Os01g0286100 - Revision history

192.168.72.52 at 04:40, 14 May 2015

2015-05-14T04:40:52Z

Chenbaohua: /* References */

2014-05-30T01:39:14Z

‎References

Chenbaohua: /* Labs working on this gene */

2014-05-30T01:39:05Z

‎Labs working on this gene

Chenbaohua: /* Labs working on this gene */

2014-05-30T01:38:27Z

‎Labs working on this gene

Chenbaohua: /* Evolution */

2014-05-30T01:35:46Z

‎Evolution

Chenbaohua: /* Evolution */

2014-05-30T01:35:04Z

‎Evolution

Chenbaohua: /* Mutation */

2014-05-30T01:32:15Z

‎Mutation

Chenbaohua: /* References */

2014-05-29T14:50:16Z

‎References

Chenbaohua: /* Expression */

2014-05-29T14:49:34Z

‎Expression

Chenbaohua: /* Function */

2014-05-29T14:34:09Z

‎Function

← Older revision		Revision as of 04:40, 14 May 2015
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	==Structured Information==		==Structured Information==
−	~~{{JaponicaGene\|~~	+	[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]
−	~~GeneName = Os01g0286100\|~~
−	~~Description = Basic helix-loop-helix dimerisation region bHLH domain containing protein\|~~
−	~~Version = NM_001049310.1 GI:115436033 GeneID:4327916\|~~
−	~~Length = 3148 bp\|~~
−	~~Definition = Oryza sativa Japonica Group Os01g0286100, complete gene.\|~~
−	~~Source = Oryza sativa Japonica Group~~
−
−	~~ORGANISM Oryza sativa Japonica Group~~
−	~~Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;~~
−	~~Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP~~
−	~~clade; Ehrhartoideae; Oryzeae; Oryza.~~
−	\|
−	~~Chromosome = [[:category:Japonica Chromosome 1\|Chromosome 1]]\|~~
−	~~AP = Chromosome 1:10319113..10322260\|~~
−	~~CDS = 10319429..10319542,10319639..10320124,10320218..10320283,10320371..10320436,10320598..10320690<br>,10320781..10321867,10321976..10321977\|~~
−	~~GCID = <gbrowseImage1>~~
−	~~name=NC_008394:10319113..10322260~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage1>\|~~
−	~~GSID = <gbrowseImage2>~~
−	~~name=NC_008394:10319113..10322260~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage2>\|~~
−	CDNA = <cdnaseq>atgtccgacggcaacgacttcgccgagctgctgtgggagaacggccaggcggtggtgcacgggaggaagaagcacccgcagccggccttcccgccgttcggcttcttcggtggcaccggcggtggcggcggcggcagcagtagtagagcccaggagaggcagcccggcggcatcgatgcgttcgccaaggtggggggcggcttcggcgccttgggcatggctccggcggtgcacgacttcgcttctggcttcggcgccaccacgcaggacaacggtgatgatgacaccgttccgtggatccattaccccataattgacgatgaagacgccgccgcccctgctgctctcgcagcagcggactatggctccgacttcttctccgagctccaggcggcggcggctgccgcggcggccgccgcgccgccgaccgatctcgcctctctgccagcctccaatcacaacggcgccaccaataacagaaatgctccggttgccaccaccaccaccagggaaccctccaaggaaagccacggcggcctgtcggttcccaccacccgagccgagccgcagccgcagccacagctcgccgcagccaagctgcctcggtcgagcggcagcggcggcggcgagggcgtgatgaacttctcgctcttctcccgcccggccgtcctggcgagggcgacgctggagagcgcgcagaggacgcagggcaccgacaataaggcgtccaatgtcaccgcgagcaaccgcgtcgagtcgacggtcgtgcagacggcgagcgggccaaggagcgcaccggcgttcgccgatcagagggcggcggcgtggccgccgcagccgaaggagatgccgttcgcgtccacggcagccgctcccatggccccggccgttaacctgcaccacgagatgggccgtgacagggcaggccgaaccatgcctgtccacaaaaccgaggcgaggaaggcacctgaggccacggtcgcgacatcgtcggtgtgctccggcaacggagctgggagtgacgagctgtggcgccagcagaagcggaagtgccaggcccaggcagagtgctcagctagccaagacgatgatcttgacgatgaacctggagtattgagaaaatctggaaccaggagcacgaaacgcagccgcacagctgaggttcacaatttatcagaaaggaggagaagggacaggatcaatgaaaagatgcgcgctctgcaagaactcattcccaactgcaacaagattgataaagcctcgatgctggatgaagctatagagtacctcaaaacccttcagcttcaagtacagatgatgtccatgggaactgggctgtgcattcctccaatgctattaccaacagccatgcagcacttgcaaattccaccgatggctcatttccctcatctcggcatgggattggggtacgggatgggcgtcttcgacatgagcaacactggagcacttcagatgccacccatgcctggtgctcactttccctgcccaatgatcccaggtgcgtcaccacaaggtcttgggatccctggcacaagcaccatgccaatgtttggggttcctgggcaaacaattccttcgtcagcgtctagtgtaccaccatttgcatctttggctggtcttcctgttaggccaagcggggtccctcaagtatcaggcgccatggctaacatggtgcaagaccagcaacaaggcatagcgaatcaacagcagcaatgtctgaacaaggaagctatacagggagcaaatccaggtgattcacaaatgcagatcatcatgcagggtgacaacgagaattttaggataccctcttcagcccaaacaaaaagcagtcaattttcagatggtaccggcaaggggaccaacgctagagagagagatggggctgaaacataa</cdnaseq>\|
−	AA = <aaseq>MSDGNDFAELLWENGQAVVHGRKKHPQPAFPPFGFFGGTGGGGG GSSSRAQERQPGGIDAFAKVGGGFGALGMAPAVHDFASGFGATTQDNGDDDTVPWIHY PIIDDEDAAAPAALAAADYGSDFFSELQAAAAAAAAAAPPTDLASLPASNHNGATNNR NAPVATTTTREPSKESHGGLSVPTTRAEPQPQPQLAAAKLPRSSGSGGGEGVMNFSLF SRPAVLARATLESAQRTQGTDNKASNVTASNRVESTVVQTASGPRSAPAFADQRAAAW PPQPKEMPFASTAAAPMAPAVNLHHEMGRDRAGRTMPVHKTEARKAPEATVATSSVCS GNGAGSDELWRQQKRKCQAQAECSASQDDDLDDEPGVLRKSGTRSTKRSRTAEVHNLS ERRRRDRINEKMRALQELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMSMGTGLCIPP MLLPTAMQHLQIPPMAHFPHLGMGLGYGMGVFDMSNTGALQMPPMPGAHFPCPMIPGA SPQGLGIPGTSTMPMFGVPGQTIPSSASSVPPFASLAGLPVRPSGVPQVSGAMANMVQ DQQQGIANQQQQCLNKEAIQGANPGDSQMQIIMQGDNENFRIPSSAQTKSSQFSDGTG KGTNARERDGAET</aaseq>\|
−	DNA = <dnaseqindica>2719..2832#2137..2622#1978..2043#1825..1890#1571..1663#394..1480#284..285#aggtccccccacgccacagcctcttatcccacacgcggaccaacagcgccgccccgcccgtcccccgcttcaccttcggcttcgacttcggcttcgtttcctcttctcttcgtctctccctccctccagcgaaagaaagagagagctcacctcgcgttgcccggccggccgcggaggagagcacggcttcgcattcggctggagctctcgtctctgcactcggagtacagctgcaaactcctccttccttgatttcttcaccctgtctccacggactgcacagatgtgggtgcaacgcgatctttcgctgcctccggtttagctctccggttgattccgatcgaggaagctgatgcatgtgtttgtatatggctcggtgttttgtgtgtgcaggtccgacggcaacgacttcgccgagctgctgtgggagaacggccaggcggtggtgcacgggaggaagaagcacccgcagccggccttcccgccgttcggcttcttcggtggcaccggcggtggcggcggcggcagcagtagtagagcccaggagaggcagcccggcggcatcgatgcgttcgccaaggtggggggcggcttcggcgccttgggcatggctccggcggtgcacgacttcgcttctggcttcggcgccaccacgcaggacaacggtgatgatgacaccgttccgtggatccattaccccataattgacgatgaagacgccgccgcccctgctgctctcgcagcagcggactatggctccgacttcttctccgagctccaggcggcggcggctgccgcggcggccgccgcgccgccgaccgatctcgcctctctgccagcctccaatcacaacggcgccaccaataacagaaatgctccggttgccaccaccaccaccagggaaccctccaaggaaagccacggcggcctgtcggttcccaccacccgagccgagccgcagccgcagccacagctcgccgcagccaagctgcctcggtcgagcggcagcggcggcggcgagggcgtgatgaacttctcgctcttctcccgcccggccgtcctggcgagggcgacgctggagagcgcgcagaggacgcagggcaccgacaataaggcgtccaatgtcaccgcgagcaaccgcgtcgagtcgacggtcgtgcagacggcgagcgggccaaggagcgcaccggcgttcgccgatcagagggcggcggcgtggccgccgcagccgaaggagatgccgttcgcgtccacggcagccgctcccatggccccggccgttaacctgcaccacgagatgggccgtgacagggcaggccgaaccatgcctgtccacaaaaccgaggcgaggaaggcacctgaggccacggtcgcgacatcgtcggtgtgctccggcaacggagctgggagtgacgagctgtggcgccagcagaagcggaagtgccaggcccaggcagagtgctcagctagccaagacgatgtaagtaaatggtatgagatagatatgcactgcataaccagctgactataccttcgctgattctcatgataaaaaactggttctattcaggatcttgacgatgaacctggagtattgagaaaatctggaaccaggagcacgaaacgcagccgcacagctgaggttcacaatttatcagaaagggtgagtagctcacatcttcagtgcatggatcatcctgcatccatttgcttcaaagttcacatgtcagtgcattgatcatcctgcatccatttgcttcaatcccatgactcgactcatgctgcaattttattgactgtattgcaacccaacaatctttgcagaggagaagggacaggatcaatgaaaagatgcgcgctctgcaagaactcattcccaactgcaacaaggtaaagataagccattccatcgtcttgctccctctgagatgcctctgaatgaacatttggtcaattcaggcatgctatgttttgcagattgataaagcctcgatgctggatgaagctatagagtacctcaaaacccttcagcttcaagtacaggtacattgaaactgccttcgaacaaatgtaccatgattgtcgggtgaatatgtacatagatgcattgacaaggtgcagttgtcattgacacagatgatgtccatgggaactgggctgtgcattcctccaatgctattaccaacagccatgcagcacttgcaaattccaccgatggctcatttccctcatctcggcatgggattggggtacgggatgggcgtcttcgacatgagcaacactggagcacttcagatgccacccatgcctggtgctcactttccctgcccaatgatcccaggtgcgtcaccacaaggtcttgggatccctggcacaagcaccatgccaatgtttggggttcctgggcaaacaattccttcgtcagcgtctagtgtaccaccatttgcatctttggctggtcttcctgttaggccaagcggggtccctcaagtatcaggcgccatggctaacatggtgcaagaccagcaacaaggcatagcgaatcaacagcagcaatgtctgaacaaggaagctatacagggagcaaatccaggtgattcacaaatgcagatcatcatgcaggtactaattaaaaattaacaaatgatgtcaagcgaatagaagacatttgctagtacttaagtgcattacttactccagtttattttaatattccagggtgacaacgagaattttaggataccctcttcagcccaaacaaaaagcagtcaattttcagatggtaccggcaaggggaccaacgctagagagagagatggggctgaaacataaagaaaggccagtaggtgtaacttgactttcatgctaaatttgagatctaccactgaaatctgcagaatgttcctgtcctaaaaagatcaatggctgaggaatttcatgtacgaccaactaacaacttccagatatgaaagttagcaattcatactgggagaacttacttgagtatcaagatccacgaggcagatgtatcagccaagatgccccaaaattttgtgtaaaatgtagatggtagaagatgctaccaggttacaagctgtaattcttgacttccagtgcagtttcctatgagtagtttttgccctatctg</dnaseqindica>\|
−	~~Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049310.1 RefSeq:Os01g0286100]\|~~
−	}}
−	[[Category:Genes]]
−	~~[[Category:Japonica mRNA]]~~
−	[[Category:Oryza Sativa Japonica Group]]
−	[[Category:Japonica ~~Genes]]~~
−	~~[[Category:Japonica Chromosome 1]]~~
−	~~[[Category:~~Chromosome 1]]

← Older revision		Revision as of 01:39, 30 May 2014
Line 36:		Line 36:

	[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.		[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.
−
−	~~==References==~~

	==Structured Information==		==Structured Information==

← Older revision		Revision as of 01:39, 30 May 2014
Line 36:		Line 36:

	[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.		[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.
−
−	~~==Labs working on this gene==~~
−

	==References==		==References==

← Older revision		Revision as of 01:38, 30 May 2014
Line 18:		Line 18:

	==Labs working on this gene==		==Labs working on this gene==
		+	[1]Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University,Chikusa-ku, Nagoya 464-8601, Japan

		+	[2]Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
		+
		+	[3]Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100, China
		+
		+	[4]Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100190, China
		+
		+	[5]Graduate School of Horticulture, Chiba University, Chiba, Japan

	==References==		==References==

@@ Line 15: / Line 15: @@
 ===Evolution===
-An extensive inspection of the entire genome sequence databases of rice (Oryza sativa) revealed six candidate genes (or codingsequences)of PILs, which were esignated OsPIL11 to OsPIL16. A non-rooted neighbor-joining phylogenetic tree was constructed using the amino acid sequence of the bHLH DNA-binding domain.A PIL family is composed of seven members in A. thaliana and six members in O. sativa. (HFR1, GL3, ICE1, and RAP1 are not PIL family, and are used as an out-group.) For these rice OsPIL genes,the annotated ID-code for each coding sequence was adopted from the Rice Annotation Project (http://rapdb.lab.nig.ac.jp/index.html), and the ID-codes are indicted in parentheses. For the Arabidopsis PIL family members, their characteristics are indicated in parentheses with regard to biological events in which they appear to be implicated: circadian rhythm, elongation of hypocotyls in red light,greening upon the onset of light exposure, shade avoidance, and germination (for details and references, see the introduction).[[File:Example.jpg]]
+An extensive inspection of the entire genome sequence databases of rice (Oryza sativa) revealed six candidate genes (or codingsequences)of PILs, which were esignated OsPIL11 to OsPIL16. A non-rooted neighbor-joining phylogenetic tree was constructed using the amino acid sequence of the bHLH DNA-binding domain.A PIL family is composed of seven members in A. thaliana and six members in O. sativa. (HFR1, GL3, ICE1, and RAP1 are not PIL family, and are used as an out-group.) For these rice OsPIL genes,the annotated ID-code for each coding sequence was adopted from the Rice Annotation Project, and the ID-codes are indicted in parentheses. For the Arabidopsis PIL family members, their characteristics are indicated in parentheses with regard to biological events in which they appear to be implicated: circadian rhythm, elongation of hypocotyls in red light,greening upon the onset of light exposure, shade avoidance, and germination.
 ==Labs working on this gene==

← Older revision		Revision as of 01:32, 30 May 2014
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	===Evolution===		===Evolution===

−
−	~~===Mutation===~~

	==Labs working on this gene==		==Labs working on this gene==

← Older revision		Revision as of 14:50, 29 May 2014
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	[3]Massari M E, Murre C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms[J]. Molecular and cellular biology, 2000, 20(2): 429-440.		[3]Massari M E, Murre C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms[J]. Molecular and cellular biology, 2000, 20(2): 429-440.
		+
		+	[4]Nakamura Y, Kato T, Yamashino T, et al. Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa[J]. Bioscience, biotechnology, and biochemistry, 2007, 71(5): 1183-1191.

	==Labs working on this gene==		==Labs working on this gene==

@@ Line 12: / Line 12: @@
 ===Expression===
+To amplify cDNAs from a rice total RNA preparation, an RT-PCR kit was used according to instructions with specific primers. The resulting PCR fragments were cloned and sequenced with an automated DNA sequencer, with the recommended sequencing kits according to instructions[https://www.jstage.jst.go.jp/article/bbb/71/5/71_60643/_article]. The following primers were used for cDNA amplification:5'-ATGAATTCATGAACCAGTTCGTCCCTGATTGGAGC-3' and 5'-AAGAATTCTTATCCTGATCCTGTGTTGGGTGCATTTTCAGG-3'.
 ===Evolution===

@@ Line 8: / Line 8: @@
 ===Function===
 Grain size is a major yield component in rice, and partly controlled by the sizes of the lemma and palea. Molecular mechanisms controlling the sizes of these organs largely remain unknown. In this study, we show that an antagonistic pair of basic helix-loop-helix (bHLH) proteins is involved in determining rice grain length by controlling cell length in the lemma/palea. Overexpression of an atypical bHLH, named POSITIVE REGULATOR OF GRAIN LENGTH 1 (PGL1), in lemma/palea increased grain length and weight in transgenic rice.Proteins with E-values of <4e−12 were selected for analysis; Os12g0610200, Os01g0286100, Os05g0139100, and Os04g0618600. Except for Os04g0618600, all candidates contained amino acids conserved in the basic domain required for binding to DNA. We found expression in the lemma/palea of these candidates. Thus, we chose these four candidates for analysis of interaction with PGL1.
 OsPIL15‐OX seedlings exhibit an exaggerated shorter aboveground part and undeveloped root system relative to wild‐type seedlings, suggesting that OsPIL15 represses seedling growth in the dark. Microarray analysis combined with gene ontology analysis revealed that OsPIL15 represses a set of genes involved in auxin pathways and cell wall organization or biogenesis.Given the important roles of the auxin pathway and cell wall properties in controlling plant growth, we speculate that OsPIL15 represses seedling growth likely by regulating the auxin pathway and suppressing cell wall organization in etiolated rice seedlings. Additionally, exposure to red light or far‐red light relieved growth retardation and promoted seedling elongation in the OsPIL15‐OX lines, despite higher levels of OsPIL15 transcripts under red light and far‐red light than in the dark.These results suggest that light regulation of OsPIL15 expression is probably involved in photomorphogenesis in rice.