing 100049, China<br />
<br />
3.Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan<br />
<br />
4.PRESTO, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan<br />
<br />
5.Imperial Cancer Research Fund, 44 Lincoln's Inn Field, London WC2A 3PX, UK<br />
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6.Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan<br />
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7.Faculty of Health Sciences for Welfare, Kansai University of Welfare Sciences, 3-11-1 Asahigaoka, Osaka 582-0026, Japan<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Zhang L, Tao J, Wang S, et al. The rice OsRad21-4, an orthologue of yeast Rec8 protein, is required for efficient meiosis[J]. Plant molecular biology, 2006, 60(4): 533-554.</ref><br />
* <ref name="ref2"><br />
Zhang L R, Tao J Y, Wang T. Molecular characterization of OsRAD21‐1, a rice homologue of yeast RAD21 essential for mitotic chromosome cohesion*[J]. Journal of experimental botany, 2004, 55(399): 1149-1152.</ref><br />
*<ref name="ref3">Nasmyth K. Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis[J]. Annual review of genetics, 2001, 35(1): 673-745.</ref><br />
*<ref name="ref4">Watanabe Y, Yokobayashi S, Yamamoto M, et al. Pre-meiotic S phase is linked to reductional chromosome segregation and recombination[J]. Nature, 2001, 409(6818): 359-363.</ref><br />
*<ref name="ref5">Ma H. Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants[J]. Annu. Rev. Plant Biol., 2005, 56: 393-434.</ref><br />
<references><br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0580500|<br />
Description = Rad21/Rec8 like protein, N-terminal domain containing protein|<br />
Version = NM_001062961.1 GI:115465652 GeneID:4339720|<br />
Length = 7262 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0580500, 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 5|Chromosome 5]]|<br />
AP = Chromosome 5:28971202..28978463|<br />
CDS = 28971255..28971307,28971498..28971566,28971665..28971723,28971819..28971863,28971950..28971969<br>,28972078..28972154,28973352..28973448,28973606..28973687,28973767..28973845<br>,28973955..28974118,28974803..28974846,28974927..28975082,28975179..28975347<br>,28975463..28975530,28975642..28975789,28975853..28975940,28976938..28977065<br>,28977165..28977249,28977333..28977445,28978161..28978243|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctgtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatgatgatgtgtctcggtttctgattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatgcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctgggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcgttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtga</cdnaseq>|<br />
AA = <aaseq>MFYSHQLLARKAPLGQIWMAATLHSKINRKRLDKLDIIKICEEI LNPSVPMALRLSGILMGGVAIVYERKVKALYDDVSRFLIEINEAWRVKPVADPTVLPK GKTQAKYEAVTLPENIMDMDVEQPMLFSEADTTRFRGMRLEDLDDQYINVNLDDDDFS RAENHHQADAENITLADNFGSGLGETDVFNRFERFDITDDDATFNVTPDGHPQVPSNL VPSPPRQEDSPQQQENHHAASSPLHEEAQQGGASVKNEQEQQKMKGQQPAKSSKRKKR RKDDEVMMDNDQIMIPGNVYQTWLKDPSSLITKRHRINSKVNLIRSIKIRDLMDLPLV SLISSLEKSPLEFYYPKELMQLWKECTEVKSPKAPSSGGQQSSSPEQQQRNLPPQAFP TQPQVDNDREMGFHPVDFADDIEKLRGNTSGEYGRDYDAFHSDHSVTPGSPGLSRRSA SSSGGSGRGFTQLDPEVQLPSGRSKRQHSSGKSFGNLDPVEEEFPFEQELRDFKMRRL SDVGPTPDLLEEIEPTQTPYEKKSNPIDQVTQSIHSYLKLHFDTPGASQSESLSQLAH GMTTAKAARLFYQACVLATHDFIKVNQLEPYGDILISRGPKM</aaseq>|<br />
DNA = <dnaseqindica>54..106#297..365#464..522#618..662#749..768#877..953#2151..2247#2405..2486#2566..2644#2754..2917#3602..3645#3726..3881#3978..4146#4262..4329#4441..4588#4652..4739#5737..5864#5964..6048#6132..6244#6960..7042#cagcgcctccactctcactcgctcatccattccctccctcctcacgatcgagaatgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggtgggtttgcttcgctctccgctcctctcgatcgcgtcctttcggcttctcttctcatgcgccgttctgcggtgctccgttctatattgttttctgcgatttctctgctcgttccgctccgaaatccgaatgttcgccacttggttggagttgattaggccgctgattactccgcttttttttttcgcaggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctggtgagcgaattagtccgaatccagttgtctctgatttcttcgtttcgaacttgacggttttttttggggggattttgtgcgtgtggtttttgggttagtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtgagtccagtttgcttgttgtctccatagttccgatcgcatttgtttggtgatattttctgatgtgggtgcttgcgtcgtgggagtgtgagtaggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatggtgagttgctccctgattgcttctcttttgtttccattttttttggattcgttatagactcaaactgtgtgagatcttcttcgcagatgatgtgtctcggtttctggtaaaattcgagttcgattttcacctaattttggtgcctcctccttgatccatttgcctgtctatgctaacatggttcagattacgcttgtactaactcctcacacagattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtaagtgccctctttgtttccatgaccttctaggactagaagtttctagatgttctgtgcacggttttgggttcgagggaagattgaagaacatgctattatgttggtgaccgaggggagtttgcttttgtttccctgctgccagggattgtgagtttgtgtgtgattttcaccatccgatgctaatctgatggactcgtcatttgacacagttgcaagttttgatatgtcatcagcttacttggttctgattagaacatgctgcatctgtgtaatgttgattttatgatgatactatctccttgcagcatagtacattgttatgttttcagatgtacctgatgttgtcatatgactgattgttctgttctacctgttgtctattggcggttcatgggaccctgctgttacttgcctcttgttgtcttgctgactttggtagcagccgatgtctgtattatgcaggagtactattctacaaatgatctgtgtttcctggcagcataaatttgtctgtatgttgttccagtatatgtaggtcctctacatttgtagggtgatgaagggcttttgcttccccacagtgtttcctcctctcttaatgaaatgatatacaactctcttgcatattcaagaaaaaaaaactggaagggcattaggcagttaggcaggcattgtcagtgagcgatacatgctttatggggatgaacatttgactttttcttgggtgtcagttactggtgccaagggagcaggtctgagggccgtctggtacttgagaaatgttgctatcttagagtctagggaattccatcacctttgggaaccggaggcaaacatttcttaatcttgtatcatgctcgaaggactgactcttgtgggtgtaccatttccttccattgtggcctgcatctgatatgtaaccatgtggctgtgccatcatccccttgatcccttcggaactatgttcgatagttactgcaatgttcacgtgatgttgatacctgtactgttgcaatgagtttaaccctcttggagtcctggatagttcctctgaatgattgtatcccaagggtcttttcaacttacttttgtaaatagcatagagtgggtataagttggtggatggagaatgatattttgtaccaagagtaaaacagtaatggtttgctcatctaaacttggggcttcatgcaggtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatggtaatccctgtaatatgtatatttcggtggtgtctgattgtatgcattgaaagatggcattaagttatgagcaataaccacgagatagtcttgctttcagtctcctgacttttgccagattgtctctattcctctgaaatccgtcatgcatgtgcagcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaaggttttcatttcttttcttatgaattactctttgtggttgcttaagaggtgtactttctgactgaaatatgttatctcagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagaggtgaagcaaaattttattcttctcttattctaccattcattttttgcacttcttgttccttattttggccagtacaattattcattgagcaatgttacaatgtcaccagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaaggtcaattcaagcacatggtttggtctatttgatcctaaatttggaaagggtactatcatcctgtaaatcgggattttttttccagtttccatgccaaaagacaacaattctcatctctgttttttagcatgccacagatgcaaatgatatttcaaacaagtaaaacttccatccaaatatatctcagtgaatttatgatttgatgtagtttcttcagggatatgaacttgatggttatgtcaatatctcttaacagctagatattctatcttatcatatactctgctatattatgttggttaagaagctaaaagttcactcatcatctcctgttgcctttctacatttccaacggttggattttcgcgaggctaggtagagatgctgagcgattgccattgaatttgctacatgttatgtcattgaatttggcttttgtcaacgggataataaaacacattgtgtaacttgtcaccattcacactagtttactgactgaaattcaatttatattatatttgaatcttttctacttgctaaacaagacttgcatatagcctcttcctcgtgactatctgtacttcagtttgctatatctgatataagtgctggacatggtttgggtacattaatatgtgccatagtgcaagtgccttgttgcaattactgacaacttttctgcagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaaggtttgtgatcaagcgagccgttagcttcaggaacatctagatgaagaagataattgttttgtttgatattgtttaaccagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtgtatgtaattgctttgattacctaattctgtgtagagttttgtaactatgcagaattttgtgaacatatctgatgttttgccgtgtaatattgcagaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggttactacacaatttgtagttttctttcacctttctggatcaccaagggaactgtaagttttttataatttaatctgctaagttcgaactgaaaaggttgcaatcttttttaaaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccaggttatttctaaatttatatgtttatggaaatgatttatgctagcttttcctattgagctgtaacatttacattcattcttgaacttgtctgataagtggttcaatttgcagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctggtaagtacaaaaaacaatatattttatttatttagacactgaatgacatcagtcctgctgcagggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtgagtgttgattaatagcaaccttcactagttttctgaaatatgacttgttcctggaataaataaaaagttatccgtgcaaacttttgaagatgcatgtctttatactggagcctctttggtttatgttccaaagcatcgaagtggttagttgtcttattgatgaagtgttaggcaagaagaaaaggaaacggagattgttaccccccccctccagcggtaaccgctgaaaaccacgtgaaattcgtcctcaaatatttgaattaaaaatcggcggttttgcgttttcggcacagtaaccgcgatattcgcgcggttactgccaattgtgtagcagaatagaaacactcttaaaaaagtttaaaaaagcacttaaatgtgtgtagaaattggggataattagaagaatatataggatacttgcaaacctaacttttgggtgtaaaatacaaaaattctgcatgacattttctatgttatggacttcgaagcaattcaacatttcgtagcataataattcaacaacaacaattcaacaacctcacatttgaaagcatgtgccgagagagagcgatagagatagatgagaggacctaggagatatttttcccacttatgggacttaatgggccagataaacagtgcaactgtgcaacctaaggtccattacatttttcttttttccattttctaatgaacattcggttttaccctcaaatttgaatttatcttactctttttcaaaaaatttcttcactgtctaccactacaaatcaagaagtttttttatttgtttggaattttgaatttgggcaaaatttatcaaaccctaccaccggtaacccttactgtacccccgcggtaagcgcggttaccggtggtaagggaaaccctggtctaggctacttgactatcaactatcaagtggcagcttcctatctatggtccttctattttcatagaggtcttagtacaactgcgtgaggtcattgaacaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccaggttgacttcttttcagtccttatttcaaatgattctatacaaaagtgtggaaatttatttccccgtcatcataccgattaacttttaatttggtcacagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtaagtattcaactatacattatgtttgttccacagattacagtagatgtatactctgtgatcatcaaactaaatccatccaggtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcggtatgagttctataatcccaatgcgagtcaacagatgatgcaatcgctagagtaaacataatgttaacatttcatttgctggtttgatggttatttataatttccgtaagttcatttcaacacttgataagccatgtgtacttcctttccatattgcaactttgcaatgaaatattccaaccattgtttcaagttatgatatcaccgaaaccttttaggctcattacgtttttcccaggcttctctcattacattgaccaagtaaatataataagttcactttattagttcatgtagtgttaagggaggaaaacaaatgtgcaatagcactatttcctgagttggataagtgggcaacacctagtttgcttagccatagacagatgttggaaaatcttgaagaagtaccttggaaattcaatcgtacatcattgtggctatgtattttttgtttctttttcagattgtagccatgtttgatggacgagttagtgattttaactatgtcaataatggttatgtttcttttctccctcgatgagagaggatgagggcctaacaccatgtgtgggcaagatcggtgttcacaaaagtttggttagtgttttatattcttagctttactgtttagcgtggcagtttgatgtttttaggtgcttgtatgtgttattattggttcagtacttgtatttactgaggaccctttgttctgcagttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtgacatcctaaatgtttaatagttggacaattttctgctgttgtggttcttgcacatctcgtgttatgtatggtgtttaagtttgcacatgaagtttagaaaaacttcgaaggaaggcttgtaggtacgttgtattggggcatgtatttaacactagttttgtgtaggaaagaaattttgtaagtatgctgaatggcttgatagctggtgcaaggttaaagtt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062961.1 RefSeq:Os05g0580500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0580500&diff=276914Os05g05805002017-03-21T08:42:17Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
'''''Rad21/Rec8''''' is an important component and key regulator of cohesins. '''''OsRAD21-4''''', a '''''RAD21'''''-like gene from rice Zhonghua 10 (Oryza sativa L. ssp.japonica), is a single-copy gene in the rice genome and essential for efficient meiosis.<br />
<br />
===Function===<br />
'''''OsRad21-4''''' is composed of 20 exons and 19 introns.<ref name="ref1" /> It encodes a relatively hydrophilic protein and contains the entire Pfam04825 and Pfam04824 domains (spanning amino acids 1–115 and 554–608, respectively) (Figure 2A), of which Pfam04825 is highly conserved in all known members and Pfam04824 present in most of the '''''Rad21/Rec8''''' family.<ref name="ref1" /><ref name="ref2" /> The two domain regions are spaced by a long linker sequence (amino acids 116-553).<ref name="ref1" /> This linker sequence contains a potential nuclear targeting motif at positions 272–279 (KRKKRRKD), 2 separase recognition sites at 411–421 (ADDIEKLRGNT) and 420–430 (NTSGEYGRDYD) and a PEST motif at 511– 534 (RLSDVGPTPDLLEEIEPTQTPYEK) (Figure 2A)<ref name="ref1" />. These motifs are proposed to be implicated in function regulation in cohesion establishment and disassociation.<ref name="ref1" /><ref name="ref3" /> The deficiency of '''''OsRad21-4''''' at the mRNA and protein is correlated with pollen cell sterility phenotype.(Figure6)<ref name="ref1" /> '''''OsRad21-4''''' was essential to meiosis. (Figure7, Figure8)<ref name="ref1" /> In addtion, '''''OsRad21-4''''' is responsible for the pairing of some homologous chromosomes.(Figure9, Figure10)<ref name="ref1" /><br />
<br />
===Expression===<br />
'''''OsRad21-4''''' is present in the rice genome as a single-copy gene.<ref name="ref1" /> The mRNA and protein of '''''OsRad21-4''''' were expressed preferentially in young flowers where the pollen mother cells (PMCs) were in pre-meiotic stages.<ref name="ref1" /> '''''OsRAD21-4''''' cDNA cloned here is 2133 bp long and has a 5' UTR of 54 bp, a 3' UTR of 255 bp and an ORF of 1824 bp encoding a deduced polypeptide of 608 amino acids (OsRad21-4).<ref name="ref1" /> OsRad21-4 has a calculated molecular mass of 68.5 kDa and an isoelectric point (pI) of 5.45.<ref name="ref1" /> The protein is a nucleus-localizing protein.(Figure 2B)<ref name="ref1" />[[File:F23.png|200px|thumb|left|Figure2(B)]] As shown in Figure 3A, '''''OsRad21-4''''' was expressed preferentially in flowers, weakly in leaves and barely in buds and roots.<ref name="ref1" /> Furthermore, '''''OsRad21-4''''' was expressed dominantly just before the premeiotic stage of PMCs.(Figure 3C)<ref name="ref1" /> This gene should function in premeiotic and meiotic PMCs, which is consistent with this notion that meiotic cohesion is established at the pre-meiotic S phase. (Figur 4)<ref name="ref4" /><br />
[[File:F3A.png|200px|thumb|left|Figure3 (A)]][[File:F3C.png|200px|thumb|left|Figure3(C)]][[File:F4.png|200px|thumb|left|Figure4]]<br />
<br />
===Evolution===<br />
'''''OsRad21-4''''' is a rice orthologue of yeast Rec8.(Figure2(C))<ref name="ref1" /> In rice, '''''OsRad21-4''''' is required for homologous pairing and segregation.<ref name="ref1" /> It might be responsible mainly for sister chromatid-arm cohesion and to a lesser extent or not at all for centromere cohesion.<ref name="ref1" /> In addition, '''''OsRad21-4''''' is required for chromosome condensation.<ref name="ref1" /> Besides, Zhang et al suggest possible link between Rec8 proteins and chromosome fragmentation in higher eukaryotes.<ref name="ref1" /> Furthermore, appearance of micronuclei and/or undetached dinuclei-containing spores and unequal cell division at anaphase I and II in the deficient plants were similar to those reported in mutants of genes related to other early events of meiosis prophase I<ref name="ref5" />, suggesting possible interaction of early events of prophase I.<br />
<br />
==Labs working on this gene==<br />
1.Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Research Center of Molecular & Developmental Biology, Institute of Botany, Chinese academy of Sciences, Beijing 100093,China<br />
<br />
2.Graduate School of the Chinese Academy of Sciences, Beijing 100049, China<br />
<br />
3.Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan<br />
<br />
4.PRESTO, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan<br />
<br />
5.Imperial Cancer Research Fund, 44 Lincoln's Inn Field, London WC2A 3PX, UK<br />
<br />
6.Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan<br />
<br />
7.Faculty of Health Sciences for Welfare, Kansai University of Welfare Sciences, 3-11-1 Asahigaoka, Osaka 582-0026, Japan<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Zhang L, Tao J, Wang S, et al. The rice OsRad21-4, an orthologue of yeast Rec8 protein, is required for efficient meiosis[J]. Plant molecular biology, 2006, 60(4): 533-554.</ref><br />
* <ref name="ref2"><br />
Zhang L R, Tao J Y, Wang T. Molecular characterization of OsRAD21‐1, a rice homologue of yeast RAD21 essential for mitotic chromosome cohesion*[J]. Journal of experimental botany, 2004, 55(399): 1149-1152.</ref><br />
*<ref name="ref3">Nasmyth K. Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis[J]. Annual review of genetics, 2001, 35(1): 673-745.</ref><br />
*<ref name="ref4">Watanabe Y, Yokobayashi S, Yamamoto M, et al. Pre-meiotic S phase is linked to reductional chromosome segregation and recombination[J]. Nature, 2001, 409(6818): 359-363.</ref><br />
*<ref name="ref5">Ma H. Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants[J]. Annu. Rev. Plant Biol., 2005, 56: 393-434.</ref><br />
<references><br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0580500|<br />
Description = Rad21/Rec8 like protein, N-terminal domain containing protein|<br />
Version = NM_001062961.1 GI:115465652 GeneID:4339720|<br />
Length = 7262 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0580500, 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 5|Chromosome 5]]|<br />
AP = Chromosome 5:28971202..28978463|<br />
CDS = 28971255..28971307,28971498..28971566,28971665..28971723,28971819..28971863,28971950..28971969<br>,28972078..28972154,28973352..28973448,28973606..28973687,28973767..28973845<br>,28973955..28974118,28974803..28974846,28974927..28975082,28975179..28975347<br>,28975463..28975530,28975642..28975789,28975853..28975940,28976938..28977065<br>,28977165..28977249,28977333..28977445,28978161..28978243|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctgtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatgatgatgtgtctcggtttctgattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatgcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctgggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcgttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtga</cdnaseq>|<br />
AA = <aaseq>MFYSHQLLARKAPLGQIWMAATLHSKINRKRLDKLDIIKICEEI LNPSVPMALRLSGILMGGVAIVYERKVKALYDDVSRFLIEINEAWRVKPVADPTVLPK GKTQAKYEAVTLPENIMDMDVEQPMLFSEADTTRFRGMRLEDLDDQYINVNLDDDDFS RAENHHQADAENITLADNFGSGLGETDVFNRFERFDITDDDATFNVTPDGHPQVPSNL VPSPPRQEDSPQQQENHHAASSPLHEEAQQGGASVKNEQEQQKMKGQQPAKSSKRKKR RKDDEVMMDNDQIMIPGNVYQTWLKDPSSLITKRHRINSKVNLIRSIKIRDLMDLPLV SLISSLEKSPLEFYYPKELMQLWKECTEVKSPKAPSSGGQQSSSPEQQQRNLPPQAFP TQPQVDNDREMGFHPVDFADDIEKLRGNTSGEYGRDYDAFHSDHSVTPGSPGLSRRSA SSSGGSGRGFTQLDPEVQLPSGRSKRQHSSGKSFGNLDPVEEEFPFEQELRDFKMRRL SDVGPTPDLLEEIEPTQTPYEKKSNPIDQVTQSIHSYLKLHFDTPGASQSESLSQLAH GMTTAKAARLFYQACVLATHDFIKVNQLEPYGDILISRGPKM</aaseq>|<br />
DNA = <dnaseqindica>54..106#297..365#464..522#618..662#749..768#877..953#2151..2247#2405..2486#2566..2644#2754..2917#3602..3645#3726..3881#3978..4146#4262..4329#4441..4588#4652..4739#5737..5864#5964..6048#6132..6244#6960..7042#cagcgcctccactctcactcgctcatccattccctccctcctcacgatcgagaatgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggtgggtttgcttcgctctccgctcctctcgatcgcgtcctttcggcttctcttctcatgcgccgttctgcggtgctccgttctatattgttttctgcgatttctctgctcgttccgctccgaaatccgaatgttcgccacttggttggagttgattaggccgctgattactccgcttttttttttcgcaggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctggtgagcgaattagtccgaatccagttgtctctgatttcttcgtttcgaacttgacggttttttttggggggattttgtgcgtgtggtttttgggttagtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtgagtccagtttgcttgttgtctccatagttccgatcgcatttgtttggtgatattttctgatgtgggtgcttgcgtcgtgggagtgtgagtaggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatggtgagttgctccctgattgcttctcttttgtttccattttttttggattcgttatagactcaaactgtgtgagatcttcttcgcagatgatgtgtctcggtttctggtaaaattcgagttcgattttcacctaattttggtgcctcctccttgatccatttgcctgtctatgctaacatggttcagattacgcttgtactaactcctcacacagattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtaagtgccctctttgtttccatgaccttctaggactagaagtttctagatgttctgtgcacggttttgggttcgagggaagattgaagaacatgctattatgttggtgaccgaggggagtttgcttttgtttccctgctgccagggattgtgagtttgtgtgtgattttcaccatccgatgctaatctgatggactcgtcatttgacacagttgcaagttttgatatgtcatcagcttacttggttctgattagaacatgctgcatctgtgtaatgttgattttatgatgatactatctccttgcagcatagtacattgttatgttttcagatgtacctgatgttgtcatatgactgattgttctgttctacctgttgtctattggcggttcatgggaccctgctgttacttgcctcttgttgtcttgctgactttggtagcagccgatgtctgtattatgcaggagtactattctacaaatgatctgtgtttcctggcagcataaatttgtctgtatgttgttccagtatatgtaggtcctctacatttgtagggtgatgaagggcttttgcttccccacagtgtttcctcctctcttaatgaaatgatatacaactctcttgcatattcaagaaaaaaaaactggaagggcattaggcagttaggcaggcattgtcagtgagcgatacatgctttatggggatgaacatttgactttttcttgggtgtcagttactggtgccaagggagcaggtctgagggccgtctggtacttgagaaatgttgctatcttagagtctagggaattccatcacctttgggaaccggaggcaaacatttcttaatcttgtatcatgctcgaaggactgactcttgtgggtgtaccatttccttccattgtggcctgcatctgatatgtaaccatgtggctgtgccatcatccccttgatcccttcggaactatgttcgatagttactgcaatgttcacgtgatgttgatacctgtactgttgcaatgagtttaaccctcttggagtcctggatagttcctctgaatgattgtatcccaagggtcttttcaacttacttttgtaaatagcatagagtgggtataagttggtggatggagaatgatattttgtaccaagagtaaaacagtaatggtttgctcatctaaacttggggcttcatgcaggtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatggtaatccctgtaatatgtatatttcggtggtgtctgattgtatgcattgaaagatggcattaagttatgagcaataaccacgagatagtcttgctttcagtctcctgacttttgccagattgtctctattcctctgaaatccgtcatgcatgtgcagcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaaggttttcatttcttttcttatgaattactctttgtggttgcttaagaggtgtactttctgactgaaatatgttatctcagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagaggtgaagcaaaattttattcttctcttattctaccattcattttttgcacttcttgttccttattttggccagtacaattattcattgagcaatgttacaatgtcaccagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaaggtcaattcaagcacatggtttggtctatttgatcctaaatttggaaagggtactatcatcctgtaaatcgggattttttttccagtttccatgccaaaagacaacaattctcatctctgttttttagcatgccacagatgcaaatgatatttcaaacaagtaaaacttccatccaaatatatctcagtgaatttatgatttgatgtagtttcttcagggatatgaacttgatggttatgtcaatatctcttaacagctagatattctatcttatcatatactctgctatattatgttggttaagaagctaaaagttcactcatcatctcctgttgcctttctacatttccaacggttggattttcgcgaggctaggtagagatgctgagcgattgccattgaatttgctacatgttatgtcattgaatttggcttttgtcaacgggataataaaacacattgtgtaacttgtcaccattcacactagtttactgactgaaattcaatttatattatatttgaatcttttctacttgctaaacaagacttgcatatagcctcttcctcgtgactatctgtacttcagtttgctatatctgatataagtgctggacatggtttgggtacattaatatgtgccatagtgcaagtgccttgttgcaattactgacaacttttctgcagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaaggtttgtgatcaagcgagccgttagcttcaggaacatctagatgaagaagataattgttttgtttgatattgtttaaccagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtgtatgtaattgctttgattacctaattctgtgtagagttttgtaactatgcagaattttgtgaacatatctgatgttttgccgtgtaatattgcagaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggttactacacaatttgtagttttctttcacctttctggatcaccaagggaactgtaagttttttataatttaatctgctaagttcgaactgaaaaggttgcaatcttttttaaaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccaggttatttctaaatttatatgtttatggaaatgatttatgctagcttttcctattgagctgtaacatttacattcattcttgaacttgtctgataagtggttcaatttgcagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctggtaagtacaaaaaacaatatattttatttatttagacactgaatgacatcagtcctgctgcagggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtgagtgttgattaatagcaaccttcactagttttctgaaatatgacttgttcctggaataaataaaaagttatccgtgcaaacttttgaagatgcatgtctttatactggagcctctttggtttatgttccaaagcatcgaagtggttagttgtcttattgatgaagtgttaggcaagaagaaaaggaaacggagattgttaccccccccctccagcggtaaccgctgaaaaccacgtgaaattcgtcctcaaatatttgaattaaaaatcggcggttttgcgttttcggcacagtaaccgcgatattcgcgcggttactgccaattgtgtagcagaatagaaacactcttaaaaaagtttaaaaaagcacttaaatgtgtgtagaaattggggataattagaagaatatataggatacttgcaaacctaacttttgggtgtaaaatacaaaaattctgcatgacattttctatgttatggacttcgaagcaattcaacatttcgtagcataataattcaacaacaacaattcaacaacctcacatttgaaagcatgtgccgagagagagcgatagagatagatgagaggacctaggagatatttttcccacttatgggacttaatgggccagataaacagtgcaactgtgcaacctaaggtccattacatttttcttttttccattttctaatgaacattcggttttaccctcaaatttgaatttatcttactctttttcaaaaaatttcttcactgtctaccactacaaatcaagaagtttttttatttgtttggaattttgaatttgggcaaaatttatcaaaccctaccaccggtaacccttactgtacccccgcggtaagcgcggttaccggtggtaagggaaaccctggtctaggctacttgactatcaactatcaagtggcagcttcctatctatggtccttctattttcatagaggtcttagtacaactgcgtgaggtcattgaacaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccaggttgacttcttttcagtccttatttcaaatgattctatacaaaagtgtggaaatttatttccccgtcatcataccgattaacttttaatttggtcacagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtaagtattcaactatacattatgtttgttccacagattacagtagatgtatactctgtgatcatcaaactaaatccatccaggtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcggtatgagttctataatcccaatgcgagtcaacagatgatgcaatcgctagagtaaacataatgttaacatttcatttgctggtttgatggttatttataatttccgtaagttcatttcaacacttgataagccatgtgtacttcctttccatattgcaactttgcaatgaaatattccaaccattgtttcaagttatgatatcaccgaaaccttttaggctcattacgtttttcccaggcttctctcattacattgaccaagtaaatataataagttcactttattagttcatgtagtgttaagggaggaaaacaaatgtgcaatagcactatttcctgagttggataagtgggcaacacctagtttgcttagccatagacagatgttggaaaatcttgaagaagtaccttggaaattcaatcgtacatcattgtggctatgtattttttgtttctttttcagattgtagccatgtttgatggacgagttagtgattttaactatgtcaataatggttatgtttcttttctccctcgatgagagaggatgagggcctaacaccatgtgtgggcaagatcggtgttcacaaaagtttggttagtgttttatattcttagctttactgtttagcgtggcagtttgatgtttttaggtgcttgtatgtgttattattggttcagtacttgtatttactgaggaccctttgttctgcagttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtgacatcctaaatgtttaatagttggacaattttctgctgttgtggttcttgcacatctcgtgttatgtatggtgtttaagtttgcacatgaagtttagaaaaacttcgaaggaaggcttgtaggtacgttgtattggggcatgtatttaacactagttttgtgtaggaaagaaattttgtaagtatgctgaatggcttgatagctggtgcaaggttaaagtt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062961.1 RefSeq:Os05g0580500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0580500&diff=276913Os05g05805002017-03-21T08:41:56Z<p>Xysj2012: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
'''''Rad21/Rec8''''' is an important component and key regulator of cohesins. '''''OsRAD21-4''''', a '''''RAD21'''''-like gene from rice Zhonghua 10 (Oryza sativa L. ssp.japonica), is a single-copy gene in the rice genome and essential for efficient meiosis.<br />
<br />
===Function===<br />
'''''OsRad21-4''''' is composed of 20 exons and 19 introns.<ref name="ref1" /> It encodes a relatively hydrophilic protein and contains the entire Pfam04825 and Pfam04824 domains (spanning amino acids 1–115 and 554–608, respectively) (Figure 2A), of which Pfam04825 is highly conserved in all known members and Pfam04824 present in most of the '''''Rad21/Rec8''''' family.<ref name="ref1" /><ref name="ref2" /> The two domain regions are spaced by a long linker sequence (amino acids 116-553).<ref name="ref1" /> This linker sequence contains a potential nuclear targeting motif at positions 272–279 (KRKKRRKD), 2 separase recognition sites at 411–421 (ADDIEKLRGNT) and 420–430 (NTSGEYGRDYD) and a PEST motif at 511– 534 (RLSDVGPTPDLLEEIEPTQTPYEK) (Figure 2A)<ref name="ref1" />. These motifs are proposed to be implicated in function regulation in cohesion establishment and disassociation.<ref name="ref1" /><ref name="ref3" /> The deficiency of '''''OsRad21-4''''' at the mRNA and protein is correlated with pollen cell sterility phenotype.(Figure6)<ref name="ref1" /> '''''OsRad21-4''''' was essential to meiosis. (Figure7, Figure8)<ref name="ref1" /> In addtion, '''''OsRad21-4''''' is responsible for the pairing of some homologous chromosomes.(Figure9, Figure10)<ref name="ref1" /><br />
<br />
===Expression===<br />
'''''OsRad21-4''''' is present in the rice genome as a single-copy gene.<ref name="ref1" /> The mRNA and protein of '''''OsRad21-4''''' were expressed preferentially in young flowers where the pollen mother cells (PMCs) were in pre-meiotic stages.<ref name="ref1" /> '''''OsRAD21-4''''' cDNA cloned here is 2133 bp long and has a 5' UTR of 54 bp, a 3' UTR of 255 bp and an ORF of 1824 bp encoding a deduced polypeptide of 608 amino acids (OsRad21-4).<ref name="ref1" /> OsRad21-4 has a calculated molecular mass of 68.5 kDa and an isoelectric point (pI) of 5.45.<ref name="ref1" /> The protein is a nucleus-localizing protein.(Figure 2B)<ref name="ref1" />[[File:F23.png|200px|thumb|left|Figure2(B)]] As shown in Figure 3A, '''''OsRad21-4''''' was expressed preferentially in flowers, weakly in leaves and barely in buds and roots.<ref name="ref1" /> Furthermore, '''''OsRad21-4''''' was expressed dominantly just before the premeiotic stage of PMCs.(Figure 3C)<ref name="ref1" /> This gene should function in premeiotic and meiotic PMCs, which is consistent with this notion that meiotic cohesion is established at the pre-meiotic S phase. (Figur 4)<ref name="ref4" /><br />
[[File:F3A.png|200px|thumb|left|Figure3 (A)]][[File:F3C.png|200px|thumb|left|Figure3(C)]][[File:F4.png|200px|thumb|left|Figure4]]<br />
<br />
===Evolution===<br />
'''''OsRad21-4''''' is a rice orthologue of yeast Rec8.(Figure2(C))<ref name="ref1" /> In rice, '''''OsRad21-4''''' is required for homologous pairing and segregation.<ref name="ref1" /> It might be responsible mainly for sister chromatid-arm cohesion and to a lesser extent or not at all for centromere cohesion.<ref name="ref1" /> In addition, '''''OsRad21-4''''' is required for chromosome condensation.<ref name="ref1" /> Besides, Zhang et al suggest possible link between Rec8 proteins and chromosome fragmentation in higher eukaryotes.<ref name="ref1" /> Furthermore, appearance of micronuclei and/or undetached dinuclei-containing spores and unequal cell division at anaphase I and II in the deficient plants were similar to those reported in mutants of genes related to other early events of meiosis prophase I<ref name="ref5" />, suggesting possible interaction of early events of prophase I.<br />
[[File:F2C.png|200px|thumb|left|Figure2(C)]]<br />
<br />
==Labs working on this gene==<br />
1.Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Research Center of Molecular & Developmental Biology, Institute of Botany, Chinese academy of Sciences, Beijing 100093,China<br />
<br />
2.Graduate School of the Chinese Academy of Sciences, Beijing 100049, China<br />
<br />
3.Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan<br />
<br />
4.PRESTO, Japan Science and Technology Corporation, Kawaguchi, Saitama 332-0012, Japan<br />
<br />
5.Imperial Cancer Research Fund, 44 Lincoln's Inn Field, London WC2A 3PX, UK<br />
<br />
6.Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan<br />
<br />
7.Faculty of Health Sciences for Welfare, Kansai University of Welfare Sciences, 3-11-1 Asahigaoka, Osaka 582-0026, Japan<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Zhang L, Tao J, Wang S, et al. The rice OsRad21-4, an orthologue of yeast Rec8 protein, is required for efficient meiosis[J]. Plant molecular biology, 2006, 60(4): 533-554.</ref><br />
* <ref name="ref2"><br />
Zhang L R, Tao J Y, Wang T. Molecular characterization of OsRAD21‐1, a rice homologue of yeast RAD21 essential for mitotic chromosome cohesion*[J]. Journal of experimental botany, 2004, 55(399): 1149-1152.</ref><br />
*<ref name="ref3">Nasmyth K. Disseminating the genome: joining, resolving, and separating sister chromatids during mitosis and meiosis[J]. Annual review of genetics, 2001, 35(1): 673-745.</ref><br />
*<ref name="ref4">Watanabe Y, Yokobayashi S, Yamamoto M, et al. Pre-meiotic S phase is linked to reductional chromosome segregation and recombination[J]. Nature, 2001, 409(6818): 359-363.</ref><br />
*<ref name="ref5">Ma H. Molecular genetic analyses of microsporogenesis and microgametogenesis in flowering plants[J]. Annu. Rev. Plant Biol., 2005, 56: 393-434.</ref><br />
<references><br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0580500|<br />
Description = Rad21/Rec8 like protein, N-terminal domain containing protein|<br />
Version = NM_001062961.1 GI:115465652 GeneID:4339720|<br />
Length = 7262 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0580500, 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 5|Chromosome 5]]|<br />
AP = Chromosome 5:28971202..28978463|<br />
CDS = 28971255..28971307,28971498..28971566,28971665..28971723,28971819..28971863,28971950..28971969<br>,28972078..28972154,28973352..28973448,28973606..28973687,28973767..28973845<br>,28973955..28974118,28974803..28974846,28974927..28975082,28975179..28975347<br>,28975463..28975530,28975642..28975789,28975853..28975940,28976938..28977065<br>,28977165..28977249,28977333..28977445,28978161..28978243|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:28971202..28978463<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctgtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatgatgatgtgtctcggtttctgattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatgcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctgggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcgttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtga</cdnaseq>|<br />
AA = <aaseq>MFYSHQLLARKAPLGQIWMAATLHSKINRKRLDKLDIIKICEEI LNPSVPMALRLSGILMGGVAIVYERKVKALYDDVSRFLIEINEAWRVKPVADPTVLPK GKTQAKYEAVTLPENIMDMDVEQPMLFSEADTTRFRGMRLEDLDDQYINVNLDDDDFS RAENHHQADAENITLADNFGSGLGETDVFNRFERFDITDDDATFNVTPDGHPQVPSNL VPSPPRQEDSPQQQENHHAASSPLHEEAQQGGASVKNEQEQQKMKGQQPAKSSKRKKR RKDDEVMMDNDQIMIPGNVYQTWLKDPSSLITKRHRINSKVNLIRSIKIRDLMDLPLV SLISSLEKSPLEFYYPKELMQLWKECTEVKSPKAPSSGGQQSSSPEQQQRNLPPQAFP TQPQVDNDREMGFHPVDFADDIEKLRGNTSGEYGRDYDAFHSDHSVTPGSPGLSRRSA SSSGGSGRGFTQLDPEVQLPSGRSKRQHSSGKSFGNLDPVEEEFPFEQELRDFKMRRL SDVGPTPDLLEEIEPTQTPYEKKSNPIDQVTQSIHSYLKLHFDTPGASQSESLSQLAH GMTTAKAARLFYQACVLATHDFIKVNQLEPYGDILISRGPKM</aaseq>|<br />
DNA = <dnaseqindica>54..106#297..365#464..522#618..662#749..768#877..953#2151..2247#2405..2486#2566..2644#2754..2917#3602..3645#3726..3881#3978..4146#4262..4329#4441..4588#4652..4739#5737..5864#5964..6048#6132..6244#6960..7042#cagcgcctccactctcactcgctcatccattccctccctcctcacgatcgagaatgttctactcgcaccagctcctcgcgcggaaggctccgctcggccagatatggtgggtttgcttcgctctccgctcctctcgatcgcgtcctttcggcttctcttctcatgcgccgttctgcggtgctccgttctatattgttttctgcgatttctctgctcgttccgctccgaaatccgaatgttcgccacttggttggagttgattaggccgctgattactccgcttttttttttcgcaggatggcggcgacgcttcactcgaagatcaaccggaagcggcttgacaagctcgacatcatcaaaatctggtgagcgaattagtccgaatccagttgtctctgatttcttcgtttcgaacttgacggttttttttggggggattttgtgcgtgtggtttttgggttagtgaggagattttgaacccgtcggtacccatggcactaaggctctccggaattctcatgggtgagtccagtttgcttgttgtctccatagttccgatcgcatttgtttggtgatattttctgatgtgggtgcttgcgtcgtgggagtgtgagtaggtggtgtggcgatcgtgtacgagaggaaggtgaaggctctgtatggtgagttgctccctgattgcttctcttttgtttccattttttttggattcgttatagactcaaactgtgtgagatcttcttcgcagatgatgtgtctcggtttctggtaaaattcgagttcgattttcacctaattttggtgcctcctccttgatccatttgcctgtctatgctaacatggttcagattacgcttgtactaactcctcacacagattgagatcaacgaggcatggcgggtcaagccagtcgcagaccccaccgtacttcccaagggcaaaacccaagccaagtaagtgccctctttgtttccatgaccttctaggactagaagtttctagatgttctgtgcacggttttgggttcgagggaagattgaagaacatgctattatgttggtgaccgaggggagtttgcttttgtttccctgctgccagggattgtgagtttgtgtgtgattttcaccatccgatgctaatctgatggactcgtcatttgacacagttgcaagttttgatatgtcatcagcttacttggttctgattagaacatgctgcatctgtgtaatgttgattttatgatgatactatctccttgcagcatagtacattgttatgttttcagatgtacctgatgttgtcatatgactgattgttctgttctacctgttgtctattggcggttcatgggaccctgctgttacttgcctcttgttgtcttgctgactttggtagcagccgatgtctgtattatgcaggagtactattctacaaatgatctgtgtttcctggcagcataaatttgtctgtatgttgttccagtatatgtaggtcctctacatttgtagggtgatgaagggcttttgcttccccacagtgtttcctcctctcttaatgaaatgatatacaactctcttgcatattcaagaaaaaaaaactggaagggcattaggcagttaggcaggcattgtcagtgagcgatacatgctttatggggatgaacatttgactttttcttgggtgtcagttactggtgccaagggagcaggtctgagggccgtctggtacttgagaaatgttgctatcttagagtctagggaattccatcacctttgggaaccggaggcaaacatttcttaatcttgtatcatgctcgaaggactgactcttgtgggtgtaccatttccttccattgtggcctgcatctgatatgtaaccatgtggctgtgccatcatccccttgatcccttcggaactatgttcgatagttactgcaatgttcacgtgatgttgatacctgtactgttgcaatgagtttaaccctcttggagtcctggatagttcctctgaatgattgtatcccaagggtcttttcaacttacttttgtaaatagcatagagtgggtataagttggtggatggagaatgatattttgtaccaagagtaaaacagtaatggtttgctcatctaaacttggggcttcatgcaggtatgaagcagtaacactgccagagaatatcatggatatggatgtggagcagcccatgcttttctcagaggctgatactacaaggttccggggaatggtaatccctgtaatatgtatatttcggtggtgtctgattgtatgcattgaaagatggcattaagttatgagcaataaccacgagatagtcttgctttcagtctcctgacttttgccagattgtctctattcctctgaaatccgtcatgcatgtgcagcgtttggaggatttggatgaccaatacattaatgtcaacctagacgatgatgacttctcgcgcgctgagaatcatcaccaaggttttcatttcttttcttatgaattactctttgtggttgcttaagaggtgtactttctgactgaaatatgttatctcagctgatgcagaaaatatcaccctggctgataatttcgggtctgggcttggagagactgatgtgttcaatcgttttgagaggtgaagcaaaattttattcttctcttattctaccattcattttttgcacttcttgttccttattttggccagtacaattattcattgagcaatgttacaatgtcaccagattcgacataacagatgatgatgcaactttcaatgtcactcctgatggacacccacaggttccaagtaatctggttccttctccacctaggcaggaagactctcctcagcaacaagaaaaccatcatgctgcctcatcccctcttcacgaagaagctcaacaaggtcaattcaagcacatggtttggtctatttgatcctaaatttggaaagggtactatcatcctgtaaatcgggattttttttccagtttccatgccaaaagacaacaattctcatctctgttttttagcatgccacagatgcaaatgatatttcaaacaagtaaaacttccatccaaatatatctcagtgaatttatgatttgatgtagtttcttcagggatatgaacttgatggttatgtcaatatctcttaacagctagatattctatcttatcatatactctgctatattatgttggttaagaagctaaaagttcactcatcatctcctgttgcctttctacatttccaacggttggattttcgcgaggctaggtagagatgctgagcgattgccattgaatttgctacatgttatgtcattgaatttggcttttgtcaacgggataataaaacacattgtgtaacttgtcaccattcacactagtttactgactgaaattcaatttatattatatttgaatcttttctacttgctaaacaagacttgcatatagcctcttcctcgtgactatctgtacttcagtttgctatatctgatataagtgctggacatggtttgggtacattaatatgtgccatagtgcaagtgccttgttgcaattactgacaacttttctgcagggggggcatctgtaaaaaatgagcaagagcagcagaagatgaaggtttgtgatcaagcgagccgttagcttcaggaacatctagatgaagaagataattgttttgtttgatattgtttaaccagggtcagcaacctgctaaatcatcaaagagaaaaaaacgtaggaaagatgatgaggtgatgatggataacgaccagataatgatcccaggaaatgtatatcaaacatggctgaaggatccatcaagcctcattaccaaaaggcacagaatcaacagtgtatgtaattgctttgattacctaattctgtgtagagttttgtaactatgcagaattttgtgaacatatctgatgttttgccgtgtaatattgcagaaagttaatcttattcggtcaatcaagataagagacctcatggacttgcccctcgtttctctaatatcttccttggagaagtcacccttagaattttattatcctaaggaacttatgcagctttggaaggaatgtactgaagtcaagtccccaaaagctccatcttcaggttactacacaatttgtagttttctttcacctttctggatcaccaagggaactgtaagttttttataatttaatctgctaagttcgaactgaaaaggttgcaatcttttttaaaggagggcagcagtcatcatcaccagaacaacagcaaagaaacttgcctcctcaggcatttccaacccaggttatttctaaatttatatgtttatggaaatgatttatgctagcttttcctattgagctgtaacatttacattcattcttgaacttgtctgataagtggttcaatttgcagcctcaggttgataatgacagggaaatgggatttcacccagtggactttgcagatgacatcgaaaaactccgaggaaacactagtggggaatatggaagagattatgatgcttttcacagtgatcatagtgttactcctggaagtcctggtaagtacaaaaaacaatatattttatttatttagacactgaatgacatcagtcctgctgcagggctaagtcgcaggtctgcttcaagctctggtggctctggacggggatttacgcagttggatccagaagtacagttgccatccggaaggtgagtgttgattaatagcaaccttcactagttttctgaaatatgacttgttcctggaataaataaaaagttatccgtgcaaacttttgaagatgcatgtctttatactggagcctctttggtttatgttccaaagcatcgaagtggttagttgtcttattgatgaagtgttaggcaagaagaaaaggaaacggagattgttaccccccccctccagcggtaaccgctgaaaaccacgtgaaattcgtcctcaaatatttgaattaaaaatcggcggttttgcgttttcggcacagtaaccgcgatattcgcgcggttactgccaattgtgtagcagaatagaaacactcttaaaaaagtttaaaaaagcacttaaatgtgtgtagaaattggggataattagaagaatatataggatacttgcaaacctaacttttgggtgtaaaatacaaaaattctgcatgacattttctatgttatggacttcgaagcaattcaacatttcgtagcataataattcaacaacaacaattcaacaacctcacatttgaaagcatgtgccgagagagagcgatagagatagatgagaggacctaggagatatttttcccacttatgggacttaatgggccagataaacagtgcaactgtgcaacctaaggtccattacatttttcttttttccattttctaatgaacattcggttttaccctcaaatttgaatttatcttactctttttcaaaaaatttcttcactgtctaccactacaaatcaagaagtttttttatttgtttggaattttgaatttgggcaaaatttatcaaaccctaccaccggtaacccttactgtacccccgcggtaagcgcggttaccggtggtaagggaaaccctggtctaggctacttgactatcaactatcaagtggcagcttcctatctatggtccttctattttcatagaggtcttagtacaactgcgtgaggtcattgaacaggtccaagaggcagcattcatctggaaaaagctttgggaacctcgatccagttgaagaagaattcccattcgagcaagaacttagagatttcaagatgagaaggctttcagatgttgggccaactccaggttgacttcttttcagtccttatttcaaatgattctatacaaaagtgtggaaatttatttccccgtcatcataccgattaacttttaatttggtcacagacctgctggaagaaatcgaacctactcaaaccccatatgaaaagaaatccaatcctatcgaccaggtcacacaatcaatccactcgtaagtattcaactatacattatgtttgttccacagattacagtagatgtatactctgtgatcatcaaactaaatccatccaggtacctcaagctacactttgacaccccaggggcctcacagtctgaatcattaagtcagctagcacatgggatgactacagcaaaggctgcccgactcttctatcaagcatgcggtatgagttctataatcccaatgcgagtcaacagatgatgcaatcgctagagtaaacataatgttaacatttcatttgctggtttgatggttatttataatttccgtaagttcatttcaacacttgataagccatgtgtacttcctttccatattgcaactttgcaatgaaatattccaaccattgtttcaagttatgatatcaccgaaaccttttaggctcattacgtttttcccaggcttctctcattacattgaccaagtaaatataataagttcactttattagttcatgtagtgttaagggaggaaaacaaatgtgcaatagcactatttcctgagttggataagtgggcaacacctagtttgcttagccatagacagatgttggaaaatcttgaagaagtaccttggaaattcaatcgtacatcattgtggctatgtattttttgtttctttttcagattgtagccatgtttgatggacgagttagtgattttaactatgtcaataatggttatgtttcttttctccctcgatgagagaggatgagggcctaacaccatgtgtgggcaagatcggtgttcacaaaagtttggttagtgttttatattcttagctttactgtttagcgtggcagtttgatgtttttaggtgcttgtatgtgttattattggttcagtacttgtatttactgaggaccctttgttctgcagttttagcaactcatgattttatcaaggttaaccagctggaaccatacggagacatcttgatctcgaggggaccaaagatgtgacatcctaaatgtttaatagttggacaattttctgctgttgtggttcttgcacatctcgtgttatgtatggtgtttaagtttgcacatgaagtttagaaaaacttcgaaggaaggcttgtaggtacgttgtattggggcatgtatttaacactagttttgtgtaggaaagaaattttgtaagtatgctgaatggcttgatagctggtgcaaggttaaagtt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062961.1 RefSeq:Os05g0580500]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0531600&diff=276912Os08g05316002017-03-21T08:38:46Z<p>Xysj2012: </p>
<hr />
<div>Os08g0531600(OsSPL16) is a very important gene that encoding a positive regulator of cell prolifertion which can pormote cell division and grain filling.<br />
<br />
==Annotated Information==<br />
qGW8 within a genetic window on the long arm of chromosome 8 defined by the markers RM80 and RM447.The progeny testing of homozygous recombinant plants allowed this region to be narrowed to an ~7.5-kb stretch flanked by RM502 and PSM711.Quantitative trait locus GW8 is synonymous with OsSPL16, which encodes a protein that is a positive regulator of cell proliferation.Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. Conversely, a loss-of-function mutation in Basmati rice is associated with the formation of a more slender grain and better quality of appearance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs. We also show that a marker-assisted strategy targeted at elite alleles of GS3 and OsSPL16 underlying grain size and shape can be effectively used to simultaneously improve grain quality and yield.<br />
===Function===<br />
[[File:Parental grains.jpg|frame|'''Figure1''' Parental grains. Scale bar, 3 mm.]]<br />
<br />
'''''OsSPL16''''' control of grain size, shape, and quality<ref name="ref1" />.<br />
'''''OsSPL16''''' encodes a protein that is a positive regulator of cell proliferation. OsSPL16contributes to organ size through its effect on the cell cycle machinery.Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. The candidate gene ''''''OsSPL16'''''' encodes squamosa promoter-binding protein-like 16, which belongs to the SBP domain family of transcription factors and shares homology with the product of '''''tga1''''',a domestication syndrome gene associated with the formation of grains in maize<ref name="ref1" />. Grain width and length were also altered in NIL-'''''qw8''''' plaints expressing the Basmati385 '''''OsSPL16''''' cDNA under the control of the native HJX74 promoter.The SPL genes have an important role in the control of flowering.The SPL genes have been shown to be regulated by microRNA miR156 (refs. 14–16,19–22), and OsSPL16contains an OsmiR156 target sequence. OsSPL16functions as a negative regulator of panicle branching.<br />
<br />
===Mutation===<br />
Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice.A loss-of-function mutation in Basmati rice is assciated with the formation of a more slender grain and better quality of apperance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs<ref name="ref1" />.<br />
<br />
===Expression===<br />
[[File: Expression of OsSPL16in NIL-GW8and NIL-gw8.jpg|frame|'''Figure2''' Expression of OsSPL16in NIL-GW8and NIL-gw8.R, root; C, culm; L, leaf blade; SAM, shoot apex meristem; BM, branch meristem; YP1–Y22, young panicles, where the number indicates the length of the panicle in centimeters. Expression levels are shown as relative number of copies per 1,000 copies of rice actin3. Data are given as mean ±s.e.m. (n= 4).]]<br />
The expression profiles of OsSPL16in various organs of HJX74 were examined by quantitative RT-PCR analysis. OsSPL16 was preferentially expressed in developing panicles, and the highest levels of OsSPL16expression were found in panicles of 7 cm in length, whereas there was less transcript accumulation in the root, culm, leaf sheath, shoot meristem and young panicle(of <1 cm in length)<ref name="ref1 " /><br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National <br />
Centre for Plant Gene Research, Beijing, China. <br />
The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural <br />
University, Guangzhou, China. <br />
The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.<br />
working<br />
Development of the SSSL population.Fine mapping of qGW8.Transgene constructs.Expression analysis.Histological analysis.Transactivation activity assay.Analysis of transgenic plants expressing OsSPL16.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Wang S, Wu K, Yuan Q, et al. Control of grain size, shape and quality by OsSPL16 in rice[J]. Nature genetics, 2012, 44(8): 950-954.<br />
</ref><br />
</references><br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os08g0531600&diff=276911Os08g05316002017-03-21T08:38:19Z<p>Xysj2012: </p>
<hr />
<div>Os08g0531600(OsSPL16) is a very important gene that encoding a positive regulator of cell prolifertion which can pormote cell division and grain filling.<br />
<br />
==Annotated Information==<br />
qGW8 within a genetic window on the long arm of chromosome 8 defined by the markers RM80 and RM447.The progeny testing of homozygous recombinant plants allowed this region to be narrowed to an ~7.5-kb stretch flanked by RM502 and PSM711.Quantitative trait locus GW8 is synonymous with OsSPL16, which encodes a protein that is a positive regulator of cell proliferation.Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. Conversely, a loss-of-function mutation in Basmati rice is associated with the formation of a more slender grain and better quality of appearance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs. We also show that a marker-assisted strategy targeted at elite alleles of GS3 and OsSPL16 underlying grain size and shape can be effectively used to simultaneously improve grain quality and yield.<br />
===Function===<br />
[[File:Parental grains.jpg|frame|'''Figure1''' Parental grains. Scale bar, 3 mm.]]<br />
<br />
'''''OsSPL16''''' control of grain size, shape, and quality<ref name="ref1" />.<br />
'''''OsSPL16''''' encodes a protein that is a positive regulator of cell proliferation. OsSPL16contributes to organ size through its effect on the cell cycle machinery.Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice. The candidate gene ''''''OsSPL16'''''' encodes squamosa promoter-binding protein-like 16, which belongs to the SBP domain family of transcription factors and shares homology with the product of '''''tga1''''',a domestication syndrome gene associated with the formation of grains in maize<ref name="ref1" />. Grain width and length were also altered in NIL-'''''qw8''''' plaints expressing the Basmati385 '''''OsSPL16''''' cDNA under the control of the native HJX74 promoter.The SPL genes have an important role in the control of flowering.The SPL genes have been shown to be regulated by microRNA miR156 (refs. 14–16,19–22), and OsSPL16contains an OsmiR156 target sequence. OsSPL16functions as a negative regulator of panicle branching.<br />
<br />
<br />
<br />
<br />
===Mutation===<br />
Higher expression of this gene promotes cell division and grain filling, with positive consequences for grain width and yield in rice.A loss-of-function mutation in Basmati rice is assciated with the formation of a more slender grain and better quality of apperance. The correlation between grain size and allelic variation at the GW8 locus suggests that mutations within the promoter region were likely selected in rice breeding programs<ref name="ref1" />.<br />
<br />
<br />
<br />
<br />
===Expression===<br />
[[File: Expression of OsSPL16in NIL-GW8and NIL-gw8.jpg|frame|'''Figure2''' Expression of OsSPL16in NIL-GW8and NIL-gw8.R, root; C, culm; L, leaf blade; SAM, shoot apex meristem; BM, branch meristem; YP1–Y22, young panicles, where the number indicates the length of the panicle in centimeters. Expression levels are shown as relative number of copies per 1,000 copies of rice actin3. Data are given as mean ±s.e.m. (n= 4).]]<br />
The expression profiles of OsSPL16in various organs of HJX74 were examined by quantitative RT-PCR analysis. OsSPL16 was preferentially expressed in developing panicles, and the highest levels of OsSPL16expression were found in panicles of 7 cm in length, whereas there was less transcript accumulation in the root, culm, leaf sheath, shoot meristem and young panicle(of <1 cm in length)<ref name="ref1 " /><br />
<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National <br />
Centre for Plant Gene Research, Beijing, China. <br />
The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural <br />
University, Guangzhou, China. <br />
The State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China.<br />
working<br />
Development of the SSSL population.Fine mapping of qGW8.Transgene constructs.Expression analysis.Histological analysis.Transactivation activity assay.Analysis of transgenic plants expressing OsSPL16.<br />
<br />
==References==<br />
<references><br />
* <ref name="ref1"><br />
Wang S, Wu K, Yuan Q, et al. Control of grain size, shape and quality by OsSPL16 in rice[J]. Nature genetics, 2012, 44(8): 950-954.<br />
</ref><br />
</references><br />
==Structured Information==<br />
<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 8]]<br />
[[Category:Chromosome 8]]</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=276759Main Page2017-03-07T04:29:11Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
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<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[RiceWiki:Curated Genes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
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|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[RiceWiki:Curated Genes|'''400 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
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<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
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<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Jun 24th, 2016''': The Upcoming Conference Note: [http://pgc.hzau.edu.cn/ The 17th Conference of Plant Genomics] in China will be held in Fuzhou China from August 19th to 22th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
* '''Jan 31th, 2016''': The staffs of BIG Data Center presented a keynote lecture at [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php the KAUST Research Conference in Saudi Arabia]. <br />
</div><br />
|}<br />
<!--------------main part two----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<br />
<!-------------Lab Information--------------><br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent; width:65%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
<div style="padding:0.5em 1em;font-size:100%"><br />
'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
</div><br />
<br />
<!------------Visitor Statistics-------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #66B3FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Visitor Statistics</div><br />
<div style="padding:0.5em 1em;text-align:center"><br />
<htmlet nocache="yes">earth</htmlet><br />
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|}</div>Xysj2012https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Main_Page&diff=276758Main Page2017-03-07T04:28:34Z<p>Xysj2012: </p>
<hr />
<div>__NOTITLE__<br />
__NOTOC__<br />
__NOEDITSECTION__<br />
<!-----------------title---------------------><br />
{|style="width:100%; margin-top:10px; background-color:#f6f6f6; border:1px solid #d2d2d2; margin-bottom: 10px;"<br />
|style="width:50%; text-align:center; white-space:nowrap; color:#000"|<br />
<div style="font-size:180%; border:none; margin:0; padding:.5em; color:#000;">Welcome to RiceWiki</div><br />
<div style="padding:0em; font-size:100%">[[:Category:Genes |86,216]] rice genes inside</div><br />
<div style="padding:0em; font-size:100%; color:#492;">'''Contribute your efforts, further our knowledge.'''</div><br />
<br />
|style="width:18%;|<br />
*<span class=plainlinks>[[RiceWiki:Curated Genes|'''Genes''']]</span><br />
*[[RiceWiki:Omics Knowledge Portal for Rice|'''Omics Knowledge''']]<br />
|style="width:18%;|<br />
*[[Special:BLAST|'''BLAST''']]<br />
*[[RiceWiki:Templates|'''Templates''']]<br />
|style="width:18%;|<br />
*[http://visual.ic4r.org/ '''Genome Browser''']<br />
*[http://databasecommons.org/browse.jsp?organism=Oryza%20sativa '''Databases''']<br />
|}<br />
<br />
<!---------------welcome Box-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|valign="top" style="border:1px solid #c6c6c6; background-color:transparent; width:100%;"|<br />
<div style="background:#f1f1f1; border-bottom:1px solid #c6c6c6; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Introduction</div><br />
<div style="padding:0.5em 0.5em;">{{:RiceWiki:Summary}}</div><br />
<div style="padding:0.2em 0.5em;text-align:center">''Nothing great is ever accomplished in isolation. – Yo-Yo Ma''</div><br />
----<br />
<div style="padding:0.5em 0.5em;"><br />
{|<br />
|style="width:70%; white-space:nowrap; color:#000"|<br />
*More than [[RiceWiki:Curated Genes|'''400 manually curated genes''']] are validated as high quality in RiceWiki.<br />
*Gene Expression Profiles retrieved from the [http://expression.ic4r.org '''''IC4R-RED'''''] are integrated in RiceWiki.<br />
*[[Special:AuthorReward |'''Quantified contributions''']] of all curators are calculated by: [http://www.ncbi.nlm.nih.gov/pubmed/23732274 ''AuthorReward'']<br />
*[http://literature.ic4r.org '''35,717 Scientific Articles'''] associated with rice are provided for curators.<br />
*Here, is a [[RiceWiki:TBC|'''List of genes ''']]to be curated for the next season. If you are interested in this project, just [[RiceWiki:Joining|'''contact us''']].<br />
|<br />
''' |*******Recently Curated Genes*******|'''<br>''' [[Os06g0683400]]''', '''[[Os03g0125100]]''', '''[[Os01g0192000]]''' <br>''' [[Os01g0848400]]''', '''[[Os06g0107700]]''', '''[[Os10g0563600]]''' <br>''' [[Os01g0919400]]''', '''[[Os03g0180800]]''', '''[[Os12g0583700]]'''<br>''' [[Os09g0306400]]''', '''[[Os10g0553300]]''', '''[[Os09g0286400]]'''<br />
|<br />
|}<br />
</div><br />
|}<br />
<!--------------main part one----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------Rice Genome Overview------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Omics Knowledge Portal for Rice (OKP4R)</div><br />
<div style="width:515px;padding:0.5em 0.5em;font-size:100%;"><br />
* '''OKP4R''': a multidisciplinary portal to share omics knowledge for rice. [[RiceWiki:Omics_Knowledge_Portal_for_Rice|'''(More...)''']]<br><br />
[[File:IC4R_Omics_Pic_Jian.png|right|505px|'''Figure 1. Omics Knowledge Portal for Rice'''|link=RiceWiki:Omics_Knowledge_Portal_for_Rice]]<br />
</div><br />
<!-----------------Rice----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #93ff93; background-color:transparent;"|<br />
<div style="background:#deffde; border-bottom:1px solid #93ff93; padding:0.2em 0.5em; font-size:120%; font-weight:bold;">Rice Story</div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
*As an important food<br />
:Rice is the seed of the monocot plants ''Oryza sativa'' (Asian rice) or ''Oryza glaberrima'' (African rice). As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies. It is the grain with the third-highest worldwide production, after maize (corn) and wheat, according to data for 2010 [http://en.wikipedia.org/wiki/Rice (Full article...)].<br><br />
*As a biological model<br />
:Rice is also a model organism for the biological study of the grass family of crops and other plants. The two most common rice cultivars, ''indica'' and ''japonica'', were completely sequenced in 2002. The genome sequences of domesticated rice provide a solid foundation for integrating biological information, including genetics, gene expression, development, physiology and evolution.</div><br />
|}<br />
<br />
<!---------------Omics Knowledge Portal for Rice-----------------><br />
{|border="0" cellspacing="0" cellpadding="0" style="margin:1em 0; background:transparent; width:100%;"<br />
|-<br />
<!-----------English------------><br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;width:40%"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Featured Research</div><br />
<br />
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<!-----------------Chinese----------------------><br />
|style="padding:0px 2px;"|<br />
|valign="top" style="border:1px solid #ACD6FF; background-color:transparent;"|<br />
<div style="background:#ACD6FF; border-bottom:1px solid #ACD6FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;"> Latest News </div><br />
<div style="padding:0.5em 0.5em;font-size:100%;"><br />
* '''Jun 24th, 2016''': The Upcoming Conference Note: [http://pgc.hzau.edu.cn/ The 17th Conference of Plant Genomics] in China will be held in Fuzhou China from August 19th to 22th.<br />
* '''Jun 22th, 2016''': [[Omics Knowledge Portal for Rice| The Omics Knowledge Portal for Rice]] was launched at RiceWiki.<br />
* '''Jun 21th, 2016''': Seminar: Dr. Haixu Tang from Indiana University will give a lecture on [http://www.big.ac.cn/xwzx/xshd/201606/t20160621_4624539.html "Computational methods for characterizing spontaneous mutations in bacterial genomes using whole genome shotgun sequencing"].<br />
* '''May 27th, 2016''': The Upcoming Conference Note: [http://wlsc2016.medmeeting.org/2920?lang=en 2016 The World Life Science Conference] will be held in Beijing China from November 1st to 3rd.<br />
* '''Apr 19th, 2016''': Dr. Zhang Zhang presented a talk at [http://bigd.big.ac.cn/news/5 the 9th International Biocuration Conference].<br />
* '''Jan 31th, 2016''': The staffs of BIG Data Center presented a keynote lecture at [http://www.cbrc.kaust.edu.sa/cbrcweb/sp/bd2016.php the KAUST Research Conference in Saudi Arabia]. <br />
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<div style="background:#ACD6FF; border-bottom:1px solid #66B3FF; padding:0.2em 0.5em; font-size:125%; font-weight:bold;">Publications</div><br />
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'''Primary publication:'''<br><br />
*'''RiceWiki: a wiki-based database for community curation of rice genes.''' ''Nucleic Acids Research'' (2014), 42(Database issue):D1222-1228. [http://www.ncbi.nlm.nih.gov/pubmed/24136999 PMID=24136999]<br />
'''Related publications:'''<br />
*'''Information Commons for Rice (IC4R).''' ''Nucleic Acids Research'' (2016), 44(D1):D1172-1180. [http://www.ncbi.nlm.nih.gov/pubmed/26519466 PMID=26519466]<br />
*'''Bringing biocuration to China.''' ''Genomics Proteomics Bioinformatics'' (2014), 12(4):153-155.[http://www.ncbi.nlm.nih.gov/pubmed/25042682 PMID=25042682]<br />
*'''AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification.''' ''Bioinformatics'' (2013), 29(14):1837-1839.[http://www.ncbi.nlm.nih.gov/pubmed/23732274 PMID=23732274]]<br />
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