http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=Jixiang 2026-05-25T03:56:01Z User contributions MediaWiki 1.30.0 https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177335 2014-06-04T10:03:05Z

<p>Jixiang: </p> <hr /> <div>''qLTG3–1'' is a key regulator of low-temperature germinability in rice.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the ''qLTG3–1'' protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177333 2014-06-04T10:02:49Z

<p>Jixiang: </p> <hr /> <div>''qLTG3–1'' is a key regulator of low-temperature germinability in rice.<br /> Italica Livorno<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the ''qLTG3–1'' protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177328 2014-06-04T09:55:33Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the ''qLTG3–1'' protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177327 2014-06-04T09:55:19Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the ''qLTG3–1'' protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177326 2014-06-04T09:53:28Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177325 2014-06-04T09:53:13Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177324 2014-06-04T09:52:49Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177322 2014-06-04T09:52:26Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177320 2014-06-04T09:52:02Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling <br /> low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative <br /> trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177318 2014-06-04T09:51:34Z

<p>Jixiang: /* References */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> 3.Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.<br /> <br /> 4.Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177317 2014-06-04T09:50:51Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano.<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda.<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> &lt;ref name=&quot;ref3&quot;&gt;Kenji Fujino;Yasuyuki Matsuda.Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice Cryobiology, 2009, 59(3): 387-388.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref4&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice Plant Molecular Biology, 2011, 75(1-2): 1-10.&lt;/ref&gt;<br /> <br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177314 2014-06-04T09:47:00Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;references&gt;<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda<br /> Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice<br /> Plant Molecular Biology, 2010, 72(1-2): 137-152.&lt;/references&gt;<br /> <br /> 3. Louis M. T. Bradbury ,Susan A. Gillies Donald J. Brushett, Daniel L. E. Waters Robert J. Henry, Encoding <br /> Betaine Aldehyde Dehydrogenase, Inhibits the Biosynthesis of 2-Acetyl-1-Pyrroline, a Major Component in Rice<br /> Fragrance,Plant Mol Biol (2008) 68:439–449.<br /> <br /> 4. Ratree Wongpanya , Nonlawat Boonyalai , Napaporn Thammachuchourat, Natharinee Horata , Siwaret Arikit, Khin <br /> Myo Myint, Biochemical and Enzymatic Study of Rice BADH Wild-Type and Mutants: An Insight into Fragrance in Rice,<br /> Protein J (2011) 30:529–538<br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177313 2014-06-04T09:44:29Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177312 2014-06-04T09:44:10Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|middle|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177311 2014-06-04T09:43:31Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|right|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177310 2014-06-04T09:43:06Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|right|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a ''qLTG3–1''-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177308 2014-06-04T09:41:12Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> [[File:FIGURE4.png|left|thumb|300px|Figure.4 (A-B)GUS expression and subcellular localization. (C–E)Subcellular localization of GFP in<br /> onion epidermal cells expressing a qLTG3–1-GFP fusion as shown by confocal microscopy.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177307 2014-06-04T09:38:25Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of ''qLTG3–1''. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177305 2014-06-04T09:37:18Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|Figure.2 the strucrure of ''qLTG3–1'' and qLTG3–1.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> [[File:FIGURE3.png|left|thumb|300px|Figure.3 Expression of qLTG3–1. (A) Tissue specificity. (B) Germination.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177299 2014-06-04T09:33:55Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.png|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177297 2014-06-04T09:33:34Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.jpg|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177295 2014-06-04T09:33:20Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.jpg|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177292 2014-06-04T09:32:39Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|400px|Figure.1 Proposed hypothetical model of the role of ''qLTG3-1'' in seed germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.jpg|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177288 2014-06-04T09:31:45Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|300px|Figure.1 Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.jpg|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177280 2014-06-04T09:29:55Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> [[File:THE STUCTURE.jpg|left|thumb|300px|'''Figure.2''' ''the strucrure of ''qLTG3–1'' and qLTG3–1 protein.&lt;ref name=&quot;ref1&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177278 2014-06-04T09:26:09Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177277 2014-06-04T09:25:44Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177276 2014-06-04T09:25:04Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177275 2014-06-04T09:24:32Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177274 2014-06-04T09:24:12Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177273 2014-06-04T09:23:57Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177271 2014-06-04T09:23:30Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|left|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177270 2014-06-04T09:22:59Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|thumb|300px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177269 2014-06-04T09:22:25Z

<p>Jixiang: </p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|thumb|400px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177267 2014-06-04T09:22:04Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;[[File:S.jpg|thumb|400px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177266 2014-06-04T09:21:38Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|thumb|400px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177265 2014-06-04T09:21:22Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|thumb|400px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.&lt;ref name=&quot;ref2&quot;/&gt;.'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177262 2014-06-04T09:20:16Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|thumb|400px|'''Figure.1''' ''Proposed hypothetical model of the role of qLTG3-1 in seed<br /> germination.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177259 2014-06-04T09:19:23Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|thumb|400px|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177257 2014-06-04T09:18:41Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|400px|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177256 2014-06-04T09:18:25Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|thumb|400px|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177254 2014-06-04T09:17:50Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|right|thumb|400px|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177253 2014-06-04T09:17:16Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.png|right|thumb|400px|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177252 2014-06-04T09:16:42Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg|'''Figure1.''' ''2AP Levels and Their Significant Differences among Nontransgenic Lines and Three Kinds of Transgenic Lines Carrying Different Badh2 CDS Driven by the CaMV35S Promoter.From(from reference &lt;ref name=&quot;ref1&quot;/&gt;).'']]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177251 2014-06-04T09:15:25Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> <br /> [[File:S.jpg]]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:S.jpg&diff=177250 2014-06-04T09:15:03Z

<p>Jixiang: </p> <hr /> <div></div>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177248 2014-06-04T09:13:58Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> [[File:hypothetical model.jpg]]<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os03g0103300&diff=177247 2014-06-04T09:10:59Z

<p>Jixiang: /* Function */</p> <hr /> <div>Please input one-sentence summary here.<br /> <br /> ==Annotated Information==<br /> ===Function===<br /> ''qLTG3–1'' ,a quantitative trait locus for low-temperature germinability on chromosome 3, has been identified as the most effective locus<br /> controlling low-temperature germinability in the rice variety Italica Livorno. Its expression is tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. The research phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.&lt;ref name=&quot;ref1&quot; /&gt;<br /> <br /> Based on the results of Genome-wide analysis, a hypothetical model of the role of ''qLTG3-1'' in seed germination is proposed. ''qLTG3-1'' has a role in the up-regulation of genes involved in phytoalexin biosynthesis and ''PBZ1'', which are inducible by elicitors and UV. It is currently unclear whether qLTG3-1 up-regulates these genes mediated by elicitors in this model. Momilactones A, ''PBZ1'', and ''PBZ1''-inducible genes of a putative phenylalanine ammonia-lyase (''PAL'') and ''COMT'', might induce PCD. Therefore, ''qLTG3-1'' may enhance seed germination by weakening the tissues covering the embryo under several stress conditions.(Figure .1)&lt;ref name=&quot;ref2&quot; /&gt;<br /> <br /> ===Gene and Protein structure===<br /> ''qLTG3–1'' consisted of one exon of 555-bp length, which encodes a novel protein of 184 aa with unknown function.(Figure .2A) <br /> <br /> Based on domain searches, the qLTG3–1 protein has two conserved domains: glycine-rich cell wall protein (GRP) of the glycine rich protein family from amino acid 1 to 100, and Tryp_alpha_amyl of the protease inhibitor/seed storage/LTP family from amino acid 100 to 182 according to Pfam analysis. (Figure .2B)<br /> <br /> ===Expression===<br /> The expression of ''qLTG3–1'' is tissue-specific to the embryo, panicle, and shoot. Northern blot analysis was used to measure the ''qLTG3–1'' expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was used as a loading control. The results indicated that the timing and level of expression of ''qLTG3–1'' were strongly associated with the promotion of seed germination.(Figure .3)<br /> <br /> The analysis of ''qLTG3–1'' promoter activity in transgenic rice plants carrying an ''qLTG3–1''::GUS reporter gene fusion indicates that GUS was expressed in both the epiblast covering the embryo and the aleurone cells.(Figure .4)<br /> <br /> The coding region of ''qLTG3–1'' fused to modified green fluorescent protein determines the subcellular localization of the ''qLTG3–1'' protein in both the cytoplasm and the nucleus in onion epidermal cells following particle bombardment.(Figure .4)<br /> <br /> ==Labs working on this gene==<br /> Plant Breeding and Production Division, Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido 0691317, Japan<br /> <br /> QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 3058602, Japan<br /> <br /> ==References==<br /> &lt;ref name=&quot;ref1&quot;&gt; Kenji Fujino;Hiroshi Sekiguchi;Yasuyuki Matsuda;Kazuhiko Sugimoto;Kazuko Ono;Masahiro Yano<br /> Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice<br /> Proceedings of the National Academy of Sciences, 2008, 105(34): 12623-12628.&lt;/ref&gt;<br /> &lt;ref name=&quot;ref2&quot;&gt; Kenji Fujino;Yasuyuki Matsuda Global expression profiling of genes targeted by qLTG3-1 controlling low temperature tolerance at the germination stage in rice<br /> Cryobiology, 2009, 59(3): 387-388<br /> &lt;/references&gt;<br /> <br /> ==Structured Information==<br /> {{JaponicaGene|<br /> GeneName = Os03g0103300|<br /> Description = Plant lipid transfer/seed storage/trypsin-alpha amylase inhibitor domain containing protein|<br /> Version = NM_001055203.2 GI:297600190 GeneID:4331303|<br /> Length = 941 bp|<br /> Definition = Oryza sativa Japonica Group Os03g0103300, 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 3|Chromosome 3]]|<br /> AP = Chromosome 3:198326..199266|<br /> CDS = 198414..198968|<br /> GCID = &lt;gbrowseImage1&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage1&gt;|<br /> GSID = &lt;gbrowseImage2&gt;<br /> name=NC_008396:198326..199266<br /> source=RiceChromosome03<br /> preset=GeneLocation<br /> &lt;/gbrowseImage2&gt;|<br /> CDNA = &lt;cdnaseq&gt;atggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaa&lt;/cdnaseq&gt;|<br /> AA = &lt;aaseq&gt;MATKAGVIATLLALNLHFFTFSDACGCQCGSCPSPGGGGGGGGG GGGGGGGRGGGGGSGGGSGGGGGSGGGGSGGGGSGGGGSGGGGGGGSGGGGGGGRCPI DTLKLGVCANVLNGLINVQLGTPPRQPCCSLIQGLADLEAAVCLCTALRANILGINLN LPINLSLLVNYCGRSVPSGFQCSN&lt;/aaseq&gt;|<br /> DNA = &lt;dnaseqindica&gt;89..643#atctgaatacactggctagcaagcaaagctaggtagaggccaggccatagatcgagatcgatctgcaggtgcagtgcggtgggtgggcatggcgacgaaagctggggtgatcgccacgctcctggccctgaacctccacttcttcaccttctccgacgcgtgcggctgccagtgcggctcatgccctagtcccggcggaggaggcggtggcggtggcggtggcggtggcggtggtggagggcgtggaggtggtggcgggagcggcggaggttcaggtggaggcggcggttcaggtggaggaggaagcggcggcggaggttcaggcggtggaggaagcggaggcggcggaggaggaggaagcggcggcggcgggggaggaggaagatgcccgatcgacacgctgaagctgggggtgtgcgcgaacgtgctgaatgggctgataaacgtgcagctggggacgccgccgcggcagccgtgttgcagcctcatccagggcctcgccgaccttgaggccgccgtgtgcctctgcaccgccctccgcgccaacatccttggcatcaacctcaacctccccatcaacctcagcctcctcgtcaactactgcggccgctccgtcccctccggcttccagtgcagcaactaatatagctgctgctccattctacttcactgcttgctacacacaagaacgtacgaagaacgaccaccaggccacgtacaactatatatctatctatgtctaatttgttccttgttcaaatcatcatatgtatctgcgtgccttaatttcctccttcatcccgtaaattaatgagatatatatgcatgcatatgattcagttccacgacgtaattaaagcatgcttcattcgtctacttgtatatgtgtatctgcataattgattaattaatttgtactcgatggatctcatcgtatatgc&lt;/dnaseqindica&gt;|<br /> Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055203.2 RefSeq:Os03g0103300]|<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>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:THE_STUCTURE.png&diff=177245 2014-06-04T09:09:11Z

<p>Jixiang: </p> <hr /> <div></div>

Jixiang https://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Hypothetical_model.jpg&diff=177244 2014-06-04T09:08:58Z

<p>Jixiang: </p> <hr /> <div></div>

Jixiang