Rice gene details
Searching for LOC_Os03g12290 [glutamine synthetase, catalytic domain containing protein, 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_Os03g12290.1 358 17 97 PF03951.11 Gln-synt_N
2 LOC_Os03g12290.1 358 103 355 PF00120.16 Gln-synt_C
  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:0005515 protein binding (RGAP)
3 GO:0005488 binding (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0009414 response to water deprivation  
2 GO:0009628 response to abiotic stimulus  
3 GO:0060359 response to ammonium ion  
4 GO:0008152 metabolic process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0005575 cellular_component (RGAP)
2 GO:0005618 cell wall (RGAP)
3 GO:0005829 cytosol (RGAP)
4 GO:0005886 plasma membrane (RGAP)
5 GO:0005840 ribosome (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007097 ammonium sulfate regimen (+)
2 EO:0007173 warm/hot temperature regimen (+)
3 MCE:1000069 dessication/dehydration stress (+)
4 MCE:1000294 ammonium chloride (NH4) (+)

Metabolic Pathway details
S. No. Pathway Id Pathway Description
1 GLNSYN-PWY glutamine biosynthesis I
2 PWY-3282 ammonia assimilation cycle II
3 PWY-381 nitrate reduction II (assimilatory)

QTL details
S. No. QTL Id QTL Associated Trait
1 AQDQ028 panicle length
2 AQDQ029 panicle length
3 AQAC032 total amylase activity
4 AQAG009 tiller number
5 AQEX008 root length
6 AQGI001 root dry weight
7 AQGI011 root dry weight
8 AQGI110 biomass yield
9 AQGI111 biomass yield
10 AQAL004 deep root dry weight
11 AQAL010 deep root to shoot ratio
12 AQGC006 penetrated root number
13 AQGC012 penetrated root number
14 AQGC015 root penetration index
15 AQDL005 stomatal closure time
16 AQCO005 spikelet fertility
17 AQCO115 spikelet fertility
18 AQCO118 spikelet fertility
19 AQCP005 spikelet fertility
20 AQGC021 root penetration index
21 AQBA010 brown planthopper resistance
22 AQBA011 brown planthopper resistance
23 AQBA014 brown planthopper resistance
24 AQW007 brown planthopper resistance
25 AQDI004 hybrid incompatibilty
26 AQDK007 grain yield
27 AQCU106 spikelet fertility
28 AQEE021 crushed grain percentage
29 CQX11 panicle length
30 AQDL002 stomatal resistance
31 AQFU015 amylose content
32 CQAS38 seed number
33 CQAS37 spikelet number
34 CQAS34 seed number
35 CQAS36 1000-seed weight
36 CQAS33 spikelet density
37 CQAS32 spikelet number
38 AQFC001 elongation ability
39 CQE15 chlorophyll content
40 CQAR8 spikelet density
41 CQAR7 tiller number

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 MCP:1000521 mature plant stage (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 MCP:1000257 xylem sap (+)
2 PO:0000003 whole plant (+)
3 PO:0008037 seedling (+)
4 PO:0009005 root (+)
5 PO:0009025 vascular leaf (+)
6 PO:0009047 stem (+)
7 PO:0009049 inflorescence (+)
8 PO:0009051 spikelet (+)
9 PO:0025034 leaf (+)
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:1000049 glutamine synthetase (GS) activity (+)
2 MCT:1000526 ripened spikelet ratio (+)
3 MCT:1000527 glutamine content (+)
4 MCT:1000528 glutamate content (+)
5 MCT:1000529 asparagine content (+)
6 MCT:1000530 aspartate content (+)
7 MCT:1000531 ammonium ion (NH4+) concentration (+)
8 TO:0000019 seedling height (+)
9 TO:0000152 panicle number (+)
10 TO:0000207 plant height (+)
11 TO:0000346 tiller number (+)
12 TO:0000352 plant dry weight (+)
13 TO:0000592 1000-dehulled grain weight (+)
14 TO:0002673 amino acid content (+)
15 TO:0002759 grain number (+)

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


Domain name/N or C term

Amino acid involved in interaction


Domain name/N or C term

involved in interaction
Reference point cis-elements [PLACE Id]
1 LOC_Os05g48010 - --- LOC_Os03g12290 - 1079 - - 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]

Ranathunge Kosala; El-Kereamy Ashraf; Gidda Satinder; Bi Yong-Mei; Rothstein Steven J; AMT1;1 transgenic rice plants with enhanced NH4 + permeability show superior growth and higher yield under optimal and suboptimal NH4 + conditions. Journal of experimental botany 2014:65
PMID [24420570]

Funayama Kazuhiro; Kojima Soichi; Tabuchi-Kobayashi Mayumi; Sawa Yuki; Nakayama Yosuke; Hayakawa Toshihiko; Yamaya Tomoyuki; Cytosolic glutamine synthetase1;2 is responsible for the primary assimilation of ammonium in rice roots. Plant & cell physiology 2013:
PMID [23509111]

El-Kereamy Ashraf; Bi Yong-Mei; Ranathunge Kosala; Beatty Perrin H; Good Allen G; Rothstein Steven J; The Rice R2R3-MYB Transcription Factor OsMYB55 Is Involved in the Tolerance to High Temperature and Modulates Amino Acid Metabolism. PloS one 2012:7
PMID [23251677]

Singh Kamal Krishna; Ghosh Shilpi; Regulation of glutamine synthetase isoforms in two differentially drought-tolerant rice (Oryza sativa L.) cultivars under water deficit conditions. Plant Cell Reports 2012:
PMID [23070303]

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