Rice gene details
Searching for LOC_Os03g44380 [9-cis-epoxycarotenoid dioxygenase 1, 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_Os03g44380.1 609 108 601 PF03055.7 RPE65
  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
  4
N22InfloresenceFC
  -2
N22 Root FC
  -2
IR64 Flag-leaf FC
  7
IR64InfloresenceFC
  27
IR64 Root FC
  3

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:0009409 response to cold  
2 GO:0009414 response to water deprivation  
3 GO:0009737 response to abscisic acid stimulus  
4 GO:0030912 response to deep water  
5 GO:0006950 response to stress (RGAP)
6 GO:0009628 response to abiotic stimulus (RGAP)
7 GO:0008152 metabolic process (RGAP)
8 GO:0009058 biosynthetic process (RGAP)
9 GO:0009987 cellular process (RGAP)
10 GO:0006629 lipid metabolic process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0016020 membrane (RGAP)
2 GO:0009536 plastid (RGAP)
3 GO:0009579 thylakoid (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007048 sodium chloride regimen (+)
2 EO:0007068 ethylene regimen (+)
3 EO:0007105 abscisic acid regimen (+)
4 EO:0007198 water environment (+)
5 EO:0007261 copper nutrient regimen (+)
6 EO:0007332 cold air temperature regimen (+)
7 EO:0007383 watering regimen (+)
8 EO:0007404 drought environment (+)
9 MCE:1000010 submergence stress (+)
10 MCE:1000016 polyethylene glycol (PEG) treatment (+)
11 MCE:1000044 mannitol (+)
12 MCE:1000069 dessication/dehydration stress (+)
13 MCE:1000241 D-glucose (+)
14 MCE:1000242 D-allose (+)

Metabolic Pathway details
S. No. Pathway Id Pathway Description
1 PWY-1042 glycolysis IV (plant cytosol)

QTL details
S. No. QTL Id QTL Associated Trait
1 AQDY056 panicle length
2 AQDY058 panicle length
3 AQGJ020 leaf nitrogen content
4 AQHE004 root length
5 DQC15 penetrated to total root ratio
6 DQC8 penetrated root number
7 AQDY054 panicle length
8 AQFE071 100-grain weight
9 AQFE072 100-grain weight
10 AQFE073 100-grain weight
11 CQE18 yield
12 AQDY051 culm length
13 CQAS27 plant height
14 CQE26 carbon content
15 CQE27 grain number
16 CQF5 soluble protein content
17 AQAL004 deep root dry weight
18 AQAL010 deep root to shoot ratio
19 AQGC006 penetrated root number
20 AQGC012 penetrated root number
21 AQGC015 root penetration index
22 AQDL005 stomatal closure time
23 AQF008 seed dormancy
24 AQF026 seed dormancy
25 AQF043 awn length
26 AQF060 anther length
27 CQAH11 seed dormancy
28 CQAH12 seed dormancy
29 CQE19 specific leaf area

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000204 5 days post-anthesis stage (+)
2 MCP:1000330 pre-anthesis stage (+)
3 MCP:1000376 15 days post-anthesis stage (+)
4 MCP:1000454 10 days post-anthesis stage (+)
5 MCP:1000473 20 days post-anthesis stage (+)
6 MCP:1000477 25 days post-anthesis stage (+)
7 MCP:1000505 30 days post-anthesis stage (+)
8 MCP:1000518 seedling development stage (+)
9 PO:0001012 G early unicellular microspore stage (+)
10 PO:0007022 imbibition (+)
11 PO:0007065 LP.05 five leaves visible (+)
12 PO:0007616 4 anthesis (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 PO:0008037 seedling (+)
2 PO:0009006 shoot system (+)
3 PO:0009010 seed (+)
4 PO:0009025 vascular leaf (+)
5 PO:0009066 anther (+)
6 PO:0025034 leaf (+)
Others
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
S. No. Primary rice gene loci

Interacting rice gene loci

Experiment type

Id

Domain name/N or C term

 Amino acid involved in interaction

Id

Domain name/N or C term

 Bases
involved in interaction		 Reference point cis-elements [PLACE Id]
1 LOC_Os04g52090 - --- LOC_Os03g44380 - 1 to -1000 TrSS Transcriptional activity assay
2 LOC_Os04g52090 - --- LOC_Os03g44380 - - - - S000430 Protein-DNA interaction analysis : Electrophoretic Mobility Shift Assay (EMSA)
      TSS - Transcriptional start site
TrSS - Translational start site		 TSS-Pu - Putative TSS by cDNA alignment
TSS-P - Predicted TSS
Related publications [Sorted by year]

1  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]


2  Endo Akira; Nelson Ken M; Thoms Ken; Abrams Suzanne R; Nambara Eiji; Sato Yutaka; Functional characterization of xanthoxin dehydrogenase in rice. Journal of plant physiology 2014:171
PMID [25014258]


3  Liu Yang; Fang Jun; Xu Fan; Chu Jinfang; Yan Cunyu; Schläppi Michael R; Wang Youping; Chu Chengcai; Expression patterns of ABA and GA metabolism genes and hormone levels during rice seed development and imbibition: a comparison of dormant and non-dormant rice cultivars. Journal of genetics and genomics = Yi chuan xue bao 2014:41
PMID [24976122]


4  Ye Nenghui; Li Haoxuan; Zhu Guohui; Liu Yinggao; Liu Rui; Xu Weifeng; Jing Yu; Peng Xinxiang; Zhang Jianhua; Copper Suppresses Abscisic Acid Catabolism and Catalase Activity and Inhibits Seed Germination of Rice. Plant & cell physiology 2014:
PMID [25273891]


5  Fukumoto Takeshi; Kano Akihito; Ohtani Kouhei; Inoue Megumi; Yoshihara Akihide; Izumori Ken; Tajima Shigeyuki; Shigematsu Yoshio; Tanaka Keiji; Ohkouchi Takeo; Ishida Yutaka; Nishizawa Yoko; Tada Yasuomi; Ichimura Kazuya; Gomi Kenji; Yoo Sang-Dong; Sheen Jen; Akimitsu Kazuya; Phosphorylation of D-allose by hexokinase involved in regulation of OsABF1 expression for growth inhibition in Oryza sativa L. Planta 2013:
PMID [23397192]


6  Liu Dongfeng; Chen Xujun; Liu Jiqin; Ye Jianchun; Guo Zejian; The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. Journal of Experimental Botany 2012:63
PMID [22442415]


7  Song Shiyong; Dai Xiaoyan; Zhang Wen-Hao; A rice F-box gene, OsFbx352, is involved in glucose-delayed seed germination in rice. Journal of experimental botany 2012:63
PMID [22859682]


8  Ye Nenghui; Zhu Guohui; Liu Yinggao; Li Yingxuan; Zhang Jianhua; ABA controls H₂O₂ accumulation through the induction of OsCATB in rice leaves under water stress. Plant & cell physiology 2011:52
PMID [21398647]


9  Yaish Mahmoud W; El-Kereamy Ashraf; Zhu Tong; Beatty Perrin H; Good Allen G; Bi Yong-Mei; Rothstein Steven J; The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice. PLoS genetics 2010:6
PMID [20838584]


10  Zhu Guohui; Ye Nenghui; Zhang Jianhua; Glucose-induced delay of seed germination in rice is mediated by the suppression of ABA catabolism rather than an enhancement of ABA biosynthesis. Plant & cell physiology 2009:50
PMID [19208695]


11  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]


12  Yang Wenqiang; Kong Zhaosheng; Omo-Ikerodah Edith; Xu Wenying; Li Qun; Xue Yongbiao; Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice (Oryza sativa L.). Journal of Genetics and Genomics 2008:35
PMID [18804072]


13  Oliver Sandra N; Dennis Elizabeth S; Dolferus Rudy; ABA regulates apoplastic sugar transport and is a potential signal for cold-induced pollen sterility in rice. Plant & cell physiology 2007:48
PMID [17693452]


14  Saika Hiroaki; Okamoto Masanori; Miyoshi Kentaro; Kushiro Tetsuo; Shinoda Shoko; Jikumaru Yusuke; Fujimoto Masaru; Arikawa Taku; Takahashi Hirokazu; Ando Miho; Arimura Shin-Ichi; Miyao Akio; Hirochika Hirohiko; Kamiya Yuji; Tsutsumi Nobuhiro; Nambara Eiji; Nakazono Mikio; Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8'-hydroxylase in rice. Plant & cell physiology 2007:48
PMID [17205969]


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