Difference between revisions of "Os03g0722400"
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The protein product of OsDDM1b gene is 849 amino acids in length. | The protein product of OsDDM1b gene is 849 amino acids in length. | ||
Both rice DDM1 OsDDM1a and OsDDM1b proteins contain the eight signature | Both rice DDM1 OsDDM1a and OsDDM1b proteins contain the eight signature | ||
| − | amino acid motifs diagnostic for SWI2/SNF2 proteins. | + | amino acid motifs diagnostic for SWI2/SNF2 proteins.Both consist of 15 exons and 14 introns, and the DNA |
| − | + | sequence similarity of these two genes is 81 %even including | |
| − | [[File:Osddm1a.jpg]][[File:E_1.jpg]] | + | introns (Fig. 1b). 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. 1b). The start codon of the Arabidopsis DDM1 is in the first exon, while it is in the second exon in the | ||
| + | OsDDM1 genes. | ||
| + | |||
| + | [[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]] | ||
| + | |||
By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the relationship is showed as below.We can see that they appear to have arisen by a relatively recent | By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the relationship is showed as below.We can see that they appear to have arisen by a relatively recent | ||
duplication event. | duplication event. | ||
| − | + | ||
| − | [[File:E_2.jpg]] | + | [[File:E_2.jpg|500px|]] |
==Labs working on this gene== | ==Labs working on this gene== | ||
Revision as of 08:14, 19 May 2014
Please input one-sentence summary here.
OsDDM1b
Contents
Annotated Information
Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon-related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize potentially active transposons for rice functional genomics.
Function
OsDDM1b is required for the maintenance of DNA methylation on newly replicated DNA strands in rice genome like OsDDM1a.
Mutant Phenotype
We can observe dwarf phenotypes in OsDDM1 mutant lines through the antisense technology. Besides it, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines reduced fertility relative to normal lines was observed.
Expression
Please input expression information here.
Evolution
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. The protein product of OsDDM1b gene is 849 amino acids in length. Both rice DDM1 OsDDM1a and OsDDM1b proteins contain the eight signature amino acid motifs diagnostic for SWI2/SNF2 proteins.Both consist of 15 exons and 14 introns, and the DNA sequence similarity of these two genes is 81 %even including introns (Fig. 1b). 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. 1b). The start codon of the Arabidopsis DDM1 is in the first exon, while it is in the second exon in the OsDDM1 genes.
By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the relationship is showed as below.We can see that they appear to have arisen by a relatively recent duplication event.
Labs working on this gene
Please input related labs here.
References
Higo, Hiromi, et al. "DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)." Molecular Genetics and Genomics 287.10 (2012): 785-792.
Structured Information
| Gene Name |
Os03g0722400 |
|---|---|
| Description |
Conserved hypothetical protein |
| Version |
NM_001057645.2 GI:297601601 GeneID:4333943 |
| Length |
3180 bp |
| Definition |
Oryza sativa Japonica Group Os03g0722400, 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 | |
| Location |
Chromosome 3:30070286..30073465 |
| Sequence Coding Region |
30072187..30072291 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008396:30070286..30073465 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008396:30070286..30073465 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq> |
| Protein Sequence |
<aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq> |
| Gene Sequence |
<dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica> |
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