Os09g0442700 - Revision history

Xysj2027: /* Function */

2017-05-07T16:30:50Z

‎Function

Chenxi Sang at 13:32, 21 October 2016

2016-10-21T13:32:00Z

Chenxi Sang at 13:30, 21 October 2016

2016-10-21T13:30:40Z

Rice2012: /* Structured Information */

2015-06-12T09:44:06Z

‎Structured Information

Zhangjie: /* Evolution */

2014-06-09T06:16:11Z

‎Evolution

Zhangjie: /* Evolution */

2014-06-09T06:14:40Z

‎Evolution

Zhangjie: /* Function */

2014-06-09T06:14:07Z

‎Function

Zhangjie: /* References */

2014-06-09T06:12:10Z

‎References

Zhangjie: /* Labs working on this gene */

2014-06-09T06:09:49Z

‎Labs working on this gene

Zhangjie: /* Labs working on this gene */

2014-06-09T06:08:40Z

‎Labs working on this gene

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 *'''''Os09g0442700''''' '''''<=>''''' '''''OsDDM1a'''''
 ===Function===
-* '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active.
+* '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active transposons in the genome remains unknown.
 * Hypomethylation induced by the antisense '''''OsDDM1''''' disturbs normal development.
 * Transgenic rice lines expressing '''''OsDDM1a''''' cDNA in antisense orientation exhibited the genomic DNA hypomethylation in repeated sequences similar to the pattern observed in Arabidopsis ddm1 mutants.

@@ Line 2: / Line 2: @@
 ==Annotated Information==
-[[File:155-Os03g0722400.png|right|thumb|427px|'''Figure 1.''' ''Expression of OsDDM1 genes during development..<ref name="ref1" />.'']]
+[[File:155-Os03g0722400.png|right|thumb|327px|'''Figure 1.''' ''Expression of OsDDM1 genes during development..<ref name="ref1" />.'']]
 ===Gene Symbol===
 *'''''Os09g0442700''''' '''''<=>''''' '''''OsDDM1a'''''

@@ Line 1: / Line 1: @@
-Please input one-sentence summary here.
+The rice '''''Os09g0442700''''' was reported as '''''OsDDM1a''''' in 2012 <ref name="ref1" /> by researchers from Japan.
 ==Annotated Information==
 ===Function===
-The gene was suggested that to silence endogenous loci including those related to retrotransposons in the rice genome.But the roles on transposition of active transposons in the genome remains unknown.
+* '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active.
-There are evidences suggested that the hypomethylation in the antisense of this gene lines is induced by the antisense transgene but not in the process of transformation that includes tissue culture for callus induction (Toki 1997).In the antisense of this gene lines, cytosine methylation is severely reduced in the repeated sequences.Reduction in cytosine methylation is more evident in the later generations.
+transposons in the genome remains unknown.
-Additional details suggest the gene occasional maintenance of the partial methylation state at the single copy locus.
+* Hypomethylation induced by the antisense '''''OsDDM1''''' disturbs normal development.
 ===Expression===
-They observed dwarf phenotypes in the antisense gene lines(Hiromi Higo ''et al''.2012)[[File:Characterization_of_the_antisense_OsDDM1_lines.png|200px|thumb|right]]
+* '''''OsDDM1a''''' and '''''OsDDM1b''''' are expressed during development with slight variations among various tissues, suggesting that there might be functional divergence of these two genes (Fig. 1c).
 ==Labs working on this gene==
-*Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
+* CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
-*Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
+* Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
-*Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada
+* Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada
-*Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan
+* Department of Integrated Genetics, National Institute of Genetics, Mishima 411-0801, Japan
 ==References==
-*Hiromi Higo ''et al.''DDM1 (Decrease in DNA Methylation) genes in rice (''Oryza sativa'').Mol Genet Genomics (2012) 287:785–792
+<references>
 ==Structured Information==

@@ Line 43: / Line 43: @@
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

@@ Line 13: / Line 13: @@
 ===Evolution===
-Relationship among DDM1-like proteins: a. An alignment(ClustalX) of the C-terminal portion of the deduced amino acid
+*Relationship among DDM1-like proteins: a. An alignment(ClustalX) of the C-terminal portion of the deduced amino acid
-sequences of OsDDM1a, OsDDM1b, Zea mays CHR101 ([www.chromdb.org]), ''Zea mays'' CHR106 ([www.chromdb.org]), Arabidopsis
+sequences of OsDDM1a, OsDDM1b, ''Zea mays'' CHR101 ([www.chromdb.org]), ''Zea mays'' CHR106 ([www.chromdb.org]), ''Arabidopsis thaliana'' DDM1 (AAD28303), and ''Mus musculus'' LSH (NP 032260).
-Genomic Southern analysis and database search using this EST revealed that the genome of rice(Oryza sativa var. Nipponbare) contains two sequences similar to DDM1 (Fig.a).
+*Genomic Southern analysis and database search using this EST revealed that the genome of rice(''Oryza sativa'' var. Nipponbare) contains two sequences similar to DDM1 (Fig.a).
-The two nucleotide sequences,which we designated OsDDM1a (LOC_Os09g27060 or Os09g0442700) and OsDDM1b (LOC_Os03g51230 or
+*The two nucleotide sequences,which we designated OsDDM1a (LOC_Os09g27060 or Os09g0442700) and OsDDM1b (LOC_Os03g51230 or
 Os03g0722400),are 93% identical to each other in the predicted amino acid sequences and show 60 % identity to Arabidopsis DDM1 (AT5G66750).
-The EST clone C30395 covers from the 945th nucleotide to the end of the OsDDM1a.
+*The EST clone C30395 covers from the 945th nucleotide to the end of the OsDDM1a.
 The structures of these two genes are closely related to each other.
 Both consist of 15 exons and 14 introns, and the DNA sequence similarity of these two genes is 81%even including
@@ Line 28: / Line 27: @@
 [[File:Relationship among DDM1-like proteins.png]]
-The exon–intron structure is similar,
+*The exon–intron structure is similar,
 although not identical, to that of the Arabidopsis DDM1,which is composed of 16 exons. The OsDDM1 genes lack the
 introns corresponding to the eighth intron of the Arabidopsis DDM1 gene (Fig. b).