Rice gene details
Searching for LOC_Os04g55080 [cyclic nucleotide-gated ion channel, 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_Os04g55080.1 725 153 418 PF00520.23 Ion_trans
2 LOC_Os04g55080.1 725 519 619 PF00027.21 cNMP_binding
  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
  1
N22InfloresenceFC
  1
N22 Root FC
  1
IR64 Flag-leaf FC
  2
IR64InfloresenceFC
  1
IR64 Root FC
  1

Functional details
Molecular Function
S. No. GO Id GO Description
1 GO:0005515 protein binding (RGAP)
Biological process
S. No. GO Id GO Description
1 GO:0009409 response to cold  
2 GO:0009617 response to bacterium  
3 GO:0009723 response to ethylene stimulus  
4 GO:0009733 response to auxin stimulus  
5 GO:0009735 response to cytokinin stimulus  
6 GO:0008150 biological_process (RGAP)
Cellular component
S. No. GO Id GO Description
1 GO:0005886 plasma membrane (RGAP)

Environment details
S. No. EO Id EO Description Presence(+) or absence(-) of gene expression /activity
1 EO:0007068 ethylene regimen (+)
2 EO:0007070 indole acetic acid regimen (+)
3 EO:0007105 abscisic acid regimen (+)
4 EO:0007198 water environment (+)
5 EO:0007234 Pseudomonas fuscovaginae (+)
6 EO:0007257 Xanthomonas oryzae pv. oryzae (+)
7 EO:0007290 kinetin regimen (+)
8 EO:0007332 cold air temperature regimen (+)

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 CQAX33 plant height
7 CQAS44 panicle number
8 CQAS46 spikelet density
9 CQAS47 seed number
10 CQAS49 1000-seed weight
11 CQAS51 seed number
12 CQAX21 plant height
13 CQAC2 blast disease resistance
14 CQN13 nadh-dependent glutamate synthase content
15 CQN32 leaf senescence
16 CQE34 panicle number
17 AQBY002 root length
18 AQP006 primary branch
19 AQP010 spikelet number
20 CQB8 grain number
21 AQDB002 chlorophyll content
22 AQDQ031 panicle number
23 AQDQ030 panicle number
24 AQDQ034 seed weight
25 AQEO011 seed length
26 AQEO021 100-seed weight
27 CQAW11 root number
28 CQO1 cold tolerance
29 CQO2 anther length
30 CQAS50 spikelet number
31 CQAS52 yield
32 AQF098 KClO3 resistance
33 CQAH18 grain shattering
34 AQCF005 spikelet number
35 AQCF006 grain yield
36 AQAL025 rooting depth
37 AQA016 root length
38 AQCN009 plant height
39 AQDQ038 grain yield per plant
40 AQGL003 sheath blight disease resistance
41 AQGL009 sheath blight disease resistance
42 AQGL015 sheath blight disease resistance
43 AQJ007 spikelet number
44 CQAI19 root length
45 CQAO11 1000-seed weight
46 CQAO5 panicle number
47 CQAQ10 primary branch
48 AQDQ033 seed weight
49 AQDQ035 seed weight
50 AQDQ036 grain yield per plant
51 AQDQ037 grain yield per plant
52 AQDQ039 plant height
53 AQFF038 spikelet sterility
54 CQH21 root pulling force
55 AQGI142 biomass yield
56 AQGI146 biomass yield
57 AQCU074 leaf length
58 AQCU216 leaf length
59 AQEA073 plant height
60 AQEA074 plant height
61 AQEA075 plant height
62 AQEA076 plant height
63 AQEA077 plant height
64 AQEA078 plant height
65 AQEA079 plant height
66 AQEA080 plant height
67 AQEA081 plant height
68 AQEA082 plant height
69 AQFW139 plant height
70 AQFW151 leaf length
71 CQAS48 seed set percent
72 CQV17 plant height
73 AQFU010 rice bran percentage
74 AQEI057 leaf senescence
75 AQEI058 leaf senescence
76 AQO039 root thickness

Plant developmental stage / tissue details
Plant development stage
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 PO:0007106 LP.03 three leaves visible (+)
Plant tissue/organ
S. No. PO Id PO Description Presence(+) or absence(-) of gene expression /activity
1 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
Not found
Related publications [Sorted by year]

Nawaz Zarqa; Kakar Kaleem Ullah; Saand Mumtaz A; Shu Qing-Yao; Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses. BMC genomics 2014:15
PMID [25280591]


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