Rice gene details
Searching for LOC_Os05g46480 [late embryogenesis abundant protein, group 3, 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_Os05g46480.1 201 5 48 PF02987.8 LEA_4
2 LOC_Os05g46480.2 201 5 48 PF02987.8 LEA_4
  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
  9
N22InfloresenceFC
  89
N22 Root FC
  7
IR64 Flag-leaf FC
  3
IR64InfloresenceFC
  31
IR64 Root FC
  43

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0003674 molecular_function (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:0009633 drought tolerance  
5 GO:0009651 response to salt stress  
6 GO:0009737 response to abscisic acid stimulus  
7 GO:0000003 reproduction (RGAP)
8 GO:0009791 post-embryonic development (RGAP)
9 GO:0009790 embryo development (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0005634 nucleus (RGAP)
2 GO:0005575 cellular_component (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007024 aerobic environment (+)
2 EO:0007048 sodium chloride regimen (+)
3 EO:0007105 abscisic acid regimen (+)
4 EO:0007332 cold air temperature regimen (-)
5 EO:0007404 drought environment (+)
6 MCE:1000010 submergence stress (+)
7 MCE:1000016 polyethylene glycol (PEG) treatment (+)
8 MCE:1000024 drought stress in PVC pipes (+)
9 MCE:1000069 dessication/dehydration stress (+)
10 MCE:1000101 severe drought stress in sheltered field (+)

Metabolic Pathway details
S. No. Pathway Id Pathway Description
1 FAO-PWY fatty acid β-oxidation I
2 PROPFERM-PWY D-lactate fermentation to propionate and acetate
3 PWY-3941 β-alanine biosynthesis II

QTL details
S. No. QTL Id QTL Associated Trait
1 AQBK013 days to heading
2 CQAS62 1000-seed weight
3 AQFP018 culm strength
4 AQBK016 days to heading
5 AQEP016 seedling vigor
6 AQE042 grain yield per panicle
7 CQX28 internode length
8 AQAD001 sheath blight disease resistance
9 AQAG034 1000-seed weight
10 AQAI021 large vascular bundle number
11 AQCQ022 grain yield per plant
12 CQAJ20 grain number
13 AQBK015 days to heading
14 AQBK018 days to heading
15 CQAA19 relative phosphorus distribution between shoot and root
16 AQDZ002 lodging incidence
17 AQDZ013 lodging incidence
18 CQAS53 plant height
19 AQBK017 days to heading
20 CQAA18 relative phosphorus distribution between shoot and root
21 AQX002 primary branch
22 CQAE10 plant height
23 AQAP043 brown planthopper resistance
24 AQCE028 primary branch length
25 AQCU197 plant height
26 AQCU212 leaf length
27 AQFW218 leaf width
28 AQFU013 milled rice ratio
29 CQAG23 setback
30 AQBV012 leaf angle
31 AQBV013 tiller angle
32 AQBV014 leaf angle
33 AQBC050 panicle tiller ratio
34 AQBC051 panicle tiller ratio
35 AQBC052 panicle tiller ratio
36 AQEA231 days to heading
37 AQEA232 days to heading
38 AQEA233 days to heading
39 AQEA234 days to heading
40 AQEA235 days to heading
41 AQEA236 days to heading
42 AQEA237 days to heading
43 AQEP005 seedling vigor
44 AQDX008 osmotic adjustment capacity
45 AQFE096 plant height
46 AQFE097 plant height
47 AQEJ075 leaf area
48 AQEJ077 root activity
49 CQAS63 spikelet number
50 CQAS54 days to heading
51 AQHF004 leaf length
52 AQHF011 leaf area
53 AQHF033 leaf width

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:0007065 LP.05 five leaves visible (+)
3 PO:0007115 LP.04 four leaves visible (+)
4 PO:0007616 4 anthesis (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 PO:0000003 whole plant (+)
2 PO:0008037 seedling (+)
3 PO:0009006 shoot system (+)
4 PO:0009025 vascular leaf (+)
5 PO:0020039 leaf lamina (+)
6 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 TO:0000180 spikelet fertility (+)
2 TO:0000449 grain yield per plant (+)

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_Os01g66120 N 1-165 LOC_Os05g46480 - -85 to -56 TSS S000413 Protein-DNA interaction analysis : Electrophoretic Mobility Shift Assay (EMSA)
2 LOC_Os11g08210 N 1-172 LOC_Os05g46480 - -85 to -56 TSS S000413 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  Luo Chengke; Guo Chiming; Wang Wujing; Wang Liangjiang; Chen Liang; Overexpression of a new stress-repressive gene OsDSR2 encoding a protein with a DUF966 domain increases salt and simulated drought stress sensitivities and reduces ABA sensitivity in rice. Plant cell reports 2014:33
PMID [24247850]


3  Nakashima Kazuo; Jan Asad; Todaka Daisuke; Maruyama Kyonoshin; Goto Shingo; Shinozaki Kazuo; Yamaguchi-Shinozaki Kazuko; Comparative functional analysis of six drought-responsive promoters in transgenic rice. Planta 2014:239
PMID [24062085]


4  Wei Shuya; Hu Wei; Deng Xiaomin; Zhang Yingying; Liu Xiaodong; Zhao Xudong; Luo Qingchen; Jin Zhengyi; Li Yin; Zhou Shiyi; Sun Tao; Wang Lianzhe; Yang Guangxiao; He Guangyuan; A rice calcium-dependent protein kinase OsCPK9 positively regulates drought stress tolerance and spikelet fertility. BMC plant biology 2014:14
PMID [24884869]


5  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]


6  Chen Hao; Chen Wei; Zhou Junli; He Hang; Chen Liangbi; Chen Haodong; Deng Xing Wang; Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice. Plant Science 2012: 193-194
PMID [22794914]


7  Yang An; Dai Xiaoyan; Zhang Wen-Hao; A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. Journal of Experimental Botany 2012:
PMID [22301384]


8  You Jun; Hu Honghong; Xiong Lizhong; An ornithine δ-aminotransferase gene OsOAT confers drought and oxidative stress tolerance in rice. Plant Science 2012:197
PMID [23116672]


9  Asano Takayuki; Hakata Makoto; Nakamura Hidemitsu; Aoki Naohiro; Komatsu Setsuko; Ichikawa Hiroaki; Hirochika Hirohiko; Ohsugi Ryu; Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice. Plant Molecular Biology 2011:75
PMID [21136139]


10  Bae Hansol; Kim Sung Keun; Cho Seok Keun; Kang Bin Goo; Kim Woo Taek; Overexpression of OsRDCP1, a rice RING domain-containing E3 ubiquitin ligase, increased tolerance to drought stress in rice (Oryza sativa L.). Plant Science 2011:180
PMID [21497713]


11  Du Hao; Liu Linhong; You Lei; Yang Mei; He Yubing; Li Xianghua; Xiong Lizhong; Characterization of an inositol 1,3,4-trisphosphate 5/6-kinase gene that is essential for drought and salt stress responses in rice. Plant Molecular Biology 2011:
PMID [22038091]


12  Fukao Takeshi; Yeung Elaine; Bailey-Serres Julia; The Submergence Tolerance Regulator SUB1A Mediates Crosstalk between Submergence and Drought Tolerance in Rice. The Plant Cell 2011:23
PMID [21239643]


13  Kim Hyunmi; Hwang Hyunsik; Hong Jung-Woo; Lee Young-Na; Ahn Il Pyung; Yoon In Sun; Yoo Sang-Dong; Lee Sukchan; Lee Sung Chul; Kim Beom-Gi; A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. Journal of Experimental Botany 2011:
PMID [22071266]


14  Liu Citao; Wu Yanbin; Wang Xiping; bZIP transcription factor OsbZIP52/RISBZ5: a potential negative regulator of cold and drought stress response in rice. Planta 2011:
PMID [22189955]


15  Amir Hossain Md; Lee Yongjoo; Cho Jung-Il; Ahn Chul-Hyun; Lee Sang-Kyu; Jeon Jong-Seong; Kang Hun; Lee Choon-Hwan; An Gynheung; Park Phun Bum; The bZIP transcription factor OsABF1 is an ABA responsive element binding factor that enhances abiotic stress signaling in rice. Plant Molecular Biology 2010:72
PMID [20039193]


16  Sun Shu-Jing; Guo Shu-Qiao; Yang Xia; Bao Yong-Mei; Tang Hai-Juan; Sun Hui; Huang Ji; Zhang Hong-Sheng; Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. Journal of Experimental Botany 2010:61
PMID [20460361]


17  Takasaki Hironori; Maruyama Kyonoshin; Kidokoro Satoshi; Ito Yusuke; Fujita Yasunari; Shinozaki Kazuo; Yamaguchi-Shinozaki Kazuko; Nakashima Kazuo; The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Molecular Genetics and Genomics 2010:284
PMID [20632034]


18  Lu Guojun; Gao Chenxi; Zheng Xingnan; Han Bin; Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 2009:229
PMID [19048288]


19  Xiang Yong; Tang Ning; Du Hao; Ye Haiyan; Xiong Lizhong; Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiology 2008:148
PMID [18931143]


20  Xiao Benze; Huang Yuemin; Tang Ning; Xiong Lizhong; Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Theoretical and Applied Genetics 2007:115
PMID [17426956]


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