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Os08g0398400

2014-06-02T16:22:17Z

Zhuo CHEN: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
OsHIR1 triggers hypersensitive cell death and its localization to the plasma membrane is enhanced by OsLRR1.HIR1 (OsHIR1) as an interacting partner of the OsLRR1 (rice Leucine-Rich Repeat protein 1).<ref name="ref1"/>
OsHIR1 E3 ligase positively regulates OsTIP4;1 related to As and Cd uptakes.<ref name="ref2"/>

[[File:1.jpg|right|thumb|150px|"Figure1.Schematic representation of the conserved structural domains in OsHIR1 and its homologues.(from reference <ref name="ref1"/>"]]===Expression===
OsHIR1 was identified as a putative interacting partner ofOsLRR1. The OsHIR1 protein exhibits high similarity (from 84% to 96% identity) to homologues from dicots and monocots (Figure 1a), including maize, barley, wheat, pepper, and A. thaliana. For all the close homologues of OsHIR1, computational analysis reveals a putative N-myristoylation site at the N-terminus, followed by a transmembrane domain that is embedded within a Band 7-domain, which covers most of the OsHIR1 protein (Figure 1). In an unrooted phylogenetic tree (Figure 2), HIR proteins can be further divided into two branches: dicots and monocots. Among HIR homologues
from monocots, the OsHIR1 shares the highest similarity with the maize ZmHIR1 (96% identity).

To show that OsHIR1 is related to the plant defense response, we investigated whether its gene expression is responsive to pathogen challenge. Northern and western blot analyses showed that both the mRNA and protein levels of OsHIR1 increased after the rice plant was inoculated with the pathogen Xoo LN44 (Figure 3). On the other hand, no such change was observed after mock treatment (Figure 3).

A transgenic line that exhibited a high level of OsLRR1 gene expression was chosen for subsequent electron microscopy analysis (Figure 4). Interestingly, in addition to the elevated level of OsLRR1 mRNA, the expression of the OsHIR1 gene in the OsLRR1
transgenic line was also enhanced (Figure 4).

Immuno-gold electron microscopy studies showed that not only the signal density of the OsLRR1 proteins, but also that of the OsHIR1 proteins, in the plasma membrane, was increased in the OsLRR1 overexpressing line by at least two folds, when compared to the untransformed control (Figure 5). On the other hand, there was no significant difference (Student’s t-test, p < 0.05) between the number of OsHIR1 signals in the tonoplast of the OsLRR1 overexpressing line and that in the untransformed control. These results indicated that OsLRR1 enhanced the plasma membrane localization of OsHIR1.

Proximal occurrences of large and small gold particles were detected in the plasma membrane (Figure 6), supporting the notion that OsLRR1 and OsHIR1 co-localized and interacted in the plasma membrane.
Ectopic expression of the OsHIR1 can cause spontaneous hypersensitive response lesions in the leaves of transgenic A. thaliana. To perform a rapid gain-of-function test of QsHIR1,transgenic A. thaliana plants ectopically expressing OsHIR1 were generated. Three weeks after germination, the leaves of about 20% of the OsHIR1 transgenic plants (Col-0/OsHIR1) exhibited white spontaneous HR lesions located randomly at the margins and tips (Figure 3a, red arrows). As negative controls, the untransformed wild type (Col-0) and transgenic plants with the empty vector (Col-0/V7) exhibited normal growth. Transgenic plants expressing OsLRR1 (Col-0/OsLRR1) did not exhibit visible differences in the size, shape, or color of the leaves, when compared to the negative controls (Figure 7).To further observe the effect of OsHIR1 on cell death, lactophenol-trypan blue staining was performed using the leaves of the transgenic A. thaliana. The expression of OsHIR1 caused extensive spontaneous cell death (Figure 8,black arrows). On the other hand, the expression of OsLRR1 only resulted in very mild spontaneous cell death (Figure 8). This explains the lack of visible lesions found in OsLRR1 transgenic plants (Figure 7). No spontaneous cell death was observed in the untransformed control and transgenic plants containing the empty vector (Figure 8).

Ectopic expression of OsHIR1 in transgenic A. thaliana enhances resistance to P. syringae pv. tomato DC3000 (Pst DC3000)
When the untransformed wild type (Col-0) or A. thaliana transformed with the empty vector cassette (Col-0/V7) was inoculated with the pathogen Pst DC3000, disease symptoms (yellowing and necrosis) gradually appeared and the infected areas spread out from the original inoculation sites (Figure 9). Such symptoms were alleviated in the transgenic line expressing OsLRR1, consistent with the
results of our previous study . The spread of pathogen infection was also suppressed by the ectopic expression of OsHIR1 (Figure 9). Consistent with these visible symptoms, transgenic plants expressing either OsLRR1 or OsHIR1 exhibited a lower titer of pathogens when compared to Col-0 and the empty vector control (Figure 10).However, the OsHIR1 transgenic lines showed a stronger
effect on lowering the pathogen titer when compared to the OsLRR1 transgenic line (Figure 10).

The expression levels of PR1 and PR2, two defense marker genes in the salicyclic acid pathway related to the defense against biotrophic pathogens such as Pst DC3000, were monitored in both mock- (Figure 11)and pathogen-inoculated (Figure 12) plants. In both mock-treated and pathogen-inoculated plants, the expression levels of PR1 and PR2 were elevated in both OsHIR1 and OsLRR1 transgenic plants when compared to Col-0 and transgenic plants containing the empty vector cassette. However, the OsHIR1 transgenic plants exhibited significantly higher levels of PR1 and PR2 gene induction than the OsLRR1 transgenic plants (p < 0.05).<ref name="ref1"/>

OsHIR1‑overexpressing Arabidopsis enhances As and Cd tolerance
The finding that the OsHIR1 gene was upregulated in response to As and Cd treatments raises the question of the function of OsHIR1 associated with both elemental stress responses. Three independent transgenic lines were selected depending on the expression level of the OsHIR1 by RT-PCR and then compared to the control plants under 150 μM As and 50 μM Cd (Figure 13). The OsHIR1-overexpressing lines exhibited no apparent phenotypic differences from the vector control lines under normal conditions. However,
OsHIR1-overexpressing plants showed significantly longer root lengths than those of the control plants under As and Cd conditions (Fig. 4a). To investigate the possible mechanism by which OsHIR1 ubiquitin E3 ligase affects As or Cd uptake in the transgenic line, we compared As and Cd accumulation between the OsHIR1-overexpressing lines and the control plants. The concentrations of As in the shoots and roots of the OsHIR1-overexpressing plants were 14.1 and 46.4 %, respectively, which were lower than those
of the control plants (Figure 14). Cd uptake by the OsHIR1-overexpressing plants was also 3.8 and 12.3 % lower than the control plants in the shoots and roots, respectively(Figure 15). These results suggest that the heterogeneous overexpression of the OsHIR1 gene in Arabidopsis may reduce both As and Cd uptakes by regulating its substrate protein.<ref name="ref2"/>

===Evolution===
The OsHIR1 protein is mainly localized to the plasma membrane, and its subcellular localization in that compartment is enhanced by OsLRR1. The expression of OsHIR1 may sensitize the plant so that it is more prone to HR and hence can react more promptly to limit the invading pathogens’ spread from the infection sites.<ref name="ref1"/>

OsHIR1 E3 ligase positively regulates OsTIP4;1 related to As and Cd uptakes.<ref name="ref2"/>

==Labs working on this gene==
*State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China

*Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University

==References==
<references>
<ref name="ref1"> Liang Zhou1, Ming-Yan Cheung1, Man-Wah Li1, Yaping Fu2, Zongxiu Sun2, Sai-Ming Sun1, Hon-Ming Lam1* （2010） Plant Biology 10:290</ref>

<ref name="ref2"> Sung Don Lim · Jin Gyu Hwang · A. Reum Han ·Yong Chan Park · Chanhui Lee · Yong Sik Ok ·Cheol Seong Jang （2014）Plant Mol Biol
DOI 10.1007/s11103-014-0190-0</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os08g0398400|
Description = Similar to Hypersensitive-induced response protein|
Version = NM_001068279.1 GI:115476295 GeneID:4345499|
Length = 4031 bp|
Definition = Oryza sativa Japonica Group Os08g0398400, 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 8|Chromosome 8]]|
AP = Chromosome 8:19099911..19103941|
CDS = 19101742..19101930,19102201..19102321,19102445..19102536,19102609..19102705,19103258..19103613 |
GCID = <gbrowseImage1>
name=NC_008401:19099911..19103941
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008401:19099911..19103941
source=RiceChromosome08
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggtcaagcactcggtttggtacaagtagatcaatcgacagtagccatcaaggagtcctttgggaagtttgatgaggttcttgagcctggatgccactttttaccctggtgcatagggaagcagatcgctggatatctttccttgcgtgtgcagcagctggatgtccgttgtgaaacaaagactaaggacaatgtttttgtcaatgttgtggcatctgtgcaataccgtgctcttgctgagaaggcatcagacgccttttacaggcttagcaacaccagggagcaaatccagtcgtatgtttttgatgtgatcagggctagtgttccaaagatgaacttggatgatgcatttgagcagaagaatgagatcgcaaaagctgtggaagatgagcttgaaaaggcaatgtcaatgtatggttatgagattgtgcaaactcttattgttgatattgaaccagatgagcatgttaagagagcaatgaatgaaatcaacgcagctgctaggctgagggtggcagccaatgagaaagctgaagcagagaagattcttcagatcaagagagctgaaggagatgcagaatccaagtacttggctggtctgggtatcgcaaggcagcgtcaggctatagtggatgggctgagagacagtgttcttgccttctccgagaacgtgcctgggacctctgccaaggatgtcatggatatggttctggttacgcaatacttcgacaccatgaaggagataggagcctcatccaagtcctcttcagtgttcatccctcacgggccaggtgccgtcaaagatatcgctgcgcagataagagatggtcagctccaggccaaattgatctaa</cdnaseq>|
AA = <aaseq>MGQALGLVQVDQSTVAIKESFGKFDEVLEPGCHFLPWCIGKQIA GYLSLRVQQLDVRCETKTKDNVFVNVVASVQYRALAEKASDAFYRLSNTREQIQSYVF DVIRASVPKMNLDDAFEQKNEIAKAVEDELEKAMSMYGYEIVQTLIVDIEPDEHVKRA MNEINAAARLRVAANEKAEAEKILQIKRAEGDAESKYLAGLGIARQRQAIVDGLRDSV LAFSENVPGTSAKDVMDMVLVTQYFDTMKEIGASSKSSSVFIPHGPGAVKDIAAQIRD GQLQAKLI</aaseq>|
DNA = <dnaseqindica>1832..2020#2291..2411#2535..2626#2699..2795#3348..3703#agaatttgccctcctcacttctatacttcaatccccttcctttatttttttttttgggaggggccgaggcaaccgtcgccactccgacgatcccgtcccatccgccgccgccgccggagatttcctcgaggtaagccctaccccgctcctctccagcctctctccccttcggcgggcgcccagcccgagccccgacctcgatttcttggaatttcttggcgagcgtttgtttcttggggtttcctctagattttttcttttttttattattttggggacggatttagctctcgtggaggagattgggcggataatttcgtcggaggggggagggggagggggatgttggaatcgggtggtgggtaatttcgtcgattctccggtccttttccttgagtttagcctgggaattgcggttggttcttggacgcggtttgagttcttggttttttccactttctgtgcggacagatttagggcttgcgctttgcgagtgggggtaaaattcgatggtgtgctgttccagctttgtccacatactgcttggaaatttcaggaggttttttcagtcaagtcaagcacatcttttttgctagactaggccatgagatggaggttaacgtcgaactgtacccacctcagctaaaaataataataattctcaacaacagtatccaagtggctgtattgtttattcttgtttagttatgacgcagatgaatactactcgctaaagattgtgactttcttagttgtcacctcgtcgtgtggagccctgtgggttcttgctcttgacttttatcaaacaatgattgcttggcaagtgtcttgtttgattcgtctgccctttggcttgcatcgccagagtttgctggcttgcgctggcatttaatcaaaagtataatcattcccccaagtataatcaggattagcataatctttagcttcaactatttatatgatatatttggcttgtctgtagtctgtagtggccaagaacatcctgaagcagatttatcctatcaggctatcagcactaagttgatcggcacgtataggttttcttttgcgtcattctttttcattactgcatttctatggtgaattgttttcttttcttttgtatggctacatctattaccctgttgacttctgtgagcctgtgatgtactccctccgggctgataatacttgtcattttggacaagcgcacggtcttcaaaaaacaactttgaccattatttcctattataatatgtaaaaaagtgttaacaaatatatgatcatattaaagtactttttaagaccaatctatatatgtagtcaccatatttgaaagacaaatattttaaaaatgatttatataatcaaatattctaaagtttgacctcacccttgtccaaaacgacaagtattatcagcccggagggagtagtaatcttaggcatttttcagggaatgattacacagtataagtttgagtaatgtgttatcatgatatgcttttcaacaagatatacatattttttgcaacactgtttggtctaagttatctgaaattgcaattgcttgacttttcatttgggatgcgttgggcaatctattgtcctgacatacattcatcttcatttgaagccatggctttatcttttttaattcatatcttttgtttctgtttgtatgtactaaaaacttgaaatatgaatttccattggagaagttaacaccaacggagtataagcaagattatggcaaaacattcagttgttagttgtttcgttagcatatggcaccatttgtaattctgcatttcttcctttctagataagccatgggtcaagcactcggtttggtacaagtagatcaatcgacagtagccatcaaggagtcctttgggaagtttgatgaggttcttgagcctggatgccactttttaccctggtgcatagggaagcagatcgctggatatctttccttgcgtgtgcagcagctggatgtccgttgtgaaacaaagactaaggttccccagtttattttcttaactctggtttcttttatatttcatggcaagtgtctggagcaattgtcaggcatgataaaaaatggttctcaaaattcttgcattttgttccattcgtttactcctttatgataacatactgatgatggttatgtgcacatatctctgttttccttattcttcacttacactaatgcatgatgcatcaaagaataaacccaccttttctgagctctctgacgatgtataccattttgtggatatctgcaggacaatgtttttgtcaatgttgtggcatctgtgcaataccgtgctcttgctgagaaggcatcagacgccttttacaggcttagcaacaccagggagcaaatccagtcgtatgtttttgatggtaaggttcctgtatgctgtgaacattcatgcatccgatgcatttgcagttcatactcttctgattaccttctctatgttttgcctctattgttcaatgctaacagaactttcttcctcgcagtgatcagggctagtgttccaaagatgaacttggatgatgcatttgagcagaagaatgagatcgcaaaagctgtggaagatgagcttgaaaaggtttgtgttcaataattggtggtcatctagagcatagtggagttttatactgacctagtatatactctgtaggcaatgtcaatgtatggttatgagattgtgcaaactcttattgttgatattgaaccagatgagcatgttaagagagcaatgaatgaaatcaacgcaggtaagtattaattaaaacatcaattcattccatttcttcagagacattatttggcttggtgtttatgcttgacatttgagcttgcattggaaacaattttctcctgtttagacatgaaaatgttaaattctctttccgagaaacaaaaccatgtttatattgtctagttttattcaagttttatactgaaacactgaaaattgttgccacaaatatttttaggctttcaacacagtaacactgtaagttatatatagatggaacactgaaaagttatatatagatgtacataacatattatgaatattaacttcgtgaatacttgcaccataacagtcataagtaacacaggcacatgtaactgcaacctattgattacattgtgtgcaacaaaaaatgtgttggtcaactagtcaagtaaatatttcgtgctttttaagggcctgcaacatatatgtttggttggtctggtgtttttctaaagatgagctgtatggctgtaaatgtgctggacggcaacatagttttaactgctgttatttgatgatacagctgctaggctgagggtggcagccaatgagaaagctgaagcagagaagattcttcagatcaagagagctgaaggagatgcagaatccaagtacttggctggtctgggtatcgcaaggcagcgtcaggctatagtggatgggctgagagacagtgttcttgccttctccgagaacgtgcctgggacctctgccaaggatgtcatggatatggttctggttacgcaatacttcgacaccatgaaggagataggagcctcatccaagtcctcttcagtgttcatccctcacgggccaggtgccgtcaaagatatcgctgcgcagataagagatggtcagctccaggccaaattgatctaagaggatggcagggaatggatgttctggatttcttgggcattacgaaagtctgcagtaataccttatctacgtattcgatattttgtgagataaaaacttaggcaaaagaagttctattgtaagtatcacatgcacgcgtgcttcagtaccgtttgttcatagtaattcctgaggttatttccctagacgagtgtcaatatacttcttgaattgcatgtttctgtaaataattcctaagtgttaccgggctgtttggaattatttgcatgttgatgttagtgaccttaagtaatgtcccatcttattatgtgatgtcatgatgatttcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001068279.1 RefSeq:Os08g0398400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 8]]
[[Category:Chromosome 8]]

Os01g0367100

2014-05-07T16:19:16Z

Zhuo CHEN: /* References */

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />
'''GO assignment(s):''' GO:0003978, GO:0019375, GO:0009507

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" /> 
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Subcellular Localization===
* Confocal micrographs showing chloroplast targeting of ''PHD1''(Figure 4A). Rice protoplasts transformed with ''35S::PHD1-GFP'' (upper panel) and ''35S::GFP'' (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. <ref name="ref1" />
* ''PHD1'' protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the ''PHD1'' antibody and specific chloroplast subcompartment protein antibodies. ''Tic 40'' is an envelope membrane protein, ''RbcL'' a stroma protein, and ''PsbA'' a thylakoid membrane protein. ''HSP82'' was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. ''RbcL'' seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)<ref name="ref1" />
* Immunogold localization of ''PHD1''. Thin sections of chloroplasts in leaf mesophyll cells were incubated with ''PHD1'' antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.<ref name="ref1" /> 
[[File:Subcellular localization of PHD1.png|center|thumb|500px|'''Figure 4.''' ''Subcellular localization of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os03g0181500

2014-05-07T16:17:07Z

Zhuo CHEN: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===

ONI1 gene is originally derived from Oryza sativa Japonica Group(cultivar: Nipponbare). It encodes an fatty acid elongase involved in the synthesis of very-long-chain fatty acids, which are the component of extracellular waxes<ref name="ref2" />.

It's the key gene for correct acid composition and normal shoot development in rice. Mutation of ONI1 will induce a reduced amount of very-long-chain fatty acids<ref name="ref1" /> and failure of the maintenance of SAM and ectopic expression of SAM-specific KNOX genes in leaf<ref name="ref3" />.

===Expression===

This gene expresse in the outermost cells of the embryo, SAM, young leaves and floral organs.

At 3 days after pollination, ONI1 expression can be detected in the outermost cells of a globular embryo.

At 4-5 days after pollination, ONI1 expression can be detected in L1 of newly developed shoot organ as well as outermost cells of the embryo.

At 7-10 days after pollination, ONI1 expression can also be detected in L1, but the quantity is reduced.

During vegetative growth phase (within one month after germination), ONI1 expression can be detected in L1 of SAM and young leaves.

During reproductive growth phase, ONI1 expression can be detected in L1 of the developing panicle and floral organs.

In conclusion, ONI1 is an L1-specific gene of the SAM and young above-ground organs<ref name="ref2" />.

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

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

==Labs working on this gene==
Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken, 411-8540 Japan

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan

State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, People’s Republic of China

Institute of Cellular and Molecular Botany, Department of Ecophysiology, University of Bonn, 53115 Bonn, Germany

==References==
<references>
<ref name="ref1">
Tsuda K, Akiba T, Kimura F, Ishibashi M, Moriya C, Nakagawa K, Kurata N, Ito Y. ONION2 fatty acid elongase is required for shoot development in rice. Plant Cell Physiol. 2013;54(2):209-17.</ref>
<ref name="ref2">
Ito Y, Kimura F, Hirakata K, Tsuda K, Takasugi T, Eiguchi M, Nakagawa K, Kurata N. Fatty acid elongase is required for shoot development in rice. Plant J. 2011;66(4):680-688.</ref>
<ref name="ref3">
Takasugi T, Ito Y. Altered expression of auxin-related genes in the fatty acid elongase mutant oni1 of rice. Plant Signal Behav. 2011;6(6):887-888.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0181500|
Description = Similar to Fiddlehead protein|
Version = NM_001055705.1 GI:115451138 GeneID:4331836|
Length = 4801 bp|
Definition = Oryza sativa Japonica Group Os03g0181500, 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 3|Chromosome 3]]|
AP = Chromosome 3:4245314..4250114|
CDS = 4245368..4245778,4248671..4249888|
GCID = <gbrowseImage1>
name=NC_008396:4245314..4250114
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:4245314..4250114
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgagggagcaggcgctgctgttgacggagatcgtgaaccgcggcgtggagccgtcggggccggacgccgggtcgccgacgttctcggtgcgggtgcggcggcggctgccggacttcctccagtcggtgaacctcaagtacgtgcggctcgggtaccactacctcatcagccacggcgtgtacctggccaccatcccggtcatcgtgctcgtctgcggcgccgaggtcggcagcctcagccgagacgagctgtggcgcaaggtctggggcgaggccacctacgacctcgccaccgtcctcgccttcctcgccgtcctcgccttcaccatctccgtctacatcatgtccaggcctaggcccgtctacctcatcgacttcgcctgctacaaaccagccgacgaactcaaggtgtcgaaggcggagttcatcgatctggcgaggaagtcgggcaagttcgacgaggatagcctggcgttccagtcgcggctgctggccaagtctggcatcggcgacgagtcctacatgccgcgctgcgtgttcgagccgggcaccaactgcgccaccatgaaggaaggccgcgccgaggcgtccgccgccatgttcgccgcgctggacgagctgttcgacaagtgccgcgtccgccccaaggacgtcggcgtgctcgtcgtcaactgcagcctcttcaacccgacgccgtcgctgtccgccatgatcgtcaaccactacaagatgcgcgggaacatcctcagctacaacctcggcggcatggggtgcagcgccggcgtcatcgcggtggacctcgcccgcgacatgctccaggccagcggcgcggggctcgccgtcgtcgtcagcacggaggccgtctccttcacctggtacgccgggaagcgccgctccatgctcatccccaacgccttcttccgcgccggctgcgccgccgtgctgctctccaaccgccgcagggacttccaccgcgccaagtaccagctcgagcacatcgtgcgcacccacaagggcgccgacgaccgcagcttccggtcggtgtaccaggaggaggacgagcagcggatcaagggcctgtccatcagccgcgacctcgtggaggtcggcggccacgcgctcaagaccaacatcaccaccctgggcccgctcgtgcttccgttctcggagcagatcctcttcttcgccggcgtgctcttccgccacctgttcccgtccaagacctccgccccgccgccgccgtccgccgacggcgacgcctccgccgccgctccctacatcccggacttcaagcgcgcgttcgagcacttctgcatgcacgcggcgagccgcgacgtgctggagcacctgcagggcaacctgggcctccgcgacggcgacctggaggcgtcgcgcgccgcgctccaccgcttcggcaacacgtcgagcagcagcatctggtacgagctggcgtacctggaggccaagggccgcgtccgccgcggcgaccgcgtgtggcagctcgccttcggctccgggttcaagtgcaacagcgccgtgtggcgcgccgtccgccgcgtgcgccgcccggcgcgcagcccgtggctggactgcgtcgagcagtacccggctcgcatgaacgcttaa</cdnaseq>|
AA = <aaseq>MAREQALLLTEIVNRGVEPSGPDAGSPTFSVRVRRRLPDFLQSV NLKYVRLGYHYLISHGVYLATIPVIVLVCGAEVGSLSRDELWRKVWGEATYDLATVLA FLAVLAFTISVYIMSRPRPVYLIDFACYKPADELKVSKAEFIDLARKSGKFDEDSLAF QSRLLAKSGIGDESYMPRCVFEPGTNCATMKEGRAEASAAMFAALDELFDKCRVRPKD VGVLVVNCSLFNPTPSLSAMIVNHYKMRGNILSYNLGGMGCSAGVIAVDLARDMLQAS GAGLAVVVSTEAVSFTWYAGKRRSMLIPNAFFRAGCAAVLLSNRRRDFHRAKYQLEHI VRTHKGADDRSFRSVYQEEDEQRIKGLSISRDLVEVGGHALKTNITTLGPLVLPFSEQ ILFFAGVLFRHLFPSKTSAPPPPSADGDASAAAPYIPDFKRAFEHFCMHAASRDVLEH LQGNLGLRDGDLEASRAALHRFGNTSSSSIWYELAYLEAKGRVRRGDRVWQLAFGSGF KCNSAVWRAVRRVRRPARSPWLDCVEQYPARMNA</aaseq>|
DNA = <dnaseqindica>55..465#3358..4575#acttcactgccttctcatttactgcagaaggtgaaggtgaaggaggaggcggccatggcgagggagcaggcgctgctgttgacggagatcgtgaaccgcggcgtggagccgtcggggccggacgccgggtcgccgacgttctcggtgcgggtgcggcggcggctgccggacttcctccagtcggtgaacctcaagtacgtgcggctcgggtaccactacctcatcagccacggcgtgtacctggccaccatcccggtcatcgtgctcgtctgcggcgccgaggtcggcagcctcagccgagacgagctgtggcgcaaggtctggggcgaggccacctacgacctcgccaccgtcctcgccttcctcgccgtcctcgccttcaccatctccgtctacatcatgtccaggcctaggcccgtctacctcatcgacttcgcctgctacaaaccagccgacgaactcaaggtaatactacttaattccatgcttaatcacgtatacacatattcggtagttcatcggagtagattagtattatattactagtattatgtttaaatgaaagcatattatgccaatgtgtgaagctcctaggatctatgatttgttactgcgcaagaaacttgttcgttctaacatttcagatctcacgtaaattgaatcggccaaggttttattctgaaacaataaaagcatatttctggtgcaaaaggatagatcggataaaacatatatattgacgttatacaaagtgctcaaggactaaatgaaggtctcatatggagctagcataggatcgaatttcatgattcatggaatccacatggtccttcagtgatctagccaactgtttttcaaacagcgccattctttttttttttttgagacgaatcaaacaacgcaaattaaaactgcaaatatacttttggatttaccggacgtagtagctgaaatctcaaaactgtgaaagctattcaaggtgaggtgtgaagagaaaactcttggaacgtgtaagccttgggcctcctttaatggttgagctagctcatgcttgtccacctcatataagagatagtaaaaagtctacctctcccatagattgtctcatagcacattgtataaaatgctttaggtttcacaatttctttagtagcttagctcttaaagaagagatagtgcattctctttccttatcttctctctcttccacatcatacaaaagctgatgtggagatttatgagctagctgacttacctttgttggaggagggtttagtattaactgctggatgaacttgcattgacaacaacaaaaaaaaaaaaactcatcatcagttgggcttttagttgtgaataactattggtatagtggtgtctatagctagtactactccgcatggtcctttaatacggtcataatccttgccagctactaccagctcaaatgcttttaatgtagcacacattcactatttgagcactgacaaatctgcccggcactgactgaaatacccgagccacgctcatacgattaccacctccattttacttgacagccctagatagaaccggtgtgattcgtcttttttttttccttgagatttcaccacattggcatatttgaaatcatcttgaattaaatttttagaaattatatcattagatccatcataaaaaaaatacttccatacttagtatacgcttgttattactccctccatttcaggttataaaatattttgactttggtcaaagtcaaactttcaagtttgaccaagtttatataaaaaaatagtaatattttcgaccgaagataaatttattataaaaatatatttaattattaatttaataaaactaatttgctaatttaaatattaccatatttttcatatttgtctataaacttagttaaatttgaagcagtttgactttgaccaaagtcaaaacatcttataacatgaaacggagggattatatcctaacacaacgttgtaaaatgtgcaatggtcaaagcaatatcttagaaattgcacaaaaaaaaaagaacggaggtagtgctattttgtatgaatcaaattcatttatcatatattgattctacacctaataagtttacactagatagatgcttttccttgtgcccgagtgcctctgttatcttgtactgtatgttacttttagtataaatactgccatcattctcaagtaaagtctttgaccactgcttttttccctgattactctatgttgactaaaggaatggtaataaaatattaactgaatattataaagtatttacatgatatattagatccaaaattgataagaagctcctccttagtagatactccaaaagaaactctagttatatctttgcagacttaggcctggtttagttctccaattttttttccctaaaacataacatcgaatctttgaacacatgcatggagcattaaatataaattacaaaaactaattgcacagttaggggggaaatcacgagacgaatcttttgagcctaattagtccataattagccatatgtgctacagtaatccacatgtgctaatgacagattaattaggctcaaaagatttgtctcgcggtttccaaacgagttatgaaattattttttcattcgtatccgaaaaccccttcgacatccggtgaaatatctgatatgacatataaaaaatttcttttcacgaaaccgcgttatgaaattagttttttcattcgtatctgaaaacctctttcgacatccggtaaaatatctgatgtgacatataaaaattttcttttcacgaactaaacaggcccttatatgctacacatcactaagttttggaaaacagtttgttggctaccattattttgttggagtcttgaatgcaagttaggaggcacctttggttgggccccagtccttggaagtgaatgggcagggcagggtcgaagttatgacgagctggtaggatgctttcggttatggccaggccagccggtgactcgatcagtcgatcgctctcacttgctcgtgtcatcaaatacggttgggcgattgggcacacacattcaatgagccgaaccgtattattaaaccgtaaatgttttgcgtgagcacacattttcttttcgaaaaatgttttgcgtgagcacacaaaccacaacctgcactatccttgcacgcacgatggatttgagtcaaacaaccaagtttacccggttcgcatgcatgaaatttcttcgatttcacttgttacttacagtttgtaatcagtttgatgcattatggtactagctggtgatttgtaagcaaggatgtgattttgcatggacaattgcttgcaggtgtcgaaggcggagttcatcgatctggcgaggaagtcgggcaagttcgacgaggatagcctggcgttccagtcgcggctgctggccaagtctggcatcggcgacgagtcctacatgccgcgctgcgtgttcgagccgggcaccaactgcgccaccatgaaggaaggccgcgccgaggcgtccgccgccatgttcgccgcgctggacgagctgttcgacaagtgccgcgtccgccccaaggacgtcggcgtgctcgtcgtcaactgcagcctcttcaacccgacgccgtcgctgtccgccatgatcgtcaaccactacaagatgcgcgggaacatcctcagctacaacctcggcggcatggggtgcagcgccggcgtcatcgcggtggacctcgcccgcgacatgctccaggccagcggcgcggggctcgccgtcgtcgtcagcacggaggccgtctccttcacctggtacgccgggaagcgccgctccatgctcatccccaacgccttcttccgcgccggctgcgccgccgtgctgctctccaaccgccgcagggacttccaccgcgccaagtaccagctcgagcacatcgtgcgcacccacaagggcgccgacgaccgcagcttccggtcggtgtaccaggaggaggacgagcagcggatcaagggcctgtccatcagccgcgacctcgtggaggtcggcggccacgcgctcaagaccaacatcaccaccctgggcccgctcgtgcttccgttctcggagcagatcctcttcttcgccggcgtgctcttccgccacctgttcccgtccaagacctccgccccgccgccgccgtccgccgacggcgacgcctccgccgccgctccctacatcccggacttcaagcgcgcgttcgagcacttctgcatgcacgcggcgagccgcgacgtgctggagcacctgcagggcaacctgggcctccgcgacggcgacctggaggcgtcgcgcgccgcgctccaccgcttcggcaacacgtcgagcagcagcatctggtacgagctggcgtacctggaggccaagggccgcgtccgccgcggcgaccgcgtgtggcagctcgccttcggctccgggttcaagtgcaacagcgccgtgtggcgcgccgtccgccgcgtgcgccgcccggcgcgcagcccgtggctggactgcgtcgagcagtacccggctcgcatgaacgcttaagctgcagtggtaagtatgcagaggctaatgaacggaaaattactgcaacgtcaaaagacgggatcggcatgcgatgccggttaaggttcaagcttgattaatttgtgttggtgtattagcaagtcggtttatgagccatagactaccataaaagttgtgcgagacatgtgtactgaaccagtgtacgcgagttcggtgatatgtgaacttatctacgtttgattct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001055705.1 RefSeq:Os03g0181500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os01g0367100

2014-05-07T15:44:54Z

Zhuo CHEN: /* Function */

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />
'''GO assignment(s):''' GO:0003978, GO:0019375, GO:0009507

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" /> 
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Subcellular Localization===
* Confocal micrographs showing chloroplast targeting of ''PHD1''(Figure 4A). Rice protoplasts transformed with ''35S::PHD1-GFP'' (upper panel) and ''35S::GFP'' (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. <ref name="ref1" />
* ''PHD1'' protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the ''PHD1'' antibody and specific chloroplast subcompartment protein antibodies. ''Tic 40'' is an envelope membrane protein, ''RbcL'' a stroma protein, and ''PsbA'' a thylakoid membrane protein. ''HSP82'' was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. ''RbcL'' seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)<ref name="ref1" />
* Immunogold localization of ''PHD1''. Thin sections of chloroplasts in leaf mesophyll cells were incubated with ''PHD1'' antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.<ref name="ref1" /> 
[[File:Subcellular localization of PHD1.png|center|thumb|500px|'''Figure 4.''' ''Subcellular localization of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0367100

2014-05-07T15:41:46Z

Zhuo CHEN: /* Function */

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />
'''GO assignment(s):'''GO:0003978, GO:0019375, GO:0009507

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" /> 
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Subcellular Localization===
* Confocal micrographs showing chloroplast targeting of ''PHD1''(Figure 4A). Rice protoplasts transformed with ''35S::PHD1-GFP'' (upper panel) and ''35S::GFP'' (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. <ref name="ref1" />
* ''PHD1'' protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the ''PHD1'' antibody and specific chloroplast subcompartment protein antibodies. ''Tic 40'' is an envelope membrane protein, ''RbcL'' a stroma protein, and ''PsbA'' a thylakoid membrane protein. ''HSP82'' was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. ''RbcL'' seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)<ref name="ref1" />
* Immunogold localization of ''PHD1''. Thin sections of chloroplasts in leaf mesophyll cells were incubated with ''PHD1'' antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.<ref name="ref1" /> 
[[File:Subcellular localization of PHD1.png|center|thumb|500px|'''Figure 4.''' ''Subcellular localization of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0367100

2014-05-07T15:34:23Z

Zhuo CHEN: /* Subcellular Localization */

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" /> 
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Subcellular Localization===
* Confocal micrographs showing chloroplast targeting of ''PHD1''(Figure 4A). Rice protoplasts transformed with ''35S::PHD1-GFP'' (upper panel) and ''35S::GFP'' (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. <ref name="ref1" />
* ''PHD1'' protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the ''PHD1'' antibody and specific chloroplast subcompartment protein antibodies. ''Tic 40'' is an envelope membrane protein, ''RbcL'' a stroma protein, and ''PsbA'' a thylakoid membrane protein. ''HSP82'' was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. ''RbcL'' seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)<ref name="ref1" />
* Immunogold localization of ''PHD1''. Thin sections of chloroplasts in leaf mesophyll cells were incubated with ''PHD1'' antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.<ref name="ref1" /> 
[[File:Subcellular localization of PHD1.png|center|thumb|500px|'''Figure 4.''' ''Subcellular localization of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0367100

2014-05-07T15:27:40Z

Zhuo CHEN:

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" /> 
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Subcellular Localization===
* Confocal micrographs showing chloroplast targeting of PHD1(Figure 4A). Rice protoplasts transformed with 35S::PHD1-GFP (upper panel) and 35S::GFP (lower panel) plasmids are shown. Chlorophyll autofluorescence (middle); GFP fluorescence (left); merged images (right). Bars = 5 µm. <ref name="ref1" />
* PHD1 protein distribution in chloroplast subfractions. Percoll-purified intact chloroplasts were lysed and subjected to differential centrifugation fractionation into envelope, stroma, and thylakoid fractions. Proteins were separated by SDS-PAGE, and blotted against the PHD1 antibody and specific chloroplast subcompartment protein antibodies. Tic 40 is an envelope membrane protein, RbcL a stroma protein, and PsbA a thylakoid membrane protein. HSP82 was used as a cytosolic protein marker. About 15 µg of total proteins from extrachloroplast (Ep), purified chloroplast (Cp), envelope (E), stroma (S), and thylakoid (T) subfractions were loaded per line. RbcL seen in the Ep fraction is most likely due to leakage from the stroma of broken chloroplasts. (Figure 4B)<ref name="ref1" />
* Immunogold localization of PHD1. Thin sections of chloroplasts in leaf mesophyll cells were incubated with PHD1 antibodies (Figure 4C and Figure 4D) and preimmune serum (Figure 4E and Figure 4F). The gold label is found preferentially associated with thylakoids of the chloroplasts as seen in (Figure 4D). Chl, chloroplast; Cyt, cytosol; Mit, mitochondria; CW, cell wall. Bar = 0.5 µm.<ref name="ref1" /> 
[[File:Subcellular localization of PHD1.png|center|thumb|500px|'''Figure 4.''' ''Subcellular localization of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Subcellular localization of PHD1.png

2014-05-07T15:26:34Z

Zhuo CHEN:

Os01g0367100

2014-05-07T15:18:26Z

Zhuo CHEN:

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (Figure 2B), leaf mesophyll cells around vascular bundles (Figure 2C), young inflorescences (Figure 2D), and axillary buds (Figure 2E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.(Figure 3)<ref name="ref1" />
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0367100

2014-05-07T15:12:13Z

Zhuo CHEN:

The rice ''Os01g0367100'' has been reported as ''PHD1'' in 2011. ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE) which plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity.<ref name="ref1" />

==Annotated Information==
===Function===
* ''PHD1'' encodes a novel chloroplast-localized UDP-glucose epimerase (UGE), which is conserved in the plant kingdom. <ref name="ref1" />
* ''PHD1'' plays an important role in supplying sufficient galactolipids to thylakoid membranes for proper chloroplast biogenesis and photosynthetic activity and will be useful for improving crop yields and for bioenergy crop engineering.<ref name="ref1" />

===Wild Type VS. Mutant===
* ''photoassimilate defective1'' (''phd1'') with both low carbohydrate contents and stunted growth was selected from rice T-DNA insertion mutant population (Oryza sativa var. Nipponbare background).<ref name="ref1" />
* Scanning electron micrograph of culms demonstrated that fewer starch granules were deposited in parenchyma cells of the ''phd1'' mutants.
* During the young seedling stage, both shoots and primary roots of the mutant were shorter and lighter than those of the wild type (Figure 1A).
* After internode elongation, the ''phd1'' mutant exhibited a semi-dwarf, less grain-filling, retarded vegetative growth, later flowering, and less tillering phenotype (Figure 1B–1E).
* In addition, although the grain number per panicle was not altered between the mutant and wild type, the seed-setting ratio of the phd1 mutant was significantly decreased, which finally led to a significant reduction of grain yield (Figure 1F, 1G).
* Compared to wild type, mature leaves of the mutant had somewhat reduced sucrose (Figure 1H) and rather low starch levels (Figure 1I) at all time-points taken during the light/dark cycle. 
[[File:Phd1_mutant_phenotypes.png|center|thumb|500px|'''Figure 1.''' ''phd1 mutant phenotypes (from reference<ref name="ref1" />).'']]

===Expression===
* ''in situ'' hybridization performed by ''Chunlai Li'' et al. showed that the ''PHD1'' signal was detected in the shoot apical meristem and young leaves (B), leaf mesophyll cells around vascular bundles (C), young inflorescences (D), and axillary buds (E).<ref name="ref1" /> 
[[File:Expression_analysis_of_PHD1.png|center|thumb|500px|'''Figure 2.''' ''Expression analysis of PHD1 (from reference<ref name="ref1" />).'']]

===Evolution===
* The phylogenetic analyses between ''PHD1'' and its 16 putative homologs made by ''Chunlai Li'' et al. in 2011 showed that ''PHD1'' is closely related to ''Sb03g014730'' from sorghum and ''LOC100193101'' from maize.<ref name="ref1" />
[[File:Phylogenetic_analysis_of_PHD1.png|center|thumb|500px|'''Figure 3.''' ''Phylogenetic analysis of PHD1 (from reference<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, China

==References==
<references>
<ref name="ref1">
Li C, Wang Y, Liu L, et al. A rice plastidial nucleotide sugar epimerase is involved in galactolipid biosynthesis and improves photosynthetic efficiency[J]. PLoS genetics, 2011, 7(7): e1002196.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0367100|
Description = Conserved hypothetical protein|
Version = NM_001049575.1 GI:115436563 GeneID:4325727|
Length = 4900 bp|
Definition = Oryza sativa Japonica Group Os01g0367100, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:15224863..15229762|
CDS = 15225149..15225258,15225348..15225412,15225538..15225623,15227720..15227808,15227921..15228032 ,15228237..15228330,15228781..15228953,15229223..15229338,15229497..15229674 |
GCID = <gbrowseImage1>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:15224863..15229762
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctataaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttga</cdnaseq>|
AA = <aaseq>MGGAAVSSLLATPTPTSRPRPVSTTTAPFSVNLSTAAARAPRLL LLSRRPRPRPAAAVLGVSDDTGVKMAGSDIVGKNDLLIVGPGVLGRLVAEKWQEEHPG CKVFGQTASTDHHNELSNIGIIPSLKGSTFPQKVPYVIFCAPPSRSDDYPGDVRVAAS NWTGEGSFVFTSSTALYDCSDNELCNEDCPSVPIGRSPRTDVLLKAENVVLEAGGCVL RLAGLYKIDRGAHFFWLRKGTLDTRPDHIINQIHYEDAASLAIAIMKKGHRGRIFLGC DNKPLSRQEIMDSVNRSGKFDTKFQGFTGTDGPLGKKMENSRTRSEIGWEPKYPSFTE FLGLDS</aaseq>|
DNA = <dnaseqindica>4505..4614#4351..4415#4140..4225#1955..2043#1731..1842#1433..1526#810..982#425..540#89..266#ctgctccaatccactctcctccgtttgcctgatccgatcccctcacctccgtccctgcttcctcccggcgaccaccgcccgccgcgcgatgggcggcgccgccgtctccagcctgcttgccaccccaacaccgacctctcgacctcgacccgtctccaccaccaccgcccccttctccgtcaacctctccaccgcagctgcccgcgcacctcgcctcctcctcctctcgcgccgccctcgccctcgccccgccgccgcggttctcggtaaccacatctctctctttctctctccacctcggattatcttgttctcctatgtttgcggtaccatgtaccatggtgagggtgagggtgcatgggaacgagatgggcttgcaatttgatgactctttgttacttgggttttggtacttccaatccaggggtgtctgatgatacaggggtcaagatggctggctccgacattgttggcaagaacgatttgctgattgttggccctggagtgcttggtcgactggtagctgagaaatggcaggaggtattattatcagattgcccgattgttatactctatctcagttatttaccttgtgtctcctattggtttaaacttcgaaaaccatattcctctttcatcgtgtggagcataatattttttttggttcaaaatggcgtatctacttttgttgcttctgtaatactaggatttttaatatttaatcttctgattaacataaaaaaatgatgccgcactgttaattcgtttaattgagtacaataataatgtacactgtccgtactctgtaggaacatccaggatgcaaagtttttggccagaccgcaagcacagatcaccacaacgaattgtcgaatattggcatcattccctccttgaagggatccacttttcctcagaaggttccatatgttattttctgtgctcccccatctcgttcggatgattaccctggggatgtgaggtaaatgagtacgattataatgatgaatccatgattatattactgttaacagtatcatcctaccttctggtatcatgtgagttcctaatggctaaggtccattggttactcctaaacatttattttctttttaacacataaactatccaaatttgtgtttatagtgtatagtggtattttgctaatgaatatgcctctggcaacatttgcttgtgggtgtaagtttcttttttgagaggaggggtttgaattcttttccttgaaggccagaaccatgatacgcaactctcttgcgtattcaagaaaaaaagaaccattccagaacaaaatattattgaatcattgttgtaatagttccattccaatgatatgaaccattcatctatcttgcactaatcgaaacgcatacatggacatgtgatgtattcttatttcagaaaatgcgtgcagagtagctgcctcaaattggactggtgaaggctctttcgtttttacatcaagtactgctctgtacgattgtagtgacaacgaattgtgcaatgaggtatccccacaagcctgcagattgtagctgtgaagtcttccatacttttctttttggctcttttcatttatagaagttctagtgacattaaaaaaaaaacaatgtatccacaagccatattatgcaactctaaatattttttcttgacggttgaaaaactttattgtttttgttttaaccataattattcctcccattatgtaggattgcccatctgtgccaattggcagaagccctcgtactgacgtccttctaaaagcagagaatgttgttcttgaggcaggaggctgtgtcctcaggctagcaggactctatatatcctcaattgatgactatttgttgttctaaagtgcaagcaatattaacgcaagttcttttacattggtatgaagagaactgatacaacgtttccttgacttggacacacaaaatagatagaggtgctcattttttttggttgaggaaaggaactttggacacacgaccagatcatattatcaatcaaattcattatgaggtaatgagctgcaagtttatctcagttatatgtcttgttatgctgttctttctttatctgtcgtatcatttgcattgtgatcacaactgtggaacttgggtttacttaccatacatagttggtactttttataatttagatctaacttgtttgattgtataaaagcatatgcaattccattttataatttatagtgcgttgagatacattcgacagtctaaattaagttgcaatatatcttattattgtaatctaggaaagaacttttcaacctactattctgtatcttatgttttggttgctttctattgtatatttcgatctctggttttatgaactcatgaggggtttccatgaccttatatatactcctaaatatgtagttatcactacattatcctaatacaaatagctgtaaactacccaaaatatcgaagaaaagaaatactgttctcacataacattttagattatactccctccatttctaaatatttgacgccgttgacttttttaaatatgtttgactgttcgtcttattcaaaaaatttaagtaattattaattcttttcctatcatttgattcattgttaaatatgcttttatgtatacatatagttttacatatttcacaaaagtttttgaataagacgaacggtcaaatatgtgctaaaaattcaacggtgtcaagaaacggagggagtatatagtaattggatatctcccaagagtcacttgcttggtcctagaaacaagctaggcaaagagtcctacattaatcagaaataatcattatcccacattaataaaaaaaatgggaacatcgtgatattgatagtccattttttagattgcacgtgacttggaggaaggttagtttattctagggagcaaaacaacagagctggtgtggcatttcagctatatttcaagcaaaagagtcaatatgtccaatataatttagttagaaatatctattgagcatttgggttaacgtgaaaaataacaaaatgtatttttacaaacagtttccagcccatggtcattgaattaaagacacaacttgttatcttttcaatagcagttttcttttctttttttaagaaaaaactggaatgacgcaaaactgtaagcaatatttctctgcaggaaacaacagttttgcacttgttttgggagagataaaatttcaaaattcgaaggtctgatgtttatggcatatctaaagggcctagggatctgtttgaccaattgtcttctttggccccgtttggtagagctccaaactccaactccagtgggagctagctcctataggagctaaggtggttgtgaaagtgtttggctagacttgttagcttcacaccaccacgtcccctgtagtcatttcgtcgaacacttggttagcgtcgccccaccgtcagcttgtgcaccaccaccgccgacgcccgccgccggcaccgccactggtcaccccgtgcgctgccaccacccagcccatgctgctgctgcccgccgctcgtgtccaccgccgtcgacgccaccagcccgcgcgccatcgcccggcacccagcccccgcgctgtcggccagccctcgcgccgccgccgaggccgcgtgctgccgctagcccgcgtgccgccatcgaggccgtgcgccgcctccgccagcctgcccgctgccggttgccgccggatctcgctagagatgatgggaggatgggaggagagagaatgtgaggaggagtttaggggtagtttagtggcatttttttggtaatacatcaaaaaaaattaaagggtagtgggtcttttggggtggagtggagctgtggagcagcaaaaacccagctccacccccgtattacaaatttgtggagcagccttgccaactctgctccaaaaaatagagaatctgtactttggcacagctctagctctaggtaagtaggagcgggagctggagctgtgccatacggggtctttatatcatcgtgtttccccatgggctttttcatgttcattgcatggggtggctatgatggctgtttaattagctgttagtattggtgtaattctttgtggtaattatttgcaggatgctgcttcccttgcaattgccataatgaaaaagggacacaggggtcgaatctttttgggctgtgacaataagcctctttccaggtcagtgctaggctacttgttttgactaattatttgtttcctacgtccacttagctgtgtatcatgactgcactaatagctgaacgggtctgtcaactgaaacaaaatttacttcaacttttcaggcaagaaataatggactctgttaacagaagtggaaaatttgacacgaagttccaaggttttactggttagtattctacatgttcatttatgcttatattttactccacaggcattcgcatctattgcataatcttcattctgccttaactgcaggtacagatggtccactgggtaagaagatggagaattcgagaactcgttctgagattggttgggagcccaagtatccaagcttcacagaattccttggtcttgacagttgacatgcttgtgtatgcttgcaaaaatcttcaactctaaatgaacagcaacacgttgtgaaccagttattttgttttgtttccattgcgttttttttaaaagacgtaaatactgtatatcttgttctgctatgtgcttatatcagttagcgttctaagtctgaccgttgtacaatggtttcggccagagaaatatttccacccgtgtcatgttggcctcgttctggtccgtccaacatctatttgtctctttgtaaccacatttgttatgaaaacttggtttcctttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001049575.1 RefSeq:Os01g0367100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Phylogenetic analysis of PHD1.png

2014-05-07T15:06:34Z

Zhuo CHEN:

File:Expression analysis of PHD1.png

2014-05-07T14:57:03Z

Zhuo CHEN:

File:Phd1 mutant phenotypes.png

2014-05-07T14:51:18Z

Zhuo CHEN: