Os01g0113350 - Revision history

192.168.72.52 at 04:29, 14 May 2015

2015-05-14T04:29:28Z

Biotitan2014: /* Evolution */

2014-05-28T09:57:59Z

‎Evolution

Biotitan2014: /* References */

2014-05-28T09:56:28Z

‎References

Biotitan2014: /* References */

2014-05-28T09:55:02Z

‎References

Biotitan2014: /* Evolution */

2014-05-28T09:07:52Z

‎Evolution

Biotitan2014: /* Evolution */

2014-05-28T09:05:39Z

‎Evolution

Biotitan2014: /* Function */

2014-05-28T09:04:02Z

‎Function

Biotitan2014: /* Function */

2014-05-28T09:01:54Z

‎Function

Biotitan2014: /* Expression */

2014-05-28T08:59:34Z

‎Expression

Biotitan2014: /* Evolution */

2014-05-28T08:57:12Z

‎Evolution

← Older revision		Revision as of 04:29, 14 May 2015
Line 42:		Line 42:

	==Structured Information==		==Structured Information==
−	~~{{JaponicaGene\|~~	+	[[Category:Genes]][[Category:Oryza Sativa Japonica Group]][[Category:Japonica Chromosome 1]]
−	~~GeneName = Os01g0113350\|~~
−	~~Description = Thaumatin-like, pathogenesis-related 5 family protein\|~~
−	~~Version = NM_001185208.1 GI:297719550 GeneID:9271284\|~~
−	~~Length = 2469 bp\|~~
−	~~Definition = Oryza sativa Japonica Group Os01g0113350, 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 1:727977..730445\|~~
−	~~CDS = 727977..729455,729750..729854,730389..730445\|~~
−	~~GCID = <gbrowseImage1>~~
−	~~name=NC_008394:727977..730445~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage1>\|~~
−	~~GSID = <gbrowseImage2>~~
−	~~name=NC_008394:727977..730445~~
−	~~source=RiceChromosome01~~
−	~~preset=GeneLocation~~
−	~~</gbrowseImage2>\|~~
−	CDNA = <cdnaseq>atggcggcagtgtctacttgttgcactcaccatctcctacctctactcctcctcgctgccatagtcgccaccaccaccaccaaccacgccgccgccgccgccacgttgaacatcaccaacctatgccccttcaccgtgtggccggccgccgtgccggtgggcggcggcaggcggctcgacccgggcacgtcgtgggcgctcgacgtgcccgccggcgccgccccgggccgcgtgtgggcgcgcacgggctgcaccttcgacgccaccggcgccaacgggacgtgcctgacgggcgactgcggcggcgcgctgtcgtgcacgggctacggcgagccgccgcagacgctcgccgagttctcgctcggccaggccgacggccaggacctcttcgacatctccctcgtcgacggcttcaacgtgcccatggacttcctcccggcgccgccgccggatcagtcaccgccgtgcagcaaggggccacggtgtccggccaacgtcacggcacagtgccccggcgagctcagagctcatggaggctgcaacagcgcgtgcagagtgttcaagcaggacaaatactgctgcactggcaacgggacgaacacctgcgaacccaccacctactcgctgccatttgtgaggatgtgcccggacgcctatagctactccaggaacgatgcatccagcccagggttcacttgcccgtcaggtacaaattaccagatcatcttctgccccccaattgatctcacatcttcatctcctgcatcaattgctgttgctgcaaataacagacaaggaaaaaaggttattgccgggatcatcatagcttctgtaatcggctccacttcagtactcaccatggttatggcttacaccagcatcaagcgaagaacacgacggcgccgggagatacgtgaagaggagcaggagcttgaggagataacccttcaaggaatgccaaggaggttcacatttcagcagctacaggaagcaaccgatcagttcagagataagctcggtgaaggaggatttgggtcggttttcttgggacagattggagacgaaagagttgcggtgaaacgcctggatcgaaatggtcaggggatgagagaattcttggcagaggttcagacgatcggcagcatccaccatatcaatctggtgaggctgattggattctgtgcagagaaatcacagaggctcttggtttatgagcatatgcccaaaggttccttggacaggtggatctatcaccagcaaggtgctgctatttttcctagtgttcctcctctagattggcaaacacgatacaaaattattacccaagtagccaaaggtctctcataccttcatgaggagtgcacaaagagaattgctcacttggatgtaaaaccacaaaatatcctcctggatgacaaattcaatgctaaactctctgattttggactatgcaagctcattgatcgagataagagccaaatcgattgcaaaaggaggcctcaaatgtctgaggttgtaaaagcattggaaggcaccataagtatcgaaactaacatagttcatgattttgtcgcagtaaatccacctcagttttacaacctacctaccaccttatctgagaaaaaacaacaaccaacttag</cdnaseq>\|
−	AA = <aaseq>MAAVSTCCTHHLLPLLLLAAIVATTTTNHAAAAATLNITNLCPF TVWPAAVPVGGGRRLDPGTSWALDVPAGAAPGRVWARTGCTFDATGANGTCLTGDCGG ALSCTGYGEPPQTLAEFSLGQADGQDLFDISLVDGFNVPMDFLPAPPPDQSPPCSKGP RCPANVTAQCPGELRAHGGCNSACRVFKQDKYCCTGNGTNTCEPTTYSLPFVRMCPDA YSYSRNDASSPGFTCPSGTNYQIIFCPPIDLTSSSPASIAVAANNRQGKKVIAGIIIA SVIGSTSVLTMVMAYTSIKRRTRRRREIREEEQELEEITLQGMPRRFTFQQLQEATDQ FRDKLGEGGFGSVFLGQIGDERVAVKRLDRNGQGMREFLAEVQTIGSIHHINLVRLIG FCAEKSQRLLVYEHMPKGSLDRWIYHQQGAAIFPSVPPLDWQTRYKIITQVAKGLSYL HEECTKRIAHLDVKPQNILLDDKFNAKLSDFGLCKLIDRDKSQIDCKRRPQMSEVVKA LEGTISIETNIVHDFVAVNPPQFYNLPTTLSEKKQQPT</aaseq>\|
−	DNA = <dnaseqindica>1..1479#1774..1878#2413..2469#atggcggcagtgtctacttgttgcactcaccatctcctacctctactcctcctcgctgccatagtcgccaccaccaccaccaaccacgccgccgccgccgccacgttgaacatcaccaacctatgccccttcaccgtgtggccggccgccgtgccggtgggcggcggcaggcggctcgacccgggcacgtcgtgggcgctcgacgtgcccgccggcgccgccccgggccgcgtgtgggcgcgcacgggctgcaccttcgacgccaccggcgccaacgggacgtgcctgacgggcgactgcggcggcgcgctgtcgtgcacgggctacggcgagccgccgcagacgctcgccgagttctcgctcggccaggccgacggccaggacctcttcgacatctccctcgtcgacggcttcaacgtgcccatggacttcctcccggcgccgccgccggatcagtcaccgccgtgcagcaaggggccacggtgtccggccaacgtcacggcacagtgccccggcgagctcagagctcatggaggctgcaacagcgcgtgcagagtgttcaagcaggacaaatactgctgcactggcaacgggacgaacacctgcgaacccaccacctactcgctgccatttgtgaggatgtgcccggacgcctatagctactccaggaacgatgcatccagcccagggttcacttgcccgtcaggtacaaattaccagatcatcttctgccccccaattgatctcacatcttcatctcctgcatcaattgctgttgctgcaaataacagacaaggaaaaaaggttattgccgggatcatcatagcttctgtaatcggctccacttcagtactcaccatggttatggcttacaccagcatcaagcgaagaacacgacggcgccgggagatacgtgaagaggagcaggagcttgaggagataacccttcaaggaatgccaaggaggttcacatttcagcagctacaggaagcaaccgatcagttcagagataagctcggtgaaggaggatttgggtcggttttcttgggacagattggagacgaaagagttgcggtgaaacgcctggatcgaaatggtcaggggatgagagaattcttggcagaggttcagacgatcggcagcatccaccatatcaatctggtgaggctgattggattctgtgcagagaaatcacagaggctcttggtttatgagcatatgcccaaaggttccttggacaggtggatctatcaccagcaaggtgctgctatttttcctagtgttcctcctctagattggcaaacacgatacaaaattattacccaagtagccaaaggtctctcataccttcatgaggagtgcacaaagagaattgctcacttggatgtaaaaccacaaaatatcctcctggatgacaaattcaatgctaaactctctgattttggactatgcaagctcattgatcgagataagagccaagtgattacaagaatgagaggcacacctggatatttagctcctgaatggctgacatcgcagatcacagaaaaggcagatgtctatagctttggcatagtagtcatggaaatcatcagcggaagaaagaatgttgacacttcccggtctgaacagagcatccatctaattaccttattgcaagaaaaggtgaagagtgatcagttggtagatttgattgacaaagataataatgacatgcaagtacacgagcaagaagtaatagagatgatgaaatttgcaatgtggtgtttgcagatcgattgcaaaaggaggcctcaaatgtctgaggttgtaaaagcattggaaggcaccataagtatcgaaactaacatagttcatgattttgtcgcagtaaatccagtaagctttggttttactgcagttgtgggctcagctccacctcttgcctcagatctatccggacccaggtgactgacgcaattttgatggtatactagaacatgtgcgcttttgggtcagaaaaaggcatagcatatacgctgttgcattctcagaaaactataatgtgatagcatcataccttcaaatcatttacattttttaatattgcaattttcgttcaagaagaacatctcaatattgtttgattgtttctgttgaacttgccctattagcaaatctgatcctggttcatacatgtgaaaccaatagctcttcttacatatcaaaatggtcatagctctcatggcactttcaaccataattcagtagtactttctcatggcacaaatacaacttttatcgtatgcaaatgaatagcgtaccacaagatcacatttttctcgttccagctttatactctgttattccctaaaaaaaatcactttcaaattacaacaatgcgatgaaacatctgtttacaacaatatgtagcctcagttttacaacctacctaccaccttatctgagaaaaaacaacaaccaacttag</dnaseqindica>\|
−	~~Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001185208.1 RefSeq:Os01g0113350]\|~~
−	}}
−	[[Category:Genes]]
−	~~[[Category:Japonica mRNA]]~~
−	[[Category:Oryza Sativa Japonica Group]]
−	[[Category:Japonica ~~Genes]]~~
−	~~[[Category:Japonica Chromosome 1]]~~
−	~~[[Category:~~Chromosome 1]]

@@ Line 15: / Line 15: @@
 ... Figure 1
 [[File:figure.png|caption]]
-Phylogenetic analysis of 118 TLPs by the neighborjoining (NJ) method[8]. ...
+Phylogenetic analysis of 118 TLPs by the neighborjoining (NJ) method[6]. ...
 ==Labs working on this gene==

@@ Line 36: / Line 36: @@
 [6]Liu JJ, Sturrock R, Ekramoddoullah AK.The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function. Plant Cell Rep. 2010;29(5):419-36.
 [7]Shatters RG Jr, Boykin LM, Lapointe SL, Hunter WB, Weathersbee AA 3rd (2006) Phylogenetic and structural relationships of the PR5 gene family reveal an ancient multigene family conserved in plants and select animal taxa. J Mol Evol 63:12–29.
 [8]Sakamoto Y, Watanabe H, Nagai M, Nakade K, Takahashi M, Sato T (2006) Lentinula edodes tlg1 encodes a thaumatin-like protein that is involved in Lentinan degradation and fruiting body senescence. Plant Physiol 141:793–801

← Older revision		Revision as of 09:55, 28 May 2014
Line 36:		Line 36:

	[6]Liu JJ, Sturrock R, Ekramoddoullah AK.The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function. Plant Cell Rep. 2010;29(5):419-36.		[6]Liu JJ, Sturrock R, Ekramoddoullah AK.The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function. Plant Cell Rep. 2010;29(5):419-36.
		+	[7]Shatters RG Jr, Boykin LM, Lapointe SL, Hunter WB, Weathersbee AA 3rd (2006) Phylogenetic and structural relationships of the PR5 gene family reveal an ancient multigene family conserved in plants and select animal taxa. J Mol Evol 63:12–29.
		+	[8]Sakamoto Y, Watanabe H, Nagai M, Nakade K, Takahashi M, Sato T (2006) Lentinula edodes tlg1 encodes a thaumatin-like protein that is involved in Lentinan degradation and fruiting body senescence. Plant Physiol 141:793–801

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

@@ Line 12: / Line 12: @@
 ===Evolution===
-    Thaumatin-like proteins appear to have originated in early eukaryotes and share a well-defined thaumatin-like protein domain[6]. Evolutionary <br /> relationships within the thaumatin-like protein superfamily are not well understood. For example, a study of phylogenetic and structural relationships[7],<br /> suggested that plant PR5  proteins are paraphyletic in angiosperms and related to animal thaumatin-like proteins from insects and nematodes. However, <br />another study indicated that thaumatin-like proteins are grouped into three major clades representing the animal, plant, and fungal kingdoms, respectively.Alignment <br />analysis was done using 118 putative TLP sequences selected from ascomycete and basidiomycete fungi, moss, gymnosperms and angiosperms, plus animals as represented<br /> by nematodes and insects. The neighbor joining algorithm was used to construct a phylogenetic tree (Fig. 3). The topological pattern of the resulting tree indicates<br /> that the TLP superfamily is highly divergent, with the possibility of nine distinct groups (I–IX), each containing proteins with relatively high identity.
+    Thaumatin-like proteins appear to have originated in early eukaryotes and share a well-defined thaumatin-like protein domain[6]. Evolutionary <br /> relationships within the thaumatin-like protein superfamily are not well understood. For example, a study of phylogenetic and structural relationships[7],<br /> suggested that plant PR5  proteins are paraphyletic in angiosperms and related to animal thaumatin-like proteins from insects and nematodes. However, <br />another study indicated that thaumatin-like proteins are grouped into three major clades representing the animal, plant, and fungal kingdoms, respectively.Alignment <br />analysis was done using 118 putative TLP sequences selected from ascomycete and basidiomycete fungi, moss, gymnosperms and angiosperms, plus animals as represented<br /> by nematodes and insects. The neighbor joining algorithm was used to construct a phylogenetic tree (Fig. 3). The topological pattern of the resulting tree indicates<br /> that the TLP superfamily is highly divergent, with the possibility of nine distinct groups (I–IX), each containing proteins with relatively high identity[8].
 ... Figure 1
 [[File:figure.png|caption]]

@@ Line 4: / Line 4: @@
 ===Function===
-    This gene encodes a thaumatin-like protein. Thaumatin belongs to the pathogen response 5(PR5) family, and is only exclusively expressed in pathological<br />
+    This gene encodes a thaumatin-like protein. Thaumatin belongs to the pathogen response 5(PR5) family, and is only exclusively expressed in pathological<br />conditions such as paramicrobe infection or mechanical damage[2]. Therefore, it is thought that this protein is involved in acquired systematic resistance<br /> and the response to  biotic stress; the latter process leads to microbe growth inhibition and spore germination reduction[2]. However, the precise mechanism<br /> in rice is unknown. In addition, this thaumatin-like peotein harbors ATP-binding potentiality and  Serine/threonine-protein kinase activity according to <br />the homology  prediction[3]. And an attractive feature of this protein is its sweet flavor, and this feature may be used in food industry[4].
 ---

@@ Line 9: / Line 9: @@
 ---
 ===Expression===
-    This thaumatin-like protein is derived from the rice cultivar Nipponbare[5]. The name 'thaumatin-like' from its homology with thaumatin. Thaumatin is firstly
+    This thaumatin-like protein is derived from the rice cultivar Nipponbare[5]. The name 'thaumatin-like' from its homology with thaumatin. Thaumatin<br /> is firstly   extracted from the fruit ''Thaumatococcus daniellii'' growing in West Africa[4]. Thaumatin-like proteins are in diverse plants, and can be <br />isolated from  Hordeum  vulgare (barley),  Actinidia deliciosa(kiwifruit), Zea mays (maize), Pseudotsuga menziesii (douglas-firs), Nicotiana tabacum (tobacco),<br />  Solanum lycopersicum (tomato) and Triticum sp. (wheat) . Most of the thaumatin-like protein have a molecular weight in the range of 18 kDa to 25 kDa and <br />have a pH in the range from  4.5  to 5.5.[2]
 ---