Rice gene details
Searching for LOC_Os09g38320 [phytoene synthase, 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_Os09g38320.1 445 156 430 PF00494.11 SQS_PSY
  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
N22 Root FC
IR64 Flag-leaf FC
IR64 Root FC

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0003824 catalytic activity (RGAP)
2 GO:0016740 transferase activity (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0006950 response to stress  
2 GO:0009414 response to water deprivation  
3 GO:0009628 response to abiotic stimulus  
4 GO:0009651 response to salt stress  
5 GO:0009725 response to hormone stimulus  
6 GO:0009737 response to abscisic acid stimulus  
7 GO:0009058 biosynthetic process (RGAP)
8 GO:0009987 cellular process (RGAP)
9 GO:0006629 lipid metabolic process (RGAP)
10 GO:0008152 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:0007048 sodium chloride regimen (+)
2 EO:0007105 abscisic acid regimen (+)
3 EO:0007132 far infra-red light regimen (+)
4 EO:0007163 day light regimen (+)
5 EO:0007196 light regimen (+)
6 EO:0007207 red light regimen (+)
7 EO:0007270 continuous dark (no light) regimen (+)
8 EO:0007404 drought environment (+)
9 MCE:1000069 dessication/dehydration stress (+)

Metabolic Pathway details
Not found

QTL details
S. No. QTL Id QTL Associated Trait
1 AQBK037 spikelet number
2 CQE74 shoot elongation rate
3 AQF004 grain shattering
4 AQF040 seed dormancy
5 AQF071 anther length
6 AQF102 KClO3 resistance
7 CQAS108 panicle length
8 AQBK052 seed set percent
9 CQAS115 spikelet number
10 CQF13 rubisco content
11 AQGS010 panicle length
12 AQGS028 seed weight
13 AQGS031 grain yield per plant
14 CQAS117 yield
15 CQAW28 root number
16 AQBK054 seed set percent
17 CQAS113 seed set percent
18 CQAS114 1000-seed weight
19 AQAF042 blast disease resistance
20 AQCY007 panicle number
21 AQGE018 cooked kernel elongation
22 AQGI004 root dry weight
23 AQGI021 root dry weight
24 AQGI028 root dry weight
25 AQHR024 tiller number
26 AQEE008 colored grain percentage
27 AQGP032 1000-seed weight
28 AQHF023 leaf senescence
29 AQHF042 leaf senescence

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000518 seedling development stage (+)
2 PO:0004506 developing seed stage (+)
3 PO:0007050 FR.03 late stage of fruit ripening (+)
4 PO:0007065 LP.05 five leaves visible (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 PO:0000003 whole plant (+)
2 PO:0006339 juvenile leaf (+)
3 PO:0006340 adult leaf (+)
4 PO:0008037 seedling (+)
5 PO:0009005 root (+)
6 PO:0009006 shoot system (+)
7 PO:0009010 seed (+)
8 PO:0009089 endosperm (-)
9 PO:0025034 leaf (+)
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
Not found

Trait details
Not found

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; 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]

Welsch Ralf; Wüst Florian; Bär Cornelia; Al-Babili Salim; Beyer Peter; A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiology 2008:147
PMID [18326788]

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