Difference between revisions of "Os12g0603700"

From RiceWiki
Jump to: navigation, search
Line 17: Line 17:
 
*''OsCIPK04'' peaked during the light period, the peak time of ''OsCIPK04'' was a little earlier than that of ''OsCIPK07'', suggesting the possibility of sequential regulation of circadian expression between them<ref name="ref1"/>.
 
*''OsCIPK04'' peaked during the light period, the peak time of ''OsCIPK04'' was a little earlier than that of ''OsCIPK07'', suggesting the possibility of sequential regulation of circadian expression between them<ref name="ref1"/>.
  
−
*The x-axis indicates sampling time used for real-time RT-PCR analysis and the y-axis indicates the relative expression level to OsUbi5. 2 h drought stress treated seedling leaves for 2 h, 2hc control for 2 h, 4 h drought stress treated seedling leaves for 4 h, 4hc control for 4 h, 6 h drought stress treated seedling leaves for 6 h, 6hc control for 6 h, 8 h drought stress treated seedling leaves
+
*The x-axis indicates sampling time used for real-time RT-PCR analysis and the y-axis indicates the relative expression level to OsUbi5. 2 h drought stress treated seedling leaves for 2 h, 2hc control for 2 h, 4 h drought stress treated seedling leaves for 4 h, 4hc control for 4 h, 6 h drought stress treated seedling leaves for 6 h, 6hc control for 6 h, 8 h drought stress treated seedling leaves for 8 h, 8hc control for 8 h(Fig. 2)<ref name="ref1"/>.
−
for 8 h, 8hc control for 8 h(Fig. 2)<ref name="ref1"/>.
 
  
 
*Real-time RT-PCR analysis confirmed the diurnal expression patterns showing a peak at daytime and a downregulation in the ''osgi'' mutant for the three marker genes and nine of the ''OsCIPK'' genes, ''OsCIPK04'' is a member of these nine genes<ref name="ref1"/>.
 
*Real-time RT-PCR analysis confirmed the diurnal expression patterns showing a peak at daytime and a downregulation in the ''osgi'' mutant for the three marker genes and nine of the ''OsCIPK'' genes, ''OsCIPK04'' is a member of these nine genes<ref name="ref1"/>.
Line 26: Line 25:
  
 
===Knowledge Extension===
 
===Knowledge Extension===
−
[[File: OsCIPK family Functional.png|right|thumb|260px|'''Figure 3.''' ''Functional gene network analysis of OsCIPK family members.(from reference <ref name="ref1"/>).'']]   
+
[[File: OsCIPK family Functional.png|left|thumb|260px|'''Figure 3.''' ''Functional gene network analysis of OsCIPK family members.(from reference <ref name="ref1"/>).'']]   
 
*From real-time RT-PCR analyses, ''Giong et al.'' identified 16 OsCIPK genes showing a significant up- or down-regulation in response to '''drought stress'''. Using the probable functional gene network tool, RiceNet, ''Giong et al.'' generated a hypothetical functional gene network based on 15 out of 16 OsCIPK proteins (Fig. 3)<ref name="ref1"/>.  
 
*From real-time RT-PCR analyses, ''Giong et al.'' identified 16 OsCIPK genes showing a significant up- or down-regulation in response to '''drought stress'''. Using the probable functional gene network tool, RiceNet, ''Giong et al.'' generated a hypothetical functional gene network based on 15 out of 16 OsCIPK proteins (Fig. 3)<ref name="ref1"/>.  
 
*More than 200 interactions mediated by these OsCIPK proteins. This network was further refined by integrating fold change data showing at least 1 log2-fold up-regulation (red colored nodes in Fig. 3) or less than -1 log2-fold down-regulation (green colored nodes in Fig. 3) under drought stress to all the elements in this network<ref name="ref1"/>.
 
*More than 200 interactions mediated by these OsCIPK proteins. This network was further refined by integrating fold change data showing at least 1 log2-fold up-regulation (red colored nodes in Fig. 3) or less than -1 log2-fold down-regulation (green colored nodes in Fig. 3) under drought stress to all the elements in this network<ref name="ref1"/>.

Revision as of 04:08, 29 January 2015

OsCIPK04 is a member of CIPK genes (CIPKs,calcineurin B-like protein interacting protein kinases)[1].

Annotated Information

Function

The function of OsCIPK04 is specific to vegetative tissues/organs according to expression pattern. OsCIPK04 might function downstream of OsGI[1].

GO assignment(s): GO:0004672,GO:0004674, GO:0006468, GO:0005524, GO:0007165

Expression

Figure 1. Validation of diurnal expression patterns for OsCIPK04.(from reference [1]).
Figure 2. Down-regulation in response to drought stress were analyzed through real-time RT-PCR analysis.(from reference [1]).
  • OsCIPK04 showed down-regulation under drought stress(Fig. 1)[1].
  • Of the two genes in subgroup VII, OsCIPK04 showed preferred expression in the root and internode while OsCIPK07 showed high expression in the root, shoot, and leaf, which indicating that the function of both genes is specific to vegetative tissues/organs according to expression pattern[1].
  • OsCIPK04 peaked during the light period, the peak time of OsCIPK04 was a little earlier than that of OsCIPK07, suggesting the possibility of sequential regulation of circadian expression between them[1].
  • The x-axis indicates sampling time used for real-time RT-PCR analysis and the y-axis indicates the relative expression level to OsUbi5. 2 h drought stress treated seedling leaves for 2 h, 2hc control for 2 h, 4 h drought stress treated seedling leaves for 4 h, 4hc control for 4 h, 6 h drought stress treated seedling leaves for 6 h, 6hc control for 6 h, 8 h drought stress treated seedling leaves for 8 h, 8hc control for 8 h(Fig. 2)[1].
  • Real-time RT-PCR analysis confirmed the diurnal expression patterns showing a peak at daytime and a downregulation in the osgi mutant for the three marker genes and nine of the OsCIPK genes, OsCIPK04 is a member of these nine genes[1].

Evolution

OsCIPK04 and OsCIPK07 belongs to Group VII of OsCIPK family[1].

Knowledge Extension

Figure 3. Functional gene network analysis of OsCIPK family members.(from reference [1]).
  • From real-time RT-PCR analyses, Giong et al. identified 16 OsCIPK genes showing a significant up- or down-regulation in response to drought stress. Using the probable functional gene network tool, RiceNet, Giong et al. generated a hypothetical functional gene network based on 15 out of 16 OsCIPK proteins (Fig. 3)[1].
  • More than 200 interactions mediated by these OsCIPK proteins. This network was further refined by integrating fold change data showing at least 1 log2-fold up-regulation (red colored nodes in Fig. 3) or less than -1 log2-fold down-regulation (green colored nodes in Fig. 3) under drought stress to all the elements in this network[1].
  • Integrated subcellular localization data further enhances the feasibility of functional modules consisting of co-expressed functional groups such as CIPK and PPC and other components in the network(Fig. 3)[1].
  • The calcineurin B-like protein–CBL-interacting protein kinase (CBL–CIPK) signaling pathway in plants is a Ca2+-related pathway that responds strongly to both abiotic and biotic environmental stimuli[2]. The CBL-CIPK system shows variety, specificity, and complexity in response to different stresses, and the CBL–CIPK signaling pathway is regulated by complex mechanisms in plant cells[2].

Labs working on this gene

  • Department of Plant Molecular Systems Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
  • Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Giong H K, Moon S, Jung K H. A systematic view of the rice calcineurin B-like protein interacting protein kinase family[J]. Genes & Genomics, 2015, 37(1): 55-68.
  2. ↑ 2.0 2.1 Yu Q, An L, Li W. The CBL–CIPK network mediates different signaling pathways in plants[J]. Plant cell reports, 2014, 33(2): 203-214.

Structured Information

Gene Name

Os12g0603700

Description

Protein kinase-like domain containing protein

Version

NM_001073746.1 GI:115489453 GeneID:4352728

Length

1360 bp

Definition

Oryza sativa Japonica Group Os12g0603700, complete gene.

Source

Oryza sativa Japonica Group 

 ORGANISM  Oryza sativa Japonica Group
           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
           Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
           clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome

Chromosome 12

Location

Chromosome 12:25671309..25672668

Sequence Coding Region

25671309..25672079,25672096..25672668

Expression

GEO Profiles:Os12g0603700

Genome Context

<gbrowseImage1> name=NC_008405:25671309..25672668 source=RiceChromosome12 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008405:25671309..25672668 source=RiceChromosome12 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atggctgccatggacgcgaggaagaagaagagcggcggcggcggcggcgagccgcttctcggcaagtatgagcttgggcggatgcttgggcgagggacgttcgccaaggtgtacctggcgcgcgcggtggccggcggcgaggcggtggcggtgaaggtgatcgacaaggcggaggtgatgggcacggcgggcatggcgccgcgcgtgctccgggaggtggcggcgatgcggcggctgcgccacccgcacgtgctgcgcctccacgaggtgctcgccacgcgcgccaggatctacctcgtcatggagctcgccaccggcggcgacctcctgtcgaggctggcggcgctgccgcggcggcgcctgcccgagagcgcggcgcgccgggtgttcgtccagctcgtcgacgcgctgtcctactgccacgcgcgcggcgtggcgcaccgtgacgtgaagccgcagaacgtcctcctcgacggcgacggcaacctcaaggtctccgacttcggcctcgccgcgctcccgggacacgctccgcgacgacggccgcctccacaccgcgtgcggcacgccggcgtgctccgccgcagggcctacgacggcgccaaggccgacgcgtggtcgtgcggcgtcatcctcttcgtcctcctcgccggccacctccccttcgacgactccaacatcgccgacatgtgccggaaggcgcaccgccgcgagtacgagctcccgcggtgggtgtcccagccggcgcgccgcctggtgagccgcctgctcgacccgaacccggacacccgcgtcgccgtcgagtcgctggcggcgcaccacccgtggttcaagcgctcgctcagcgtcgactcccagctcgacggcctcctcaacggcgagccagagcgcgccgtggcgttccaggcggcgccgccgccgccgctgaacgcgttcgacatcatctccatgtctcccgggctcgacctgtccgggctgttcggcgaacacgacaagagcctaagggagaagcggttcacgacgacggcgtcgccggagaagacgctggagcagctcggcctcgccggcgggaagctcgggtacgtggtggtggtggggaagaaaggggtggagtgcttgccgctggcgggggggcggctgtcgtcggggatcgccgcgatgtcggtggagatgtcggaggtggcgccgccgctgttgctcgtcgagctgaggctggaggtcgccgccggcgacgtcgacggcggcgacggcgaggtgaaggggtttgggtgggagcagctgagaatggagctaggtgatgtagttagggcttggcatagttgtgaggatttgtgtgaaatttag</cdnaseq>

Protein Sequence

<aaseq>MAAMDARKKKSGGGGGEPLLGKYELGRMLGRGTFAKVYLARAVA GGEAVAVKVIDKAEVMGTAGMAPRVLREVAAMRRLRHPHVLRLHEVLATRARIYLVME LATGGDLLSRLAALPRRRLPESAARRVFVQLVDALSYCHARGVAHRDVKPQNVLLDGD GNLKVSDFGLAALPGHAPRRRPPPHRVRHAGVLRRRAYDGAKADAWSCGVILFVLLAG HLPFDDSNIADMCRKAHRREYELPRWVSQPARRLVSRLLDPNPDTRVAVESLAAHHPW FKRSLSVDSQLDGLLNGEPERAVAFQAAPPPPLNAFDIISMSPGLDLSGLFGEHDKSL REKRFTTTASPEKTLEQLGLAGGKLGYVVVVGKKGVECLPLAGGRLSSGIAAMSVEMS EVAPPLLLVELRLEVAAGDVDGGDGEVKGFGWEQLRMELGDVVRAWHSCEDLCEI</aaseq>

Gene Sequence

<dnaseqindica>590..1360#1..573#atggctgccatggacgcgaggaagaagaagagcggcggcggcggcggcgagccgcttctcggcaagtatgagcttgggcggatgcttgggcgagggacgttcgccaaggtgtacctggcgcgcgcggtggccggcggcgaggcggtggcggtgaaggtgatcgacaaggcggaggtgatgggcacggcgggcatggcgccgcgcgtgctccgggaggtggcggcgatgcggcggctgcgccacccgcacgtgctgcgcctccacgaggtgctcgccacgcgcgccaggatctacctcgtcatggagctcgccaccggcggcgacctcctgtcgaggctggcggcgctgccgcggcggcgcctgcccgagagcgcggcgcgccgggtgttcgtccagctcgtcgacgcgctgtcctactgccacgcgcgcggcgtggcgcaccgtgacgtgaagccgcagaacgtcctcctcgacggcgacggcaacctcaaggtctccgacttcggcctcgccgcgctcccgggacacgctccgcgacgacggccgcctccacaccgcgtgcggcacgccggcgtacgcggcgcccgaggtgctccgccgcagggcctacgacggcgccaaggccgacgcgtggtcgtgcggcgtcatcctcttcgtcctcctcgccggccacctccccttcgacgactccaacatcgccgacatgtgccggaaggcgcaccgccgcgagtacgagctcccgcggtgggtgtcccagccggcgcgccgcctggtgagccgcctgctcgacccgaacccggacacccgcgtcgccgtcgagtcgctggcggcgcaccacccgtggttcaagcgctcgctcagcgtcgactcccagctcgacggcctcctcaacggcgagccagagcgcgccgtggcgttccaggcggcgccgccgccgccgctgaacgcgttcgacatcatctccatgtctcccgggctcgacctgtccgggctgttcggcgaacacgacaagagcctaagggagaagcggttcacgacgacggcgtcgccggagaagacgctggagcagctcggcctcgccggcgggaagctcgggtacgtggtggtggtggggaagaaaggggtggagtgcttgccgctggcgggggggcggctgtcgtcggggatcgccgcgatgtcggtggagatgtcggaggtggcgccgccgctgttgctcgtcgagctgaggctggaggtcgccgccggcgacgtcgacggcggcgacggcgaggtgaaggggtttgggtgggagcagctgagaatggagctaggtgatgtagttagggcttggcatagttgtgaggatttgtgtgaaatttag</dnaseqindica>

External Link(s)

NCBI Gene:Os12g0603700, RefSeq:Os12g0603700

Retrieved from "https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os12g0603700&oldid=184788"