RiceWiki - User contributions [en]

Os07g0585700

2014-06-09T15:14:19Z

Zongyuan:

Sdr4 is a gene related with seed dormancy.

==Annotated Information==
===Function===
　　Seed dormancy 4 (''Sdr4''), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. ''Sdr4'' expression is positively regulated by ''OsVP1'', a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that ''Sdr4'' acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (''Sdr4-n''), which endows reduced dormancy, whereas both the Kasalath allele (''Srd4-k'') and ''Sdr4-n'' are widely distributed in the indica group, indicating prevalent introgression. ''Srd4-k'' also is found in the wild ancestor Oryza rufipogon, whereas ''Sdr4-n'' appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the ''Sdr4'' region has revealed that ''Sdr4'' acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.

　　The seeds of two independent ''sdr4'' mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 1C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 1E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of ''sdr4'' seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 1F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

[[File:Figure4.jpg|left|thumb|400px|Figure.1 Morphological andphysiologicalanalysisof sdr4mutant.<ref name="ref1"/>]]

===Expression===

　　''Sdr4'' mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that ''Sdr4'' mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 1A). ''Sdr4'' mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 1B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the ''Sdr4'' promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors , along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes.

　　The presence of ABREs and RY repeats in the ''Sdr4'' promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether ''Sdr4'' expression is regulated by ''OsVP1'', a global regulator of seed maturation. ''Sdr4'' expression in embryos at 28 DAF were substantially reduced in ''Osvp1'' mutant embryos (Fig. 2B and Fig. 3B). This ﬁnding suggests that the regulation exerted by ''Sdr4'' was, at least in part, integrated into the global seed maturation program directed by ''OsVP1''.To relate ''Sdr4'' more closely to known seed dormancy and germination mechanisms, we examined the effects of ''sdr4'' mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[''Sdr4''] (Fig. 2A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[''Sdr4''] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[''Sdr4''] suggest that ''OsDOG1L-1'' is a positive regulator of dormancy in rice, and that ''Sdr4'', at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed . Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1), aquaporin genes (PIP1;3 and PIP2;2), and an expansin gene (OsEXPB3) (Fig. 2A). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of ''Sdr4'' by ''OsVP1''. The foregoing expression analysis results suggest that ''Sdr4'' plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

[[File:Figure5.jpg|left|thumb|400px|Figure.2 Expression analysis of dormancy andgermination relatedgenes in ''sdr4'' and ''Osvp1'' mutants.<ref name="ref1"/>]]

[[File:3.jpg|right|thumb|500px|Figure.3 Natural variations in the Sdr4 coding region.<ref name="ref1"/>]]

===Evolution===
　　Sequence analysis of 59 cultivars from the world rice core collection revealed the existence of only three haplotypes, ''Sdr4-n'', ''Sdr4-k'', and ''Sdr4-k''′, in the coding sequences. Interestingly, all japonica cultivars had only ''Sdr4-n'', whereas both ''Sdr4-n'' and ''Sdr4-k'' were found in indica In-2, and all three haplotypes were found in indica In-1. SNP analysis of the chromosomal regions containing ''Sdr4-n'' in indica cultivars revealed that in most cases, the japonica haplotypes with ''Sdr4-n'' were ﬂanked by indica haplotypes, although some complex haplotypes were found as well . Therefore, we considered the Sdr4-n in indica cultivars to be the result of introgression from japonica sources. The seeds of cultivars with ''Sdr4-n'' had lower dormancy than those of cultivars with ''Sdr4-k'' (P = 0.012 by the F test). These results strongly suggest that the functional differences in ''Sdr4'' contribute substantially to the variations in dormancy of Asian rice accessions, although the involvement of other loci is suggested by the presence of some indica cultivars with ''Sdr4-k''(k′) showing high germination rates and some indica cultivars with ''Sdr4-n'' showing low germination rates.(Figure .3)

==Labs working on this gene==
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;

National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;

BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;

Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
<references>
<ref name="ref1">Kazuhiko Sugimoto;Yoshinobu Takeuchi;Kaworu Ebana;Akio Miyao;Hirohiko Hirochika;Naho Hara;Kanako Ishiyama;Masatomo Kobayashi;Yoshinori Ban;Tsukaho Hattori;Masahiro Yano. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences, 2010, 107(13): 5792-5797</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

File:3.png

2014-06-09T15:06:09Z

Zongyuan: uploaded a new version of "File:3.png"

[[File:3.png]]

Os07g0585700

2014-06-08T11:06:23Z

Zongyuan: /* Evolution */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
[[File:Figure4.jpg|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
[[File:Figure5.jpg|right|thumb|150px|]]

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

You can also add sub-section(s) at will.
　　Sequence analysis of 59 cultivars from the world rice core collection revealed the existence of only three haplotypes, Sdr4-n, Sdr4-k, and Sdr4-k′, in the coding sequences. Interestingly, all japonica cultivars had only Sdr4-n, whereas both Sdr4-n and Sdr4-k were found in indica In-2, and all three haplotypes were found in indica In-1. SNP analysis of the chromosomal regions containing Sdr4-n in indica cultivars revealed that in most cases, the japonica haplotypes with Sdr4-n were ﬂanked by indica haplotypes, although some complex haplotypes were found as well . Therefore, we considered the Sdr4-n in indica cultivars to be the result of introgression from japonica sources. The seeds of cultivars with Sdr4-n had lower dormancy than those of cultivars with Sdr4-k (P = 0.012 by the F test). These results strongly suggest that the functional differences in Sdr4 contribute substantially to the variations in dormancy of Asian rice accessions, although the involvement of other loci is suggested by the presence of some indica cultivars with Sdr4-k(k′) showing high germination rates and some indica cultivars with Sdr4-n showing low germination rates.

==Labs working on this gene==
Please input related labs here.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-08T11:03:03Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
[[File:Figure4.jpg|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
[[File:Figure5.jpg|right|thumb|150px|]]

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-08T11:02:46Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
[[File:Figure.jpg|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
[[File:Figure5.jpg|right|thumb|150px|]]

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-08T11:02:28Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19)
[[File:Figure.jpgjpg|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
[[File:Figure5.jpg|right|thumb|150px|]]

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

File:Figure5.jpg

2014-06-08T11:00:16Z

Zongyuan: uploaded a new version of "File:Figure5.jpg"

[[File:Figure4.jpg|right|thumb|150px|''Semidwarf VS. normal-
type rice plants at ripening (from reference <ref name="ref3" />)

File:Figure4.jpg

2014-06-08T11:00:03Z

Zongyuan: uploaded a new version of "File:Figure4.jpg"

Os07g0585700

2014-06-08T10:58:15Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19). [[File:Figure4|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.[[File:Figure5 |right|thumb|150px|]]

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-05T15:36:35Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19).
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-05T15:27:07Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19).[[File:Figure4.jpg|right|thumb|150px|]]
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.
[[File:Figure5.jpg|right|thumb|150px|]]

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

File:Figure4.jpg

2014-06-05T11:04:08Z

Zongyuan: uploaded a new version of "File:Figure4.jpg"

File:Figure5.jpg

2014-06-05T11:02:37Z

Zongyuan:

[[File:Figure4.jpg|right|thumb|150px|''Semidwarf VS. normal-
type rice plants at ripening (from reference <ref name="ref3" />)

File:Figure5.jpg

2014-06-05T11:02:15Z

Zongyuan:

[[File:Figure5.jpg|right|thumb|150px|''Semidwarf VS. normal-
type rice plants at ripening (from reference <ref name="ref3" />)

File:Figure5.jpg

2014-06-05T11:01:23Z

Zongyuan: uploaded a new version of "File:Figure5.jpg"

File:Figure4.jpg

2014-06-05T11:00:55Z

Zongyuan: uploaded a new version of "File:Figure4.jpg"

Os07g0585700

2014-06-05T10:57:33Z

Zongyuan:

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19).
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

===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.
National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan;
BioResources Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan;
Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya 464-8601,Japan

==References==
Please input cited references here.
<ref name="ref1"> Baumlein H, Nagy I, Villarroel R, Inze D, Wobus U (1992) Cis-analysis of a seed protein gene promoter: The conservative RY repeat CATGCATG within the legumin box is essential for tissue-speciﬁc expression of a legumin gene. Plant J 2:233–239.</ref>
<ref name="ref2">Shen Q, Zhang P, Ho TH (1996) Modular nature of abscisic acid (ABA) response complexes: Composite promoter units that are necessary and sufﬁcient for ABA induction of gene expression in barley. Plant Cell 8:1107–1119.</ref>
<ref name="ref3">Hobo T, Asada M, Kowyama Y, Hattori T (1999) ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.Plant J 19:679–689.</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-05T10:46:48Z

Zongyuan: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.
　　Seed dormancy 4 (Sdr4), encodes a novel protein with an amino acid sequence that has no similarity to proteins with known functions, it contributes substantially to differences in seed dormancy between japonica (Nipponbare) and indica (Kasalath) cultivars. Sdr4 expression is positively regulated by OsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting that Sdr4 acts as an intermediate regulator of dormancy in the seed maturation program. Japonica cultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) and Sdr4-n are widely distributed in the indica group, indicating prevalent introgression. Srd4-k also is found in the wild ancestor Oryza rufipogon, whereas Sdr4-n appears to have been produced through at least two mutation events from the closest O. rufipogon allele among the accessions examined. Furthermore, haplotype analysis of the Sdr4 region has revealed that Sdr4 acts as an important determinant of seed dormancy in rice cultivars and might have been involved in rice domestication.
　　The seeds of two independent sdr4 mutant lines, M25 and M100, contained embryos larger than those of the wild type (Fig. 4 C and D) and were completely nondormant (nearly 100% germination at 4WAH; Fig. 4E). The loss of dormancy was associated with severely reduced ABA sensitivity. Germination of sdr4 seeds at 6 WAH was not inhibited by ABA at 100 μM, whereas that of Nipponbare seeds was completely inhibited (Fig. 4F); however, no signiﬁcant differences in the ABA content of seeds sampled at 6 WAH were seen (83 ng/g fresh weight for Nipponbare, 87 ng/g for NIL(Sdr4), 83 ng/g for M25, and 78 ng/g for M100).

===Expression===
Please input expression information here.
　　
　　Sdr4 mRNA was detected preferentially in the seed tissues 14 days after ﬂowering (DAF). Promoter-GUS transgenics and in situ hybridization suggest that Sdr4 mRNA was expressed throughout the embryo but preferentially in the radicle; the in situ hybridization signals suggest that it also was expressed in the shoot (Fig. 4A). Sdr4 mRNA began to accumulate in the seed at 7 DAF, and its level increased as the seed matured (Fig. 4B). These expression patterns during the course of seed maturation were in accordance with the set of cis-elements predicted in the Sdr4 promoter; there were seven RY repeats (CATGCA), which are important for seed-speciﬁc gene expression and are the target of the VP1/ABI3 subfamily of B3 domain transcription factors (15), along with an ABA response element [ABRE; ACGTGG/T(C)] and an ABRE-related coupling element (CE) (16–18). One RY repeat is closely linked to an ABRE, and another is closely linked to an ABRE-CE and an ABRE. The combination of these elements and the close linkages are frequently seen in seed maturation-related genes (19).
　　The presence of ABREs and RY repeats in the Sdr4 promoter, together with an expression pattern typical of that of maturation-related genes, prompted us to investigate whether Sdr4 expression is regulated by OsVP1, a global regulator of seed maturation(6). Sdr4 expression in embryos at 28 DAF were substantially reduced in Osvp1 mutant embryos (Fig. 5B and Fig. S6B). This ﬁnding suggests that the regulation exerted by Sdr4 was, at least in part, integrated into the global seed maturation program directed by OsVP1.To relate Sdr4 more closely to known seed dormancy and germination mechanisms, we examined the effects of sdr4 mutation on the expression of several genes potentially related to dormancy and germination. Although little is known about regulators of embryonic dormancy other than those of seed maturation and ABA signaling in cereals, we examined the expression of the three closest rice homologs of Arabidopsis DOG1(8)(a QTL identified as a positive regulator of seed dormancy) as potential positive regulators of seed dormancy. the levels of expression of two of the three OsDOG1-like genes were lower in sdr4 mutant embryos than in wild-type Nipponbare or NIL[Sdr4] (Fig. 5A ). In addition, OsDOG1-like-1(OsDOG1L-1)expression was signiﬁcantly higher in NIL[Sdr4] than in Nipponbare. It was difﬁcult to judge this gene to be orthologous to Arabidopsis DOG1 from the phylogenetic relationships, due to the presence of three highly related DOG1-like genes in Arabidopsis, some of whose mutations were reported to not affect dormancy. However, the observed down-regulation in the mutant and up-regulation in NIL[Sdr4] suggest that OsDOG1L-1 is a positive regulator of dormancy in rice, and that Sdr4, at least in part, controls seed dormancy via the regulation of these OsDOG1-like genes.
　　In Arabidopsis nondormant mutants with mutations in seed maturation regulators such as abi3, germinative and postgerminative programs operate prematurely in the developing seed (22). Consequently, we examined the expression of several germination-related genes: a gibberellin biosynthesis gene (OsGA20ox-1) (23), aquaporin genes (PIP1;3 and PIP2;2) (24), and an expansin gene (OsEXPB3) (Fig. 5A ). Expression of these genes is induced in nondormant seeds on imbibition (26). Expression levels of all of these genes were signiﬁcantly higher in the sdr4 mutant than in the wild-type Nipponbare or NIL[Sdr4], consistent with the positive regulation of Sdr4 by OsVP1. The foregoing expression analysis results suggest that Sdr4 plays a regulatory, rather than a structural or metabolic, role in the promotion of dormancy and inhibition of germination, as also suggested by the nuclear localization of the gene product.

===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 = Os07g0585700|
Description = Conserved hypothetical protein|
Version = NM_001188348.1 GI:297725826 GeneID:9269794|
Length = 1032 bp|
Definition = Oryza sativa Japonica Group Os07g0585700, 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 7|Chromosome 7]]|
AP = Chromosome 7:24456768..24457799|
CDS = 24456768..24457799|
GCID = <gbrowseImage1>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:24456768..24457799
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</cdnaseq>|
AA = <aaseq>MAMVQPVDMAVKANEIMARFRPIAPKPVLPAAAAGVTGGGDGAA AVAATNRVLCQLQSRPCRARKRGRPSVVPPVSPPAGAKRKRAPAYPVPVAPLRCAAVA TATRARVSVVVVPAPESAGGVSALAPVSPSAGDSTRLSPTVVEVEDEDEERGVVLVER DLLRKLLEPRKLLEPRAVRPVGSTIHVESVHIDVGRTTAAAAAAAPKTAEEVEAELES DSLPAVVSDSSNRVRLVNDAYKRMVGQPECPWLDAVATAASRRISGEVALVVSEPAAA AAALPETCKGFSCSAKIAWERDGKWSSVHAPCDVTRLQCESRDYVFAWRFRAAGDECN THRRAAGDA</aaseq>|
DNA = <dnaseqindica>1..1032#atggccatggtgcagccggtggacatggccgtgaaggccaacgagatcatggcgaggttcaggcccatcgcgcccaagcccgtgctgccggcggcggcggcgggggtgacgggtggtggtgacggtgctgcggcggtggcggcgacgaaccgcgtgctctgccagctgcagagcaggccgtgccgggcgcggaagcgggggcggcccagcgtagtgccgccggtgtccccgccggcgggggccaagaggaagagggcgccggcgtacccggtccccgtggcgccgctccggtgcgcggcggtggccacggcgacgagggcgcgcgtgtcggtggtggtcgtcccggccccggagagtgcgggcggggttagtgcgctggcgccggtgtcgccgagtgccggggactcgacgaggctctcgccgacggtggtggaggtggaggacgaggacgaggagaggggcgtggtgctcgtggagcgcgacctgctgcggaagctgctggagccgcggaagctgctggagccgcgcgcggtgcgccccgtgggctccaccatccacgtcgagtcagtccacatcgacgtcggccgcaccaccgccgccgccgccgcagccgccccgaagacggcggaggaggtggaggcggagctggagtcggactccctcccggcggtggtctcggactccagcaaccgcgtccggctggtgaacgacgcgtacaagcgaatggtggggcagcccgagtgcccgtggctcgacgccgtggccaccgccgcgtccaggaggatcagcggcgaggtggcgctggtagtgtccgagccggcggcggcggcggcggcgctgccggagacatgcaaggggttctcgtgctcggccaagatcgcgtgggagcgcgacggcaagtggtcatccgtccatgcaccgtgcgacgtcacccggctgcagtgcgagtcgagggactacgtcttcgcctggaggttccgcgccgccggcgacgaatgcaacacccaccgccgcgccgccggcgacgcgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188348.1 RefSeq:Os07g0585700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

Os07g0585700

2014-06-05T10:42:52Z

Zongyuan: /* Function */