Difference between revisions of "Os09g0442700"
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==References== | ==References== | ||
| − | + | *Hiromi Higo ''et al.''DDM1 (Decrease in DNA Methylation) genes in rice (''Oryza sativa'').Mol Genet Genomics (2012) 287:785–792 | |
==Structured Information== | ==Structured Information== | ||
Revision as of 06:12, 9 June 2014
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Contents
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. 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. Additional details suggest the gene occasional maintenance of the partial methylation state at the single copy locus.
Expression
They observed dwarf phenotypes in the antisense gene lines(Hiromi Higo et al.2012)
The figure shows A dwarf phenotype appeared in a later generation of line 17. Right wild type; left line 17 (the fifth generation)
Evolution
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 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).
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 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
introns (Fig.b).
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). The start codon of the Arabidopsis DDM1 is in the first exon, while it is in the second exon in the OsDDM1 genes. OsDDM1a and OsDDM1b are transcribed during development with slight variations in their relative abundance among different issues.Both OsDDM1 transcripts are more abundant in proliferating young tissues than in mature tissues that are consistent with the expected function of DDM1 for maintenance of DNA methylation on newly replicated DNA strands.
Labs working on this gene
- Japan Science and Technology Agency,Kawaguchi 332-0012, 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 Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan
- Genetic Strains Research Center, 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
Structured Information
| Gene Name |
Os09g0442700 |
|---|---|
| Description |
SNF2-related domain containing protein |
| Version |
NM_001069827.2 GI:297609541 GeneID:4347183 |
| Length |
5977 bp |
| Definition |
Oryza sativa Japonica Group Os09g0442700, 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 9:17115362..17121338 |
| Sequence Coding Region |
17118477..17118737 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008402:17115362..17121338 source=RiceChromosome09 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008402:17115362..17121338 source=RiceChromosome09 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>ttatcatccttctggttttctgttttagttttgtatttacatgtttacttcgatggctttttccaggggcatcggctaaagaattccaagtgtttattattaagggagctaaagcgcctgccaatggataataagctccttttgactggaactcctcttcagaataatctagcagaactgtggtccctgctgaacttcattttgcctgatatattctcttcacaccaagaatttgagtcatggtattattcattttgctga</cdnaseq> |
| Protein Sequence |
<aaseq>LSSFWFSVLVLYLHVYFDGFFQGHRLKNSKCLLLRELKRLPMDN KLLLTGTPLQNNLAELWSLLNFILPDIFSSHQEFESWYYSFC</aaseq> |
| Gene Sequence |
<dnaseqindica>2602..2862#gttcaaaagaaaaacctcccatctcgtctcccccctcctccgcctccgccgcgccggccgccgatctccatctcctcgcgagcagggagcgcggcaggggcgccgtcgtcctgctgcttcccgccacaatcctggctggtgagcattccgcatcctctctttttctctcgcccactttttttctcgatcttttcttttcttggagtgtcgagttcacgtgcgttaaaccctagcttctctagcgtttcctattgatttgccttaacattaatacgagtactaacggcttgtttttgtttgttctccaaaaagtttggaggggcggtttaagaaggttcatctgacccccacaatgtcggaagttagatccgtccctgggatgaaggtggaagcatccccggccgcggccgccgctgccaccgtggattccccgacatccgttctggaggatgatgaggtgatttatttgtgaatgcctttttttttttcagatatctctatttctgttttatgcttccgcatttcgggttttttttggttgacgttgagttgttgttgttagaagatttctgaatgtaagaatggggatgtcttggataccaccgaggcgattaagcaagaggaggatcatctcgatgtgcttattgaggagaaagttgatggttttgtggatgcaagttcttccctgaatgtggaacctgcggctaacaacagtgatttgtcacctctcactgtgccggtgaaggaagaaggtcagttattggagcctgtcaaggaggaaaaagctgatgattttgtggatgcagttccatctctaccgattgaccttgaggccaagaatggtgatgcatccctcatcactgatgcgatgaaggaggaggaagagaagttgcacgacgcccgggttaaggctgaagaagaagaggtagcacggaagagggaagaggctgcaagacttgcttttgatccaaatgcacgttttaacaagttggacgagctactatcacagacacaactctattcagaatttctacttgagaagatggaaacgatcgctgatgtatgtattgtttctccacgcgccacatgactctttttgcttcttcctatgctttatttgatttttctgttgatggttgtgctgttggctaaggtggagggcgtccaaactcatgctgaagaggagccagtagaagagaagaagaatgggcgtggcagaaagaggaaagctacttctgcaccaaagtacaatgatgtgagttctagcttcatacatggagtaatttggtttcctatattctaaattaatgggatatgcttatgttgaccttgctcatctggatttcaaatagtactaatgttgccagtttttcaatatttactaaatagctttccacctgtagtacattgttagaaaatcataattagaaggggtgtttaaagactcgccataacacatttgcaaccgccttcttctggtaccctgatatttttaggggtttgaatgtggggcacaaatttgtggcaaatgttagcgattagtatatcaatcaaataggctcttttgactgttagatagtgaaccaggaggttagagaagcaagaaaataccagagtaaaatgctcaatactagtgagtgtcagaggaaaatcaccttatatatgttattactatcttgctaattagaggttgtttattcatgaatgctgaagatagagggacaccgtatgaaggaaaaaagtttaaaaaccattaacttttgcttgtgccttatatttttgggcttgtttcaaatttctctagaaccatgcacacttattcagaatttcagatcctttcgtaggatcaattatattatttaagtgaatagcttgctcagtgttctgtatgaatgtggcaacttgttttatacatagatcaaaatttcaagcaaaccatttcatttctaaccgacaaaataaaatattgttcagaaaaaagccaagaaagcagtggcagtcatgcttacaagatctcatgaagattgctcacctgaggattgtactctcacagaagaagaaaggtgggaaaaagagcaagccagacttgttcctctaatgactggcgggaagttgaagtcctaccagataaagggtgttaagtggttaatatcactttggcagaatgggcttaatgggatattggctgatcaaatgggccttgggaaaacaatacagactatcggttttcttgcccatctcaaggggaagggtcttgatggtccatacctgataattgctcccctatccactctctcaaactgggtgaacgagatctcaaggtaacatatccatattattctttcattatccttgattgatattcttaagtgaagctgcttgctttcaggtttgttccatctatgactggtctgatttatcatggggacaaagcagcccgggcagagataaggagaaaattcatgcccaaaaccactggcccagattttccattaatcgtaacttcctatgagatggctatgtcagatgcaaagcatcttgctcactataagtggaagtatgttattgtggatgaggtacatggagaaaccttgcaattagttatcatccttctggttttctgttttagttttgtatttacatgtttacttcgatggctttttccaggggcatcggctaaagaattccaagtgtttattattaagggagctaaagcgcctgccaatggataataagctccttttgactggaactcctcttcagaataatctagcagaactgtggtccctgctgaacttcattttgcctgatatattctcttcacaccaagaatttgagtcatggtattattcattttgctgataatagtaccaccctttccccatatataccttcactagtgcggtttgtgcttttatagtctcacgtctcagcactgaaatacaaatatgatagtaactgaagattttcataccatgcaatcattcctataaccatcttaacctttccggcaaataattgttagtctcacgtttgaatcatttcctgactgtttattgtcaacttgttcatttgtgtatgcattgagcagagcagatattctttttctcaagtcgagacatttgtcagcatctgtctgggtccttgagggctagcaatttggtcaaaacaatgtaaaagaacctcttaaactgcttaacagcaatttcaattatattcccatcaactaaccctgtctatatatatgttattccattagtttgttgctactcttaagacattgctttaatttttctcattgcctttacttatgaagtgtaaagttgaatgccctatgtgttgttgtgagtatgcatattattttgtatgtggtgtctgctaatgtgtcttttgaatattagcagaaatttatgctgtacacctactgatttctatggtgtactgacatgatattttacttttgcgtctaccattgactatttagatggattttgctgcgattaacatgtttgatcattctttgctacaaagaatatactaatgcattttaggtaccctatgcattaaaattgatttgttttgcctgcattggccttacgagtgccatacaggtttgacttttctgcgaaaggaggtgaagaagaacaagaggatagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgcccgttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttacgctaacatgactgaccatcagaaacaaatccagaatcacttggttgaacaaacatttgatcaatacctgcatgaaaaatcagaaattggtatggatgcttgtacacctagtctcctacacacacattcctgtaggcttgacaagttaatctgacaagtgctgaggaatattgcagttctgcggaaacctggcattaaggcaaagctaaataatctgttaattcagttgaggaaaaattgcaaccatcctgatcttctggagtctgcgtatgactcatcaggttgttccacattggacatctgttatcaattgattcacatgctcgtttcctaacacttatttgctttattgtctttctgtaggtctgtatccacctgttgagaagctcttggaacagtgcggcaaatttcagctcttgaacagattgctaagtttgctgcttgcacggaagcacaaggtatattgttctctcctattctgtttaattcagggattacattaatgcaaatgctagctcgaactctttaaggaaaaaaactagacctcaaccggtattttgtgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatgggagtgttaagttggaagagaggaggaggcaggtaaagcaggctgtgccagtgcattactgattactacttggcgtgtaaagttctagacgcatatacgttgactatactatcctaaaatacaattaggattctcatttttcgccatgttaccttttaacatccatttttagtctaatactgttctcaccattttgtgcactactcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggcgggcttggtatcaatcttacttcagcggatacctgtatcctatatgatagtgactgggtaattccctattgatattattgtatttcttcaggctaaatattcatattacagcaagaacattacaagatgtttttgcacgccgcctgcctgtttgaatgggtggaatgtaggcacgtagcgacttcttcgctcctgcctactgtaactttacttaaaattagctaactgcctgtttgaatgggtggaatgtaggcatgtagtgacttcttcgctcctgcctactgtaactttactttctattagctggtttagttgtgatttgttaaacttttgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgtcaccggattggtcaaacacgcccagttcacgtctatcggttagcaacatcacattctgttgaggtatgttagatgatcctttatcttcagacgtcggctaaacctgttggatagttgctcatcttaatgatgttgcagggccggatcatcaagaaagcatttggcaagttgaggttggagcatgtggtgatcgggaagggtcagtttgaacaagacagagccaagcctaatgccctagatgtaatgtttctttgtttggactatttttgtacactgaaagaatgtcgacaccacgaaaatcctctctgacagtgacatttcttatgattatgcaggaagcggagttgctggcgctgctcagggacgagcagggcgacgaggaccggatgatccagacggacatcagcgatgaggacctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaatgccgacgccgcccctctcgtccccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggaatgctgacgtcgctcaccagttagcttcttcattcgctcgctgttgccgtctatgcatgccgaccgggtggggtgcctacttcacctgtgctgatgagacgatgcttttgtgatatacaatatcccccaagtaattgactgactgggcgttgcacttgcacctactgactaggagtaggaggtgatgtagtagtgtgcactgttataggctcagctgctggaattcattttgcaaggccagaagccttttccagcaagccgtgcaaggaagtggtttttgtcatgatacaattgtctacccagcttatgtgtaagcaagctatgcaatgcaatgctataaatagtttc</dnaseqindica> 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