Rice gene details
Searching for LOC_Os01g55940 [OsGH3.2 - Probable indole-3-acetic acid-amido synthetase, 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_Os01g55940.1 615 31 592 PF03321.5 GH3
  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
  39
N22InfloresenceFC
  1
N22 Root FC
  -18
IR64 Flag-leaf FC
  2
IR64InfloresenceFC
  2
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:0006979 response to oxidative stress  
2 GO:0009409 response to cold  
3 GO:0009414 response to water deprivation  
4 GO:0009416 response to light stimulus  
5 GO:0009628 response to abiotic stimulus  
6 GO:0009725 response to hormone stimulus  
7 GO:0009733 response to auxin stimulus  
8 GO:0009737 response to abscisic acid stimulus  
9 GO:0048589 developmental growth  
10 GO:0009719 response to endogenous stimulus (RGAP)
11 GO:0008152 metabolic process (RGAP)
12 GO:0008150 biological_process (RGAP)
Cellular component
S. No. GO Id GO Description

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007070 indole acetic acid regimen (+)
2 EO:0007105 abscisic acid regimen (+)
3 EO:0007180 2,4-dichlorophenoxyacetic acid (+)
4 EO:0007270 continuous dark (no light) regimen (+)
5 EO:0007332 cold air temperature regimen (+)
6 EO:0007404 drought environment (+)
7 MCE:1000069 dessication/dehydration stress (+)
8 MCE:1000075 recovery treatment (+)
9 MCE:1000091 methyl viologen/paraquat (+)
10 MCE:1000103 fluridone (+)

Metabolic Pathway details
Not found

QTL details
S. No. QTL Id QTL Associated Trait
1 AQCF026 grain yield
2 AQCF025 spikelet fertility
3 AQT001 culm length
4 AQFU001 brown rice ratio
5 AQFU020 protein content
6 CQAA6 cold tolerance
7 AQDU006 cold tolerance
8 AQDJ006 internode length
9 AQBM006 green plantlet differentiation frequency
10 AQHH019 plant height
11 CQX5 culm length
12 CQX22 internode length
13 CQX17 internode length
14 AQR018 deep root to shoot ratio
15 AQR017 deep root to shoot ratio
16 AQR032 rooting depth
17 AQR025 deep root dry weight
18 AQO040 root thickness
19 AQR009 deep root dry weight
20 AQF001 grain shattering
21 AQDY026 culm length
22 AQDY024 culm length
23 AQDY025 culm length
24 AQDY023 culm length
25 AQDY022 culm length
26 AQDY021 culm length
27 AQBV009 leaf angle
28 CQQ24 root thickness
29 CQQ1 root weight
30 AQCU132 leaf length
31 AQAQ008 blast disease resistance
32 CQAR4 seed number
33 CQAR2 spikelet number
34 CQAR3 spikelet density
35 CQAR1 plant height
36 AQHP001 root thickness
37 AQGB107 chalkiness of endosperm
38 AQGB075 chalkiness of endosperm
39 AQGB074 chalkiness of endosperm
40 AQGB073 chalkiness of endosperm
41 AQGB072 chalkiness of endosperm
42 AQDQ005 spikelet fertility
43 AQDQ006 seed weight
44 CQAR6 spikelet density
45 CQAR5 spikelet number
46 AQED035 seed set percent
47 CQN1 nadh-dependent glutamate synthase content
48 CQN4 soluble protein content
49 AQCS004 ultraviolet-b resistance
50 AQED013 plant height
51 AQED012 plant height
52 CQAE5 plant height
53 CQAE24 grain yield per plant
54 CQAE20 1000-grain weight
55 CQAE19 1000-grain weight
56 CQAE15 grain number
57 AQE068 plant height
58 AQFP016 culm strength
59 AQBK040 seed number
60 CQC1 plant height
61 AQBK003 plant height
62 AQBK008 days to heading
63 AQBK044 seed set percent
64 AQCR001 grain yield
65 AQCS001 ultraviolet-b resistance
66 CQG1 adaxial stomatal frequency
67 AQEN001 blast disease resistance
68 CQX6 culm length
69 CQX21 internode length
70 CQN51 spikelet number
71 CQN5 soluble protein content
72 CQN43 panicle weight
73 CQN26 leaf senescence
74 CQN49 spikelet number
75 CQN3 soluble protein content
76 CQE3 plant height
77 CQE2 plant height
78 CQE6 specific leaf area
79 CQF2 soluble protein content
80 AQCW010 H2O2 content
81 AQCW002 chlorophyll content

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000107 post-germination stage (+)
2 MCP:1000518 seedling development stage (+)
3 PO:0001083 inflorescence development stages (+)
4 PO:0007041 inflorescence emergence from flag leaf sheath (+)
5 PO:0007065 LP.05 five leaves visible (+)
6 PO:0007098 LP.02 two leaves visible (+)
7 PO:0007106 LP.03 three leaves visible (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000058 etiolated seedling (+)
2 MCP:1000096 first shoot internode (+)
3 MCP:1000097 third shoot internode (+)
4 MCP:1000237 second shoot internode (+)
5 MCP:1000246 fourth shoot internode (+)
6 MCP:1000315 second leaf from base (+)
7 MCP:1000440 first shoot node (+)
8 MCP:1000527 etiolated shoot (+)
9 PO:0000003 whole plant (+)
10 PO:0000043 crown root (+)
11 PO:0000047 leaf lamina epidermis (+)
12 PO:0005004 shoot node (+)
13 PO:0005020 vascular bundle (+)
14 PO:0005052 plant callus (+)
15 PO:0006000 Poaceae hull (+)
16 PO:0008037 seedling (+)
17 PO:0009000 pulvinus (+)
18 PO:0009005 root (+)
19 PO:0009006 shoot system (+)
20 PO:0009010 seed (+)
21 PO:0009046 flower (+)
22 PO:0009047 stem (+)
23 PO:0009049 inflorescence (+)
24 PO:0009066 anther (+)
25 PO:0020039 leaf lamina (+)
26 PO:0020103 flag leaf (+)
27 PO:0020104 leaf sheath (+)
28 PO:0025034 leaf (+)
29 PO:0025240 second order inflorescence (+)
30 PO:0025287 seedling coleoptile (+)
Others
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000239 calli induction stage (+)
2 MCP:1000240 calli screening stage (+)
3 MCP:1000241 calli differentiation stage (+)

Trait details
S. No. TO Id TO Description Presence(+) or absence(-) of gene expression /activity
1 MCT:1000012 survival rate (+)
2 MCT:1000034 superoxide dismutase (SOD) activity (+)
3 MCT:1000039 water loss (+)
4 MCT:1000063 percent membrane conductance (+)
5 MCT:1000433 percentage of open stomata (+)
6 MCT:1000434 trans-violaxanthin content (+)
7 MCT:1000435 cis-violaxanthin content (+)
8 MCT:1000436 trans-beta-carotene content (+)
9 MCT:1000437 cis beta-carotene content (+)
10 TO:0000145 internode length (+)
11 TO:0000206 leaf angle (+)
12 TO:0000207 plant height (+)
13 TO:0000227 root length (+)
14 TO:0000258 leaf thickness (+)
15 TO:0000391 seed size (+)
16 TO:0000495 chlorophyll content (+)
17 TO:0000731 lignin content (+)
18 TO:0002667 abscisic acid content (+)
19 TO:0002684 plant cell size (+)
20 TO:0002685 crown root number (+)
21 TO:0002696 alpha carotene content (+)
22 TO:0002701 lutein content (+)
23 TO:0002757 flag leaf length (+)
24 TO:0006032 panicle size (+)
25 TO:0020106 Indole-3-acetic acid content (+)

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

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]


Jain Mukesh; Kaur Navneet; Tyagi Akhilesh K; Khurana Jitendra P; The auxin-responsive GH3 gene family in rice (Oryza sativa). Functional & Integrative Genomics 2006:6
PMID [15856348]


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