RiceWiki - User contributions [en]

Phr1

2014-05-14T00:29:05Z

Chuhaibuyu:

Phr1 gene

2014-05-14T00:28:28Z

Chuhaibuyu:

Phr1 gne

2014-05-13T17:07:51Z

Chuhaibuyu: /* Labs working on this gene */

Phr1 gne

2014-05-13T17:07:19Z

Chuhaibuyu: /* Evolution */

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

== Labs working on this gene ==
*Bioscience Center, and Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan
*Honda R&D, Wako Research Center, Wako 351-0193, Japan
*International Rice Research Institute, Manila, DAPO Box 7777, Philippines
*BioResources Center, and Plant Molecular Biology Laboratory, Riken, Tsukuba 305-0074, Japan
*Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, GPO Box 1600, Canberra ACT 2601, Australia
*Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

Phr1 gne

2014-05-13T17:06:25Z

Chuhaibuyu:

Phr1

2014-05-13T17:03:10Z

Chuhaibuyu: /* Structured Information */

Phr1

2014-05-13T17:03:04Z

Chuhaibuyu: /* References */

==Structured Information==

Phr1

2014-05-13T17:02:56Z

Chuhaibuyu: /* Annotated Information */

== References ==

==Structured Information==

Os04g0624500

2014-05-13T16:59:20Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" /><ref name="ref4" /> <ref name="ref5" /><ref name="ref6" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>
<ref name="ref4">Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.</ref>
<ref name="ref5">Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.</ref>
<ref name="ref6">Demeke, T., and Morris, F. (2002). Molecular characterization of wheat polyphenol oxidase (PPO). Theor. Appl. Genet. 104: 813–818.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:57:40Z

Chuhaibuyu: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" /><ref name="ref4" /> <ref name="ref5" /><ref name="ref6" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>
<ref name="ref4">Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.</ref>
<ref name="ref5">Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.</ref>
<ref name="ref6">Demeke, T., and Morris, F. (2002). Molecular characterization of wheat polyphenol oxidase (PPO). Theor. Appl. Genet. 104: 813–818.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:57:15Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" /><ref name="ref4" /> <ref name="ref5" /><ref name="ref6" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:56:49Z

Chuhaibuyu: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" /><ref name="ref4" /> <ref name="ref5" /><ref name="ref6" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>
<ref name="ref4">Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.</ref>
<ref name="ref5">Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.</ref>
<ref name="ref6">Demeke, T., and Morris, F. (2002). Molecular characterization of wheat polyphenol oxidase (PPO). Theor. Appl. Genet. 104: 813–818.</ref>

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:55:33Z

Chuhaibuyu: /* Homology */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" /><ref name="ref4" /> <ref name="ref5" /><ref name="ref6" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>
<ref name="ref4">Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.</ref>
<ref name="ref5">Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.</ref>
<ref name="ref6">Demeke, T., and Morris, F. (2002). Molecular characterization of wheat polyphenol oxidase (PPO). Theor. Appl. Genet. 104: 813–818.</ref>

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:54:55Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>
<ref name="ref4">Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.</ref>
<ref name="ref5">Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.</ref>
<ref name="ref6">Demeke, T., and Morris, F. (2002). Molecular characterization of wheat polyphenol oxidase (PPO). Theor. Appl. Genet. 104: 813–818.</ref>

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:52:41Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.

Gooding, P.S., Bird, C., and Robinson, S.P. (2001). Molecular cloning and characterisation of banana fruit polyphenol oxidase. Planta 213:748–757.

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:51:44Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

Constabel, C.P., Yip, L., Patton, J.J., and Christopher, M.E. (2000).Polyphenol oxidase from hybrid poplar. Cloning and expression in response to wounding and herbivory. Plant Physiol. 124: 285–295.

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:50:07Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:49:53Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

===References===
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

===Structured Information===
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:49:34Z

Chuhaibuyu: /* Labs working on this gene */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

===Labs working on this gene===
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:49:04Z

Chuhaibuyu: /* Homology */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> <ref name="ref3" />The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:48:44Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>
<ref name="ref3">Chevalier, T., de Rigal, D., Mbeguie, A.M.D., Gauillard, F., RichardForget, F., and Fils-Lycaon, B.R. (1999). Molecular cloning and characterization of apricot fruit polyphenol oxidase. Plant Physiol.119: 1261–1270.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:46:37Z

Chuhaibuyu: /* Homology */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002).<ref name="ref2" /> The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:45:59Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:45:04Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
2.Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T16:30:35Z

Chuhaibuyu: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>
<ref name="ref2">Cary, J.W., Lax, A.R., and Flurkey, W.H. (1992). Cloning and characterization of cDNAs coding for Vicia faba polyphenol oxidase. Plant Mol. Biol. 20: 245–253.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:43:09Z

Chuhaibuyu: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.<ref name="ref1" />

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:42:58Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.<ref name="ref1" />

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:42:31Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, 35 japonica and 20 indica lines were genotyped using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:40:57Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===
To measure the occurrence of Phr1 deﬁciency among rice cultivars, we ﬁrst genotyped 35 japonica and 20 indica lines using the molecular marker pSTS18, which speciﬁcally detects D18. All 20 indica lines examined are PHR-positive, although one line appears to be heterozygous for both the wild-type and D18 alleles.

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:36:05Z

Chuhaibuyu: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
In the haplotype tree, three of the four non D18-bearing haplotypes are embedded among H18 types, and each is most closely related to anotherH18 haplotype. Amore parsimonious explanation may be that these non-D18-bearing alleles were originally H18s themselves but have subsequently lost the D18 deﬁciency by recombination with a rice strain carrying a functional Phr1 allele.

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:32:43Z

Chuhaibuyu: /* location */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone(OSJNBa0053K19).<ref name="ref1" />

[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:32:12Z

Chuhaibuyu: /* location */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />
[[File:Example111.jpg]]

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:31:04Z

Chuhaibuyu: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===

[[File:Example1111.jpg]]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:29:58Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
[[File:Example1111.jpg|right|thumb|150px|''The Genealogy of Phr1 Alleles in Cultivars and Their Wild Relatives <ref name="ref1" />).'']]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T15:29:31Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg|right|thumb|150px|''Summary of Phr1 Variations and PHR Phenotypes (from reference <ref name="ref1" />).'']]

[[File:Example11111.jpg]]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
[[File:Example1111.jpg|right|thumb|150px|''The Genealogy of Phr1 Alleles in Cultivars and Their Wild Relatives <ref name="ref1" />).'']]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:Example1111.jpg

2014-05-13T15:27:30Z

Chuhaibuyu: The Genealogy of Phr1 Alleles in Cultivars and Their Wild Relatives

The Genealogy of Phr1 Alleles in Cultivars and Their Wild Relatives

Os04g0624500

2014-05-13T15:27:13Z

Chuhaibuyu: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg|right|thumb|150px|''Summary of Phr1 Variations and PHR Phenotypes (from reference <ref name="ref1" />).'']]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
[[File:Example1111.jpg|right|thumb|150px|''The Genealogy of Phr1 Alleles in Cultivars and Their Wild Relatives <ref name="ref1" />).'']]

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:Example11111.jpg

2014-05-13T15:24:21Z

Chuhaibuyu: Summary of Phr1 Variations and PHR Phenotypes

Summary of Phr1 Variations and PHR Phenotypes

Os04g0624500

2014-05-13T15:23:16Z

Chuhaibuyu: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

[[File:Example11111.jpg|right|thumb|150px|''Summary of Phr1 Variations and PHR Phenotypes (from reference <ref name="ref1" />).'']]

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:59:06Z

Chuhaibuyu: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:57:03Z

Chuhaibuyu: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.<ref name="ref1" />

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:56:29Z

Chuhaibuyu: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

===Expression===
The steady state level of Phr1 mRNA was not detectable by RNA gel blot analysis; nevertheless, by RT-PCR,the Phr1 express in grains at the early ﬂowering stage (G1) and at the mature stage (G2).The Phr1 gene appears to encode an ;62.6-kD precursor protein, which is processed into amature PPO of ;56.3 kD after
removal of the NH2-terminal signal peptide. The deduced Phr1 amino acid sequence shows 68% identity to wheat PPO (GenBank AAS00454), indicating that Phr1 is a rice homolog of the wheat PPO.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:52:36Z

Chuhaibuyu: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

=== Mutation ===

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:Example11.jpg

2014-05-13T14:40:17Z

Chuhaibuyu: PHR of Grains of Asian Cultivated Rice Subspecies

PHR of Grains of Asian Cultivated Rice Subspecies

Os04g0624500

2014-05-13T14:38:39Z

Chuhaibuyu: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Example11.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:38:03Z

Chuhaibuyu: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:34:55Z

Chuhaibuyu: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Oryza_sativa.jpg|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

File:Example111.jpg

2014-05-13T14:34:20Z

Chuhaibuyu: Map-Based Cloning and Conﬁrmation of Phr1

Map-Based Cloning and Conﬁrmation of Phr1

Os04g0624500

2014-05-13T14:33:52Z

Chuhaibuyu: /* location */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Oryza_sativa|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example111.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os04g0624500

2014-05-13T14:32:52Z

Chuhaibuyu: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
[[File:Oryza_sativa|right|thumb|150px|''PHR of Grains of Asian Cultivated Rice Subspecies (from reference <ref name="ref1" />).'']]
The Phr1 gene control oryza sativa classification. That means the phr1 gene decides Oryza sativa becoming indica rice or japonica rice. Genetically modified function complementary experiments show that oryza sativa are classified to indica rice or japonica rice by Phr1 gene. When the Phr1 gene is knockdown or over expressed in rice, the transgenic rice get different disease-resistant ability. That means the Phr1 gene can regulate plant resistance.

Asian rice (Oryza sativa) cultivars originated from wild rice and can be divided into two subspecies by several criteria, one of which is the phenol reaction (PHR) phenotype. Grains of indica cultivars turn brown in a phenol solution that accelerates a similar process that occurs during prolonged storage. By contrast, the grains of japonica do not discolor. This distinction may reﬂect the divergent domestication of these two subspecies. The PHR is controlled by a single gene, Phr1. The Phr1 encodes a polyphenol oxidase. The Phr1 gene is indeed responsible for the PHR phenotype, as transformation with a functional Phr1 can complement a PHR negative cultivar.<ref name="ref1" />

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

===Homology===
The Phr1 gene is highly similar to plant PPO genes (Cary et al., 1992; Chevalier et al., 1999; Constabel et al., 2000; Gooding et al., 2001; Demeke andMorris,2002). The similarity in protein sequence ranges from 43 to 68%, and the highest is found with wheat PPO. In higher plants, PPOs have been proposed to be responsible for the browning of damaged kernels, fruits, or vegetables, which may be response for disease resistance (Nicolas et al., 1994;
Thipyapong et al., 1995; Gooding et al., 2001; Demeke and Morris, 2002; Li and Steffens, 2002).<ref name="ref1" />

===location===
[[File:Example.jpg|right|thumb|150px|''Map-Based Cloning and Conﬁrmation of Phr1 (from reference <ref name="ref1" />).'']]
The Phr1 gene was mapped to the interval between markers S100 and S115 with genetic distances of 9.3 and 8.5 centimorgan (cM) to Phr1, respectively. The breakpoints can be ﬁnely delineated. The Phr1 locus was pinpointed to an 88-kb interval between markers P80 and P168 on a single BAC clone (OSJNBa0053K19).<ref name="ref1" />

==Labs working on this gene==
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

*State Key Laboratory of Biocontrol, School of Life Sciences, Zhongshan (Sun Yat-Sen) University, Guangzhou 510275, China

*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China

*National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200002, China

*Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China

*Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637

==References==
<references>
<ref name="ref1">Yanchun Yu,Tian Tang, Qian Qian, YonghongWang,Meixian Yan,Dali Zeng, Bin Han, Chung-IWu,Suhua Shi, and Jiayang Lia,Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication.The Plant Cell, 2008.Vol. 20: 2946–2959.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0624500|
Description = Similar to Polyphenol oxidase (EC 1.10.3.1) (Fragment)|
Version = NM_001060467.1 GI:115460663 GeneID:4337055|
Length = 2464 bp|
Definition = Oryza sativa Japonica Group Os04g0624500, 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 4|Chromosome 4]]|
AP = Chromosome 4:32147679..32150142|
CDS = 32147695..32148299,32148781..32149039,32149149..32149997|
GCID = <gbrowseImage1>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:32147679..32150142
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtga</cdnaseq>|
AA = <aaseq>MESINVAPGTTATPRMAPPPPPPCITNLQSTLRYNNLLLHRKTK GWKPRNVSCRVDRRDVLLGISGAAAMVATQGGGGALAAPIQAPDLGDCHQPVDVPATA PAINCCPTYSAGTVAVDFAPPPASSPLRVRPAAHLADRAYLAKYERAVSLMKKLPADD PRSFEQQWRVHCAYCDGAYDQVGFPGLEIQIHSCWLFFPWHRMYLYFHERILGKLIGD ETFALPFWNWDAPDGMSFPAMYANRWSPLYDPRRNQAHLPPFPLDLDYSGTDTNIPKD QLIDQNLNIMYRQMISGARKAELFMGQPYRAGDQPEPGAGTVESVPHNPVHRWTGDPR QPNGEDMGIFYSAARDPVFFAHHGNVDRMWHIRRGLLFPGDTDFTDPDWLDASFFFYD EEARLVRVRVRDTLDPSALRFTYQDVGLPWLNAKPSTGAASTPAPAAGAFPATLDKTV RVAVTRPRASRSREEKEEEEEVEIPDHSTYVKFDVFVNAPESGDGAATCAATCAGSVA LAPHGIHREGQLSPRKTEARFGICDLLDDIGADGDKTIVVSIVPRCGCDSVTVAGVSI GYAK</aaseq>|
DNA = <dnaseqindica>17..621#1103..1361#1471..2319#acagcgcagtgccgccatggagagcatcaacgtagcaccaggaacaaccgctacgcctcgcatggcgccgccgccgccgccgccgtgcatcaccaacctccagagtacccttcgctacaacaacctgctcttgcaccgcaagacgaaggggtggaagccgcggaacgtgtcctgcagggtcgaccgccgcgacgtgctcctcggcatcagcggcgcggccgccatggtggccacgcagggcggcggcggcgcgctcgcggcgcccatccaggccccggacctcggcgactgccaccagcccgtggacgtccccgccacggcgccggcgatcaactgctgcccgacgtacagcgccggcaccgtcgccgtcgacttcgcgccgccgccggcgtcctcgccgctccgcgtgcggccggcggctcacctggcggacagggcgtacctggccaagtacgagagggccgtgtcgctcatgaagaagctccccgccgacgacccccgcagcttcgagcagcagtggcgcgtccactgcgcctactgcgacggcgcgtacgaccaggtcggcttccccggcttggagatccagatacacagctgctggctcttcttcccatggcacaggtacgtgacattgtgacaacatggctgcatcacgttcacgtctcgcgttgttcgtgtacagttgcatgcatgatatatatggggagtggattttttacgacttcctcttattttgtacatgtcattcaaaaagttatcaaaaaatttaaaaaatttgtcaagatagatcaatatacggtatatctttttcgcaaacatacgagttaaaattcgacttatacaattcgaaacaaaaacaacaaatttgaccgtgatttacgcagttaaatttgttatttttgtttctacttgtataagttgaatttgaatttgtatgtttgtgaaataacatattatatattgatgtaatattgatctatactgctatatttttttaatttttttgatgactttttacttgacatgtaaaaatgagaggattatttgagtggctcatgagattctgtgaacgctggacgcatgcgtgtgaacgtacgtgcaggatgtacctgtacttccatgagaggatactgggcaagctgatcggcgacgagacgttcgcgctgccgttctggaactgggacgcgccggacggcatgtcgttccccgcgatgtacgccaacaggtggtcgccgctgtacgacccgcggcgcaaccaggctcacctgccaccgttcccgctcgacctcgactacagtggaaccgacacgaacatcccgaaagaccagctgatcgatcagaacctcaacatcatgtaccgccaggccagtaatcacatacaaattttgatataaataataatagatgacaaaaactccaaattaatcgacttatgagttaagattggacgaacaaaattttatgatgtttcagatgatttcgggagctaggaaggcggagctgttcatggggcagccgtaccgcgccggcgaccagccggagccgggggcgggcaccgtcgagagcgtgccgcacaaccccgtccacagatggaccggcgacccgaggcagccgaacggcgaggacatgggcatcttctactcggcggcgcgcgacccggtgttcttcgcgcaccacggcaacgtcgaccgcatgtggcacatccgccgcggcctcctcttccccggcgacaccgacttcaccgaccccgactggctcgacgccagcttcttcttctacgacgaggaggcccgcctcgtccgcgtccgcgtccgcgacaccctcgacccgtcggcgctgcgcttcacgtaccaggacgtgggtctcccgtggctgaacgccaagccgtccacgggagcagccagcacgccggcgcccgcggccggcgcgttcccggcgaccctggacaagaccgtgcgggtggccgtgacgaggcccagggcgtcgaggagccgcgaggagaaggaggaggaggaggaggtcgagatccccgaccactccacgtacgtcaagttcgacgtgttcgtgaacgcgcccgagagcggggacggcgcggcgacgtgcgcggcgacgtgcgccggcagcgtcgcgctggcgccgcacgggatccaccgcgaggggcagctgtcgccgaggaagacggaggcgaggttcggcatatgcgacttgctggacgacatcggcgccgacggcgacaagacgatcgtcgtgtcgatcgtgccgaggtgtggctgcgattcggtcaccgtcgccggcgtcagcatcggctacgctaagtgaagcacaacgtgaaccgtggacgtatatttatcatctatacatgtgaacccagatggagagacggatttgtgtttgatatgtgtgtgactaatgattgtatacaaaataatgccagtaatataatgagcatggatgatattggctt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060467.1 RefSeq:Os04g0624500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]