RiceWiki - User contributions [en]

File:Expression.jpg

2014-07-03T13:14:40Z

Chenxuepeng: uploaded a new version of "File:Expression.jpg": Reverted to version as of 09:07, 19 May 2014

Os03g0722400

2014-05-19T09:41:14Z

Chenxuepeng: /* Annotated Information */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.
===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.
[[File:expression.jpg|300px]]

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.
[[File:Osddm1a.jpg|right|thumb|200px|''Structure of OsDDM1 and Arabidopsis DDM1 (from reference <ref name="ref1" />).'']]
[[File:E_1.jpg|right|thumb|300px|''Alignment of proteins encoded by DDM1-like genes among speciecs (from reference <ref name="ref1" />).'']]
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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.
[[File:E_2.jpg|right|thumb|200px|''envolution relationship in rice,maize,Arabidopsis and mouse (from reference <ref name="ref1" />).'']]

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:40:31Z

Chenxuepeng: /* Annotated Information */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.
===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.
[[File:expression.jpg|300px]]

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.
[[File:Osddm1a.jpg|left|thumb|200px|''Structure of OsDDM1 and Arabidopsis DDM1 (from reference <ref name="ref1" />).'']]
[[File:E_1.jpg|left|thumb|300px|''Alignment of proteins encoded by DDM1-like genes among speciecs (from reference <ref name="ref1" />).'']]
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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.
[[File:E_2.jpg|right|thumb|200px|''envolution relationship in rice,maize,Arabidopsis and mouse (from reference <ref name="ref1" />).'']]

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:26:25Z

Chenxuepeng: /* Annotated Information */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.
===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:25:32Z

Chenxuepeng: /* Annotated Information */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:24:29Z

Chenxuepeng: /* Mutant Phenotype */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|left|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:23:46Z

Chenxuepeng: /* Mutant Phenotype */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
[[File:dwarf phenotype.jpg|left|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:23:19Z

Chenxuepeng: /* Mutant Phenotype */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
[[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:15:13Z

Chenxuepeng: /* Expression */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:13:41Z

Chenxuepeng: /* Function */

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:12:40Z

Chenxuepeng:

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:10:12Z

Chenxuepeng:

The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:08:34Z

Chenxuepeng: /* Expression */

Please input one-sentence summary here.

OsDDM1b
The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

[[File:expression.jpg|300px]]

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

File:Expression.jpg

2014-05-19T09:07:58Z

Chenxuepeng:

Os03g0722400

2014-05-19T09:05:49Z

Chenxuepeng: /* Labs working on this gene */

Please input one-sentence summary here.

OsDDM1b
The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T09:05:10Z

Chenxuepeng: /* Labs working on this gene */

Please input one-sentence summary here.

OsDDM1b
The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

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 Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:57:16Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

OsDDM1b
The rice semidwarf-1 (sd1) gene is well known as the "green revolution gene" and controls the plant height of rice.
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:55:55Z

Chenxuepeng: /* Labs working on this gene */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==Labs working on this gene==

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:55:33Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated
DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:55:15Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:54:49Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated
sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:54:07Z

Chenxuepeng: /* Expression */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated
sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===Expression===
Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
cytosine methylation in genomic DNA. Higo, Hiromi, et al identified two rice genes with high 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 silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
variations among various tissues, suggesting that there might be functional divergence of these two genes.

===Evolution===
OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:53:31Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

OsDDM1b
==Annotated Information==

===Function===
OsDDM1b is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated
sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===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. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:40:57Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==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.It mainly keeps the methylation level on repeated
sequences rather than single copy sequence.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===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. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:39:52Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

OsDDM1b
==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.It mainly keeps the methylation level on repeated
sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===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. However, considering maize, no simple orthologous relationships
exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:37:06Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==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.It mainly keeps the methylation level on repeated
sequences.

===Mutant Phenotype===
We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===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.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:32:02Z

Chenxuepeng: /* Mutant Phenotype */

Please input one-sentence summary here.

OsDDM1b
==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 generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

[[File:dwarf phenotype.jpg|150px]]

===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.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:31:41Z

Chenxuepeng: /* Mutant Phenotype */

Please input one-sentence summary here.

OsDDM1b
==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 generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
----
[[File:dwarf phenotype.jpg|150px]]

===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.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:28:30Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg|150px]]
===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.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
sequence similarity shared by these two genes is 81%, even including
intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
OsDDM1 genes.
The protein product of OsDDM1b gene is 849 amino acids in length.
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
amino acid motifs diagnostic for SWI2/SNF2 proteins.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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 envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
duplication event.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:19:31Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg|150px]]
===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.

[[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]

(Higo, Hiromi, et al.,2012)

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.

[[File:E_2.jpg|500px|]]

(Higo, Hiromi, et al.,2012)

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:18:06Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg|150px]]
===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.

[[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
duplication event.

[[File:E_2.jpg|500px|]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:15:05Z

Chenxuepeng: /* Mutant Phenotype */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg|150px]]

===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.

[[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
duplication event.

[[File:E_2.jpg|500px|]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:14:19Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg]]

===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.

[[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
duplication event.

[[File:E_2.jpg|500px|]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:07:05Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:dwarf phenotype.jpg]]

===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.
----
[[File:Osddm1a.jpg]][[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:06:24Z

Chenxuepeng: /* Function */

Please input one-sentence summary here.

OsDDM1b
==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.
----
[[File:Osddm1a.jpg]]

===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.
----
[[File:dwarf phenotype.jpg]]

===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.
----
[[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:04:40Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

OsDDM1b
==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, with another gene OsDDM1a, both of which are similar to Arabidopsis
DDM1, is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome.
----
[[File:Osddm1a.jpg]]
===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.
----
[[File:dwarf phenotype.jpg]]

===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.
----
[[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0722400

2014-05-19T08:03:41Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

OsDDM1b
==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, with another gene OsDDM1a, both of which are similar to Arabidopsis
DDM1, is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome.
----
[[File:Osddm1a.jpg]]
===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.
----
[[File:dwarf phenotype.jpg]]

===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 toArabidopsis DDM1.
the protein product of OsDDM1b 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.
----
[[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os09g0442400

2014-05-19T08:00:20Z

Chenxuepeng: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0442400|
Description = contains InterPro domain(s): IPR010989|
Version = NM_001069825.1 GI:115479392 GeneID:4347181|
Length = 3626 bp|
Definition = Oryza sativa Japonica Group Os09g0442400, 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17098053..17101678|
CDS = 17099148..17099653,17099732..17100319,17100396..17100522,17100653..17100839,17100947..17101103<br>,17101209..17101563|
GCID = <gbrowseImage1>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcaagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtga</cdnaseq>|
AA = <aaseq>MRRHAGTIILLLILACLWLCPGRSSGFSWNIFSSSSSSSPPTAG ESRAAPMLELDGAVADFLMDGADDPRAVKLLENARSKLAGPSNCWQEAYRRLFASCGD IMADKEMQSRLAWHLSSCFQEDSGRPPFPRCGEVSDMVHCRKRLGVSEDQVFLEFFLE TNTLCHQLQAEAFKHNTERLVNDLTRTSKSAEEKLEVIEERSDQIIQESRKVQETISS IEMQADHLAEASKNVGDQIDDVLAHSKAIFEQSKEIADSQAKLREGQTEMRETIDAGM THIQESYESLGNGMDKLKEEAVDIQREIKTVGDSMSTKMQDLQSTANDIGSVAGKSLE NQMQLLDGQSKAMDGLNNLYSFQAQALEESRETVQKLAQFGQRQQEELLSRQEEIRQA HEHLIHNSHSILEAQEEFRAKQANIFAALDKLYILHNAILAESRFIKAFFFYCCIVFL IYMLTSAKQTFSIRGHLYFGLCITLLLEIGLIKLGADDIDKQFWVISKVFLVRSVFLA LATVQMLHAIFTFRDYELLNHHLLQTLVEKVRALEETAAAGEKMLPYGGGGAESERSL MDYSWVFDELADEVDSNADPSYALPGDEQRQVAVVAPRRRHCASPEEVVGENSITTSA GRRYNLRPRSSYRQT</aaseq>|
DNA = <dnaseqindica>1096..1601#1680..2267#2344..2470#2601..2787#2895..3051#3157..3511#ttcgcctcccgtcgcgctccgtcgccttcaacctctgccaacgtcaggcgatccggtgagtaagttcttcctccatttttttcctctgctcttgcctctcttttccgaatcaaaatacagcgagatttctttcttctctctgaacttcaccggtgcaacaaaattgaaccatcgttgtaggttcgttcgttctgaacttttcagaatttcgcggtatatgttcagtgttcatgtcagtaaagatagcccgcaaggtataggagaggagaatttgattggccctctgtcactggcatggtgggccaagcgcttgcgcctcttggagtagtatcttgtggtgtaagccagtgcatgcaaccgacttaaattagcaccgacttgatttgtcattaactgatcaagatcttccttgctgggaacggaacatagaaacggcaagagatctgtgccccaccattcaacttggcatccaagtagctttccacacttccattggtgtaaccgtgtaagataactagcacattccaaatgtaaaccgccattactaatatcaagttcagtgctgttcaccgtgtgtttgcgtgcgtgtcgctgtcattttcggtgtcaaaagttctaaacatttggtttagtttagggtgattctctcttaatcttcccctgcatgtgatgtgacaggctcatctggatctctctggcttgccggctaaggaacaccgggtgctatttatcagggagcccttcacaccgcaggggaaagttgcagctattttgtcactgccccttgttgcatcttgctccggcgatttgatttagaattttaggttgttactggcttcgattaatcatattttagtctgaacaaatttgcaagttaattcctattctgttcaattcggtgattcaattcgattggggtctttgggtttaagaatttcagaatgttattaacacggggcgtaacaatctgcatcaaatgaataggctttaattcttgccttcttgattgttccttcctggcaggaactgcaattaacccgtgattttactcaccaagatcgcttcttgcccggtgcaaagttcaccgatttcaccatgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcagtaagtgcaattctcccattttcagtttgcaattcacttctgcttcttgaatttttcatgttttgttgatttgtgtagagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcaggtattttaacttctcgcttccattattctttttttatttcattgtaaaatatactgattttgactggaattttcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggttattgtctcctcctgcatatcagaatacgagaatagttttccttttgtttgactgcttaaccatgatcaatcagtaggcataggattgacttctttttcaactgatcttttttccttttgtcctgcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggtaaaaaaaaaaacatctcaggatatttcacatactattagcagttactacctgtatttacaccttgtaaaatgctcaattgctattgctttttactctcctggcaggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcaggtaaccaccaaatccagtccatgttcatcacgatcagatctttgcatgcattcgtgattcatctcaatctcctggtaattaattagcctgtaaacttttcttcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtgagtttggttggagaattaactggagatcgctttgtgcgcgtaatactgtgaacgttgttgtttctgggtttccagtgtgagtttggtttgggagaggtaaagtcgtcgtgtaccgt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069825.1 RefSeq:Os09g0442400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0442400

2014-05-19T07:55:01Z

Chenxuepeng: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0442400|
Description = contains InterPro domain(s): IPR010989|
Version = NM_001069825.1 GI:115479392 GeneID:4347181|
Length = 3626 bp|
Definition = Oryza sativa Japonica Group Os09g0442400, 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17098053..17101678|
CDS = 17099148..17099653,17099732..17100319,17100396..17100522,17100653..17100839,17100947..17101103<br>,17101209..17101563|
GCID = <gbrowseImage1>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcaagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtga</cdnaseq>|
AA = <aaseq>MRRHAGTIILLLILACLWLCPGRSSGFSWNIFSSSSSSSPPTAG ESRAAPMLELDGAVADFLMDGADDPRAVKLLENARSKLAGPSNCWQEAYRRLFASCGD IMADKEMQSRLAWHLSSCFQEDSGRPPFPRCGEVSDMVHCRKRLGVSEDQVFLEFFLE TNTLCHQLQAEAFKHNTERLVNDLTRTSKSAEEKLEVIEERSDQIIQESRKVQETISS IEMQADHLAEASKNVGDQIDDVLAHSKAIFEQSKEIADSQAKLREGQTEMRETIDAGM THIQESYESLGNGMDKLKEEAVDIQREIKTVGDSMSTKMQDLQSTANDIGSVAGKSLE NQMQLLDGQSKAMDGLNNLYSFQAQALEESRETVQKLAQFGQRQQEELLSRQEEIRQA HEHLIHNSHSILEAQEEFRAKQANIFAALDKLYILHNAILAESRFIKAFFFYCCIVFL IYMLTSAKQTFSIRGHLYFGLCITLLLEIGLIKLGADDIDKQFWVISKVFLVRSVFLA LATVQMLHAIFTFRDYELLNHHLLQTLVEKVRALEETAAAGEKMLPYGGGGAESERSL MDYSWVFDELADEVDSNADPSYALPGDEQRQVAVVAPRRRHCASPEEVVGENSITTSA GRRYNLRPRSSYRQT</aaseq>|
DNA = <dnaseqindica>1096..1601#1680..2267#2344..2470#2601..2787#2895..3051#3157..3511#ttcgcctcccgtcgcgctccgtcgccttcaacctctgccaacgtcaggcgatccggtgagtaagttcttcctccatttttttcctctgctcttgcctctcttttccgaatcaaaatacagcgagatttctttcttctctctgaacttcaccggtgcaacaaaattgaaccatcgttgtaggttcgttcgttctgaacttttcagaatttcgcggtatatgttcagtgttcatgtcagtaaagatagcccgcaaggtataggagaggagaatttgattggccctctgtcactggcatggtgggccaagcgcttgcgcctcttggagtagtatcttgtggtgtaagccagtgcatgcaaccgacttaaattagcaccgacttgatttgtcattaactgatcaagatcttccttgctgggaacggaacatagaaacggcaagagatctgtgccccaccattcaacttggcatccaagtagctttccacacttccattggtgtaaccgtgtaagataactagcacattccaaatgtaaaccgccattactaatatcaagttcagtgctgttcaccgtgtgtttgcgtgcgtgtcgctgtcattttcggtgtcaaaagttctaaacatttggtttagtttagggtgattctctcttaatcttcccctgcatgtgatgtgacaggctcatctggatctctctggcttgccggctaaggaacaccgggtgctatttatcagggagcccttcacaccgcaggggaaagttgcagctattttgtcactgccccttgttgcatcttgctccggcgatttgatttagaattttaggttgttactggcttcgattaatcatattttagtctgaacaaatttgcaagttaattcctattctgttcaattcggtgattcaattcgattggggtctttgggtttaagaatttcagaatgttattaacacggggcgtaacaatctgcatcaaatgaataggctttaattcttgccttcttgattgttccttcctggcaggaactgcaattaacccgtgattttactcaccaagatcgcttcttgcccggtgcaaagttcaccgatttcaccatgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcagtaagtgcaattctcccattttcagtttgcaattcacttctgcttcttgaatttttcatgttttgttgatttgtgtagagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcaggtattttaacttctcgcttccattattctttttttatttcattgtaaaatatactgattttgactggaattttcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggttattgtctcctcctgcatatcagaatacgagaatagttttccttttgtttgactgcttaaccatgatcaatcagtaggcataggattgacttctttttcaactgatcttttttccttttgtcctgcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggtaaaaaaaaaaacatctcaggatatttcacatactattagcagttactacctgtatttacaccttgtaaaatgctcaattgctattgctttttactctcctggcaggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcaggtaaccaccaaatccagtccatgttcatcacgatcagatctttgcatgcattcgtgattcatctcaatctcctggtaattaattagcctgtaaacttttcttcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtgagtttggttggagaattaactggagatcgctttgtgcgcgtaatactgtgaacgttgttgtttctgggtttccagtgtgagtttggtttgggagaggtaaagtcgtcgtgtaccgt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069825.1 RefSeq:Os09g0442400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os03g0722400

2014-05-19T07:54:14Z

Chenxuepeng: /* References */

Please input one-sentence summary here.

==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, with another gene OsDDM1a, both of which are similar to Arabidopsis
DDM1, is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome.
----
[[File:Osddm1a.jpg]]
===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.
----
[[File:dwarf phenotype.jpg]]

===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 toArabidopsis DDM1.
the protein product of OsDDM1b 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.
----
[[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==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==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os09g0442400

2014-05-19T07:51:33Z

Chenxuepeng: /* References */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==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==
{{JaponicaGene|
GeneName = Os09g0442400|
Description = contains InterPro domain(s): IPR010989|
Version = NM_001069825.1 GI:115479392 GeneID:4347181|
Length = 3626 bp|
Definition = Oryza sativa Japonica Group Os09g0442400, 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 = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:17098053..17101678|
CDS = 17099148..17099653,17099732..17100319,17100396..17100522,17100653..17100839,17100947..17101103<br>,17101209..17101563|
GCID = <gbrowseImage1>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:17098053..17101678
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcaagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtga</cdnaseq>|
AA = <aaseq>MRRHAGTIILLLILACLWLCPGRSSGFSWNIFSSSSSSSPPTAG ESRAAPMLELDGAVADFLMDGADDPRAVKLLENARSKLAGPSNCWQEAYRRLFASCGD IMADKEMQSRLAWHLSSCFQEDSGRPPFPRCGEVSDMVHCRKRLGVSEDQVFLEFFLE TNTLCHQLQAEAFKHNTERLVNDLTRTSKSAEEKLEVIEERSDQIIQESRKVQETISS IEMQADHLAEASKNVGDQIDDVLAHSKAIFEQSKEIADSQAKLREGQTEMRETIDAGM THIQESYESLGNGMDKLKEEAVDIQREIKTVGDSMSTKMQDLQSTANDIGSVAGKSLE NQMQLLDGQSKAMDGLNNLYSFQAQALEESRETVQKLAQFGQRQQEELLSRQEEIRQA HEHLIHNSHSILEAQEEFRAKQANIFAALDKLYILHNAILAESRFIKAFFFYCCIVFL IYMLTSAKQTFSIRGHLYFGLCITLLLEIGLIKLGADDIDKQFWVISKVFLVRSVFLA LATVQMLHAIFTFRDYELLNHHLLQTLVEKVRALEETAAAGEKMLPYGGGGAESERSL MDYSWVFDELADEVDSNADPSYALPGDEQRQVAVVAPRRRHCASPEEVVGENSITTSA GRRYNLRPRSSYRQT</aaseq>|
DNA = <dnaseqindica>1096..1601#1680..2267#2344..2470#2601..2787#2895..3051#3157..3511#ttcgcctcccgtcgcgctccgtcgccttcaacctctgccaacgtcaggcgatccggtgagtaagttcttcctccatttttttcctctgctcttgcctctcttttccgaatcaaaatacagcgagatttctttcttctctctgaacttcaccggtgcaacaaaattgaaccatcgttgtaggttcgttcgttctgaacttttcagaatttcgcggtatatgttcagtgttcatgtcagtaaagatagcccgcaaggtataggagaggagaatttgattggccctctgtcactggcatggtgggccaagcgcttgcgcctcttggagtagtatcttgtggtgtaagccagtgcatgcaaccgacttaaattagcaccgacttgatttgtcattaactgatcaagatcttccttgctgggaacggaacatagaaacggcaagagatctgtgccccaccattcaacttggcatccaagtagctttccacacttccattggtgtaaccgtgtaagataactagcacattccaaatgtaaaccgccattactaatatcaagttcagtgctgttcaccgtgtgtttgcgtgcgtgtcgctgtcattttcggtgtcaaaagttctaaacatttggtttagtttagggtgattctctcttaatcttcccctgcatgtgatgtgacaggctcatctggatctctctggcttgccggctaaggaacaccgggtgctatttatcagggagcccttcacaccgcaggggaaagttgcagctattttgtcactgccccttgttgcatcttgctccggcgatttgatttagaattttaggttgttactggcttcgattaatcatattttagtctgaacaaatttgcaagttaattcctattctgttcaattcggtgattcaattcgattggggtctttgggtttaagaatttcagaatgttattaacacggggcgtaacaatctgcatcaaatgaataggctttaattcttgccttcttgattgttccttcctggcaggaactgcaattaacccgtgattttactcaccaagatcgcttcttgcccggtgcaaagttcaccgatttcaccatgaggagacacgcagggacgattatcctgttgttgatcttggcctgcctatggctgtgccctgggaggagcagcggcttctcgtggaacattttctcctcgtcgtcgtcgtcttcgccgccgacggccggcgagagccgcgccgccccgatgctggagctggacggcgcggtggccgacttcttgatggacggggccgacgacccgagggcggtgaagctgctggagaacgcgaggagcaagctcgccgggccgagcaactgctggcaggaggcgtaccggaggctgttcgccagctgcggcgacatcatggccgacaaggagatgcagtcgcggctggcgtggcacctcagcagctgcttccaggaggactccggccgccccccgttccctcgctgcggcgaggtctccgacatggtgcactgccgcaagaggctcggcgtctccgaggaccaggtgttcctcgagttcttcctcgagaccaacaccctgtgccaccaattgcagtaagtgcaattctcccattttcagtttgcaattcacttctgcttcttgaatttttcatgttttgttgatttgtgtagagctgaagcgttcaagcataacacggagaggcttgtcaacgacctgacaaggacatccaagtcagccgaggagaagctggaggtgatcgaggagaggtcagaccagatcatacaagaatcacgcaaagttcaggagacgatctcgtcgatcgaaatgcaggcagatcatctcgcagaggcgtcgaagaatgtcggagaccagatcgacgacgtgctggctcactccaaggccatctttgagcagtccaaggagattgcagactctcaggcaaagctcagagaagggcagaccgagatgagggagacgatcgatgccggcatgacgcatattcaggagtcgtatgagagccttggcaatgggatggataagctgaaggaagaggctgttgatattcagagggagatcaaaactgttggtgattccatgtccaccaagatgcaggatttgcagagcactgcaaatgatattgggagtgtggctggcaaatcattggagaatcagatgcaacttttggatggacagagcaaggccatggacggtctgaataatctgtacagctttcaggcacaagctcttgaggaaagcaggtattttaacttctcgcttccattattctttttttatttcattgtaaaatatactgattttgactggaattttcagggagactgtgcaaaaacttgcacagtttggccagcgtcagcaggaagagttattgtccaggcaggaagaaatccggcaagctcatgaacacctgattcataattcacactcaatactggaagctcaggttattgtctcctcctgcatatcagaatacgagaatagttttccttttgtttgactgcttaaccatgatcaatcagtaggcataggattgacttctttttcaactgatcttttttccttttgtcctgcaggaagagttcagagcaaagcaggccaacatttttgctgctctggacaaactttacatcctccacaacgccatcttagccgagtcacgtttcatcaaggcgttcttcttctactgctgcatcgtgtttctcatctacatgctcacaagcgcgaagcaaactttcagcatcaggggacatctttactttggtaaaaaaaaaaacatctcaggatatttcacatactattagcagttactacctgtatttacaccttgtaaaatgctcaattgctattgctttttactctcctggcaggcttgtgcatcacgcttctgctcgaaattggcctgatcaagctcggagctgacgacatcgacaagcaattctgggtcatatccaaggtgttccttgtcagatcagtgttccttgcacttgccaccgttcagatgttgcatgccatattcacattcaggtaaccaccaaatccagtccatgttcatcacgatcagatctttgcatgcattcgtgattcatctcaatctcctggtaattaattagcctgtaaacttttcttcagggattacgaactactcaaccatcacctgctccagacgctggtcgagaaggtccgggcgctggaggaaaccgccgccgccggcgagaagatgctgccctacggcggcggcggcgcggagagcgagaggagcctgatggactactcgtgggtgttcgacgagttggccgacgaggtggacagcaatgcggatccgagctacgccttgccgggggatgagcagcggcaggtggcggtggtcgctcctcgccggaggcactgcgcctcgccggaggaggtcgtcggcgagaactccatcacgacgtcggctggccggaggtacaacctgcggccacggagtagttacaggcagacgtgagtttggttggagaattaactggagatcgctttgtgcgcgtaatactgtgaacgttgttgtttctgggtttccagtgtgagtttggtttgggagaggtaaagtcgtcgtgtaccgt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069825.1 RefSeq:Os09g0442400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os03g0722400

2014-05-19T07:44:14Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

==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, with another gene OsDDM1a, both of which are similar to Arabidopsis
DDM1, is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome.
----
[[File:Osddm1a.jpg]]
===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.
----
[[File:dwarf phenotype.jpg]]

===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 toArabidopsis DDM1.
the protein product of OsDDM1b 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.
----
[[File:E_1.jpg]]
----
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.
----
[[File:E_2.jpg]]

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

File:E 2.jpg

2014-05-19T07:38:09Z

Chenxuepeng:

File:E 1.jpg

2014-05-19T07:37:50Z

Chenxuepeng:

Os03g0722400

2014-05-19T07:26:52Z

Chenxuepeng: /* Annotated Information */

Please input one-sentence summary here.

==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, with another gene OsDDM1a, both of which are similar to Arabidopsis
DDM1, is required for the maintenance of DNA methylation on
newly replicated DNA strands in rice genome.
===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.
----
[[File:dwarf phenotype.jpg]]

===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.
----
[[File:Osddm1a.jpg]]

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

File:Dwarf phenotype.jpg

2014-05-19T07:05:49Z

Chenxuepeng:

Os03g0722400

2014-05-19T06:16:42Z

Chenxuepeng: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.

===Evolution===
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).
----
[[File:Osddm1a.jpg]]

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = 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 = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:30070286..30073465|
CDS = 30072187..30072291|
GCID = <gbrowseImage1>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:30070286..30073465
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

File:Osddm1a.jpg

2014-05-19T06:13:50Z

Chenxuepeng: