Rice gene details
Searching for LOC_Os02g09750 [lycopene beta cyclase, chloroplast precursor, putative, expressed ]

Basic information [Pfam DB] Graphical representation of the protein domains
S. No. Locus Id Protein Length Doman Start Domain End Pfam ID Domain Name
1 LOC_Os02g09750.1 490 69 466 PF05834.4 Lycopene_cycl
  The basic information is from RGAP and Pfam/InterPro databases

Gene model (download)
IR64 N22

Gene Expression (RNASeq data) in two varieties N22 & IR64 [FC=Fold Change]
N22 Flag-leaf FC
  1
N22InfloresenceFC
  -2
N22 Root FC
  3
IR64 Flag-leaf FC
  2
IR64InfloresenceFC
  1
IR64 Root FC
  1

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0003824 catalytic activity (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0009414 response to water deprivation  
2 GO:0009416 response to light stimulus  
3 GO:0009058 biosynthetic process (RGAP)
4 GO:0009987 cellular process (RGAP)
5 GO:0006629 lipid metabolic process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0009536 plastid (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007196 light regimen (+)
2 EO:0007224 light intensity regimen (+)
3 EO:0007270 continuous dark (no light) regimen (+)
4 EO:0007404 drought environment (+)

Metabolic Pathway details
S. No. Pathway Id Pathway Description
1 CAROTENOID-PWY carotenoid biosynthesis

QTL details
S. No. QTL Id QTL Associated Trait
1 AQFP026 culm thickness
2 AQFP004 culm thickness
3 AQDK017 1000-seed weight
4 AQFW170 spikelet number
5 AQFW102 panicle length
6 AQAP041 brown planthopper resistance
7 CQY1 germination speed
8 AQGB109 chalkiness of endosperm
9 AQGB108 chalkiness of endosperm
10 AQGB084 chalkiness of endosperm
11 AQBK012 days to heading
12 CQAA17 relative phosphorus distribution between shoot and root
13 CQAA16 relative phosphorus distribution between shoot and root
14 AQBK041 seed number
15 AQBK031 spikelet number
16 AQBK025 plant height
17 CQAS26 yield
18 AQDR009 1000-seed weight
19 AQE024 grain yield per plant
20 AQE001 days to flower
21 CQN31 leaf senescence
22 CQN56 spikelet number

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000505 30 days post-anthesis stage (+)
2 MCP:1000518 seedling development stage (+)
3 MCP:1000521 mature plant stage (+)
4 PO:0001053 3 leaf fully expanded (+)
5 PO:0004506 developing seed stage (+)
6 PO:0007050 FR.03 late stage of fruit ripening (+)
7 PO:0007065 LP.05 five leaves visible (+)
8 PO:0007115 LP.04 four leaves visible (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000100 upper leaf (+)
2 PO:0000003 whole plant (+)
3 PO:0008037 seedling (+)
4 PO:0009005 root (+)
5 PO:0009006 shoot system (+)
6 PO:0009010 seed (+)
7 PO:0009025 vascular leaf (+)
8 PO:0009049 inflorescence (+)
9 PO:0025034 leaf (+)
Others
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
Not found

Trait details
S. No. TO Id TO Description Presence(+) or absence(-) of gene expression /activity
1 MCT:1000015 photochemical efficiency (+)
2 MCT:1000208 leaf whitening (+)
3 MCT:1000433 percentage of open stomata (+)
4 MCT:1000434 trans-violaxanthin content (+)
5 MCT:1000435 cis-violaxanthin content (+)
6 MCT:1000436 trans-beta-carotene content (+)
7 MCT:1000437 cis beta-carotene content (+)
8 MCT:1000564 presence of pink coloured embryo (+)
9 MCT:1000567 seedling whitening (+)
10 MCT:1000568 reactive oxygen species accumulation (+)
11 TO:0000478 abscisic acid concentration (+)
12 TO:0000495 chlorophyll content (+)
13 TO:0000619 vivipary (+)
14 TO:0002667 abscisic acid content (+)
15 TO:0002675 gibberellic acid content (+)
16 TO:0002696 alpha carotene content (+)
17 TO:0002701 lutein content (+)
18 TO:0002715 chloroplast development trait (+)
19 TO:0020106 Indole-3-acetic acid content (+)
20 TO:0020117 non photochemical quenching (+)

Physical interaction details
Interaction type: protein-protein
Not found
Interaction type: protein-DNA
Not found
Related publications [Sorted by year]

Du Hao; Chang Yu; Huang Fei; Xiong Lizhong; GID1 modulates stomatal response and submergence tolerance involving ABA and GA signaling in rice. Journal of integrative plant biology 2014:
PMID [25418692]


Du Hao; Wu Nai; Chang Yu; Li Xianghua; Xiao Jinghua; Xiong Lizhong; Carotenoid deficiency impairs ABA and IAA biosynthesis and differentially affects drought and cold tolerance in rice. Plant molecular biology 2013:83
PMID [23846670]


Du Hao; Wu Nai; Fu Jing; Wang Shiping; Li Xianghua; Xiao Jinghua; Xiong Lizhong; A GH3 family member, OsGH3-2, modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice. Journal of Experimental Botany 2012:
PMID [23112280]


Chaudhary Neetu; Nijhawan Aashima; Khurana Jitendra P; Khurana Paramjit; Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis. Molecular Genetics and Genomics 2010:283
PMID [19890663]


Du Hao; Wang Nili; Cui Fei; Li Xianghua; Xiao Jinghua; Xiong Lizhong; Characterization of the beta-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice. Plant Physiology 2010:154
PMID [20852032]


Fang Jun; Chai Chenglin; Qian Qian; Li Chunlai; Tang Jiuyou; Sun Lei; Huang Zejun; Guo Xiaoli; Sun Changhui; Liu Min; Zhang Yan; Lu Qingtao; Wang Yiqin; Lu Congming; Han Bin; Chen Fan; Cheng Zhukuan; Chu Chengcai; Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice. The Plant journal : for cell and molecular biology 2008:54
PMID [18208525]


Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi-110021, India