Rice gene details
Searching for LOC_Os04g52090 [AP2 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_Os04g52090.1 223 24 75 PF00847.12 AP2
  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
  10
N22InfloresenceFC
  -2
N22 Root FC
  1
IR64 Flag-leaf FC
  3
IR64InfloresenceFC
  4
IR64 Root FC
  1

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0003677 DNA binding  
2 GO:0016563 transcription activator activity  
3 GO:0003677 DNA binding (RGAP)
4 GO:0005515 protein binding (RGAP)
5 GO:0003700 sequence-specific DNA binding transcription factor activity (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0009414 response to water deprivation  
2 GO:0009737 response to abscisic acid stimulus  
3 GO:0009739 response to gibberellin stimulus  
4 GO:0010628 positive regulation of gene expression  
5 GO:0048589 developmental growth  
6 GO:0080050 regulation of seed development  
7 GO:0007165 signal transduction (RGAP)
8 GO:0009719 response to endogenous stimulus (RGAP)
9 GO:0009058 biosynthetic process (RGAP)
10 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (RGAP)
11 GO:0006950 response to stress (RGAP)
12 GO:0009607 response to biotic stimulus (RGAP)
13 GO:0008150 biological_process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0005634 nucleus  
2 GO:0005634 nucleus (RGAP)
3 GO:0005654 nucleoplasm (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007105 abscisic acid regimen (+)
2 EO:0007383 watering regimen (+)
3 EO:0007404 drought environment (+)
4 MCE:1000010 submergence stress (+)
5 MCE:1000069 dessication/dehydration stress (+)
6 MCE:1000170 paclobutrazol (PBZ) (+)
7 MCE:1000288 GA3 gibberellin (+)

Metabolic Pathway details
Not found

QTL details
S. No. QTL Id QTL Associated Trait
1 CQN14 soluble protein content
2 AQBK014 days to heading
3 AQGD023 hull color
4 AQGD025 hull color
5 AQGD027 hull color
6 AQFA016 grain length to width ratio
7 CQAP2 scent
8 CQAX33 plant height
9 AQFF047 panicle number
10 AQFF052 panicle number
11 CQAS44 panicle number
12 CQAS46 spikelet density
13 CQAS47 seed number
14 CQAS49 1000-seed weight
15 CQAS51 seed number
16 CQAX21 plant height
17 CQB10 grain number
18 CQB9 plant height
19 CQAC2 blast disease resistance
20 AQCF031 spikelet fertility
21 AQFF031 spikelet number
22 AQFF036 spikelet number
23 CQAW13 tiller number
24 AQFE031 grain number
25 AQFE059 seed set percent
26 AQFE060 seed set percent
27 AQFE061 seed set percent
28 AQFB001 seed dormancy
29 AQFB002 seed dormancy
30 AQFB003 seed dormancy
31 CQG4 leaf rolling time
32 CQN13 nadh-dependent glutamate synthase content
33 AQA017 root length
34 AQG010 panicle number
35 AQG011 spikelet number
36 AQG012 spikelet number
37 CQN32 leaf senescence
38 CQZ7 plant height
39 AQAI041 leaf area to spikelet number ratio
40 AQAI053 large vascular bundle number to leaf area ratio
41 AQAI080 grain yield
42 CQR10 flour color
43 CQE34 panicle number
44 CQB41 spikelet number
45 CQB6 spikelet number
46 AQBY002 root length
47 AQP006 primary branch
48 AQP010 spikelet number
49 CQB8 grain number
50 AQHF002 leaf length
51 AQHF006 leaf width
52 AQHF010 leaf area
53 AQHF030 leaf length
54 AQHF032 leaf width
55 AQHF035 leaf area
56 AQDU001 cold tolerance
57 AQFJ070 grain yield per plant
58 CQAA1 leaf rolloing tolerance
59 CQAW12 root penetration index
60 AQDB002 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 MCP:1000521 mature plant stage (+)
4 PO:0007115 LP.04 four leaves visible (+)
5 PO:0007130 B reproductive growth (+)
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:0009010 seed (+)
5 PO:0009049 inflorescence (+)
6 PO:0025034 leaf (+)
7 PO:0025281 pollen (+)
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 MCT:1000039 water loss (+)
2 MCT:1000144 presence of regular shaped pollen grain (+)
3 MCT:1000209 ethylene content (+)
4 MCT:1000295 dihydrophaseic acid content (+)
5 MCT:1000297 abscisic acid- glucose ester content (+)
6 MCT:1000354 gibberellin 1 (GA1) content (+)
7 MCT:1000380 delayed flowering (+)
8 MCT:1000566 development of pale green leaves (+)
9 MCT:1000584 gibberellic acid (GA3) content (+)
10 MCT:1000585 gibberellin 4 (GA4) content (-)
11 MCT:1000586 gibberellin 8 (GA8) content (+)
12 MCT:1000587 gibberellin 19 (GA19) content (+)
13 MCT:1000588 gibberellin 20 (GA20) content (+)
14 MCT:1000589 gibberellin 29 (GA29) content (+)
15 MCT:1000590 gibberellin 34 (GA34) content (-)
16 MCT:1000591 gibberellin 53 (GA53) content (+)
17 MCT:1000592 gibberellin 51 (GA51) content (-)
18 TO:0000019 seedling height (+)
19 TO:0000128 harvest index (+)
20 TO:0000152 panicle number (+)
21 TO:0000227 root length (+)
22 TO:0000241 leaf number (+)
23 TO:0000276 drought tolerance (+)
24 TO:0000346 tiller number (+)
25 TO:0000352 plant dry weight (+)
26 TO:0000396 grain yield (+)
27 TO:0000430 germination rate (+)
28 TO:0000447 filled grain number (+)
29 TO:0002667 abscisic acid content (+)

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_Os05g40384 - 1 to -2498 TrSS Transcriptional activity assay
3 LOC_Os04g52090 - --- LOC_Os03g44380 - - - - S000430 Protein-DNA interaction analysis : Electrophoretic Mobility Shift Assay (EMSA)
4 LOC_Os08g35240 - --- LOC_Os04g52090 - - - - S000430 Protein-DNA interaction analysis : Chromatin Immunoprecipitation (ChIP)
5 LOC_Os08g35240 - LOC_Os04g52090 - to - 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  Wan Liyun; Zhang Jianfei; Zhang Haiwen; Zhang Zhijin; Quan Ruidang; Zhou Shirong; Huang Rongfeng; Transcriptional activation of OsDERF1 in OsERF3 and OsAP2-39 negatively modulates ethylene synthesis and drought tolerance in rice. Plos One 2011:6
PMID [21966459]


2  Jung Ki-Hong; Seo Young-Su; Walia Harkamal; Cao Peijian; Fukao Takeshi; Canlas Patrick E; Amonpant Fawn; Bailey-Serres Julia; Ronald Pamela C; The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiology 2010:152
PMID [20107022]


3  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]


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