RiceWiki - User contributions [en]

Os01g0883800

2014-05-22T11:46:48Z

Yimoukong:

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

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

This gene is originally derived from the Chinese cultivar Dee-Geo-Woo-Gen (DGWG). It encodes an oxidase enzyme involved in the biosynthesis of gibberellin, which is a plant growth hormone. The rice genome carries at least two GA20ox genes (GA20ox-1 and GA20ox-2). SD1 corresponds to GA20ox-2. Mutation of SD1 will cause a semi-dwarf phenotype of rice without seed yield being affected <ref name="ref1" />. It is not surprising that a rice semidwarfing gene encodes GA20-ox since successful production of semidwarf plants using antisense or overexpressed GA20-ox genes has been reported in Arabidopsis, Solanum dulcamara, potato, and lettuce <ref name="ref3" />.
It is a key enzyme in the biosynthesis of gibberellin that catalyses the three steps GA53->GA44->GA19->GA20. Impaired GA 20-oxidase activity will cause elevated content of GA53, and reduced amount of G20<ref name="ref3" />. However, there is slight difference between different strains. The extent of GA1 is lower in Doongara (semi-dwarf rice strain) when compared with Kyeema (tall), while there is no significant difference between Calrose76 (semi-dwarf rice strain) and Calrose (tall). Calrose76 has lower contents of GA44 and of GA19 than Calrose, while there is no significant difference between Doongara (semi-dwarf rice strain) and Kyeema (tall) <ref name="ref2" />.

'''GO assignment(s):''' GO:0005506, GO:0016216, GO:0017000

=== Mutation ===
'Dee-Geo-Woo-Gen' (semi-dwarf rice strain): A 383-base-pair deletion from the genome (A 280-bp deletion within the coding region), which induces a frameshift that creates a stop codon in SD1, may be related with the semi-dwarf phenotype <ref name="ref1" /><ref name="ref2" />.

Calrose76 (semi-dwarf rice strain): The DNA sequence of Calrose76 is identical to Calrose (tall) except for a C to T transition at position 798 that resulted in a change of the predicted amino acid leucine (Leu-266) in Calrose to phenylalanine in Calrose76 <ref name="ref2" />.

It has been found that introgression of a chromosomal block containing the SD1 allele from tropical japonica is associated with a change in growth patterns in BHA1 (one weedy rice population) <ref name="ref7" />.

=== Expression ===
This gene is strongly expressed in the leaf blade, stem and unopened flower, whereas GA20ox-1 is predominantly expressed in the unopened flower <ref name="ref1" />.

Among the DGWG-type sd-1 mutants, IR24 and Habataki have little transcript of this gene, while Milyang 23 expresses a normal or greater amount of truncated transcript. No significant difference is observed between Calrose and its single-nucleotide-substitution mutant Calrose 76 <ref name="ref3" />.

Analysis of the tissue- and stage-specificity of transcription of sd1 in Nipponbare revealed that this
gene was expressed within 48 hr after sowing, as well as in 10-day-old plants, 30-day-old leaves, and flowering panicles; no transcription is detected in 24-hr-old seedlings or in 14-day-old roots. Transcript accumulates predominantly in adult leaves <ref name="ref3" />.

{| class='wikitable' style="text-align:center"
|-
! | Primer
! | Forward primer
! | Reverse primer
|-
| rowspan="3"|Gene amplication
| | 5'-CAACTCACTCCCGCTCAACACAGC-3'
| | 5'-TTTGAAATGCAATGTCGTCCACC-3' (used to amplify exon 1 <ref name="ref2" />)
|-
| | 5'-GCGCCAATGGGGTAATTAAAACG-3'
| | 5'-GGCATTCCATTGTTTGTGATTGG-3' (used to amplify exon 2 <ref name="ref2" />)
|-
| | 5'-GTTTGTCCTTGTCGCGTTGCTCAG-3'
| | 5'-TCTGTTCGTTCCGTTTCGTTCCG-3' (used to amplify exon 3 <ref name="ref2" />)
|-
| rowspan="2"|RT-PCR
| | 5'-CAACTCACTCCCGCTCAACACAGC-3'
| | 5'-GTTCGTTCCGTTTCGGTTCCG-3' <ref name="ref3" />
|-
| | 5'-AGCTGGACATGCCCGTGGTC-3'
| | 5'-TTGAGCTGCTGTCCGCGAAG-3' <ref name="ref3" />
|}

=== Evolution ===
This gene is conserved in ''Arabidopsis'' (47% identity) and pea (50% identity). GA20ox-2 shows 47.8% identity to
GA20ox-1 in rice. There are at least three GA20-ox genes in Arabidopsis <ref name="ref1" /><ref name="ref2" />.

=== Knowledge Extension ===

[[File:Gibberellin SD1 RHT Signal.PNG|right|thumb|500px|''Gibberellin signalling pathway (from reference <ref name="ref4" />).'']]

Except ''sd1'', another ‘green revolution’ gene named ''Rht1'', which encodes a GA signal suppressor DELLA protein. The deletion in the N-terminal region of the native RHT1 constitutively suppresses GA signaling, consequently resulting in a dominant semi-dwarf phenotype <ref name="ref5" />. Both sd1 and Rht1 are associated with GA pathway, indicating the importance of GA in the regulation of developmental processes and making it a prime target for improving crop yield <ref name="ref4" />.

The wheat green-revolution gene Rht (for ‘reduced height’) <ref name="ref5" /> is a gain-of-function allele caused by a mutation in a transcription factor that is associated with the gibberellin signalling pathway. As wheat has a hexaploid genome, it does not contain recessive alleles such as ''sd1'' in rice that might otherwise be used to produce a semi-dwarf strain of wheat. Although the genetic and biochemical functions of the rice SD1 and wheat RHT proteins are completely different (that is, recessive versus dominant, loss-of-function versus gain-offunction events, enzyme versus transcription factor, respectively), the products of both genes are linked with gibberellin malfunction <ref name="ref1" />.

In rice, ''Slr1'' gene encodes the DELLA protein. Three semi-dominant dwarf mutants (''Slr1-d1'', ''Slr1-d2'' and ''Slr1-d3'') associated with this gene have been identified, which were caused by gain-of-function mutations in the N-terminal region of SLR1. These three mutants are responsive to GA at a reduced rate, with later SLRl degradation, and showing reduced interaction activity with GID1 (GA receptor) comparing with wild type rice <ref name="ref6" />.

== Labs working on this gene ==
*Bioscience Center, and Graduate School of Bioagricultural Science, Nagoya University, Nagoya 464-8601, Japan
*Honda R&D, Wako Research Center, Wako 351-0193, Japan
*International Rice Research Institute, Manila, DAPO Box 7777, Philippines
*BioResources Center, and Plant Molecular Biology Laboratory, Riken, Tsukuba 305-0074, Japan
*Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, GPO Box 1600, Canberra ACT 2601, Australia
*Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan

== References ==
<references>
<ref name="ref1">Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, et al. (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416: 701-702.</ref>
<ref name="ref2">Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci U S A 99: 9043-9048.</ref>
<ref name="ref3">Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, et al. (2002) Positional cloning of rice semidwarfing gene, sd-1: rice "green revolution gene" encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9: 11-17.</ref>
<ref name="ref4">Hedden P. (2003) The genes of the Green Revolution. Trends Genet 19: 5-9.</ref>
<ref name="ref5">Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, et al. (1999) 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400: 256-261.</ref>
<ref name="ref6">Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, et al. (2009) Isolation and characterization of dominant dwarf mutants, ''Slr1-d'', in rice. Mol Genet Genomics 281: 223-231.</ref>
<ref name="ref7">Reagon M, Thurber CS, Olsen KM, Jia Y, Caicedo AL (2011) The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Mol Ecol 20: 3743-3756.</ref>
</references>

== Structured Information ==
{{JaponicaGene|
GeneName = Os01g0883800|
Description = Gibberellin 20 oxidase 2 (EC 1.14.11.-) (Gibberellin C-20 oxidase 2) (GA 20-oxidase 2) (Os20ox2) (Semidwarf-1 protein)|
Version = NM_001051549.1 GI:115441468 GeneID:4325003|
Length = 2743 bp|
Definition = Oryza sativa Japonica Group Os01g0883800, 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 1|Chromosome 1]]|
AP = Chromosome 1:40138313..40141055|
CDS = 40138313..40138869,40138972..40139293,40140765..40141055|
GCID = <gbrowseImage1>
name=NC_008394:40138313..40141055
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:40138313..40141055
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</cdnaseq>|
AA = <aaseq>MVAEHPTPPQPHQPPPMDSTAGSGIAAPAAAAVCDLRMEPKIPE PFVWPNGDARPASAAELDMPVVDVGVLRDGDAEGLRRAAAQVAAACATHGFFQVSEHG VDAALARAALDGASDFFRLPLAEKRRARRVPGTVSGYTSAHADRFASKLPWKETLSFG FHDRAAAPVVADYFSSTLGPDFAPMGRVYQKYCEEMKELSLTIMELLELSLGVERGYY REFFADSSSIMRCNYYPPCPEPERTLGTGPHCDPTALTILLQDDVGGLEVLVDGEWRP VSPVPGAMVINIGDTFMALSNGRYKSCLHRAVVNQRRERRSLAFFLCPREDRVVRPPP SAATPQHYPDFTWADLMRFTQRHYRADTRTLDAFTRWLAPPAADAAATAQVEAAS</aaseq>|
DNA = <dnaseqindica>1..557#660..981#2453..2743#atggtggccgagcaccccacgccaccacagccgcaccaaccaccgcccatggactccaccgccggctctggcattgccgccccggcggcggcggcggtgtgcgacctgaggatggagcccaagatcccggagccattcgtgtggccgaacggcgacgcgaggccggcgtcggcggcggagctggacatgcccgtggtcgacgtgggcgtgctccgcgacggcgacgccgaggggctgcgccgcgccgcggcgcaggtggccgccgcgtgcgccacgcacgggttcttccaggtgtccgagcacggcgtcgacgccgctctggcgcgcgccgcgctcgacggcgccagcgacttcttccgcctcccgctcgccgagaagcgccgcgcgcgccgcgtcccgggcaccgtgtccggctacaccagcgcccacgccgaccgcttcgcctccaagctcccatggaaggagaccctctccttcggcttccacgaccgcgccgccgcccccgtcgtcgccgactacttctccagcaccctcggccccgacttcgcgccaatggggtaattaaaacgatggtggacgacattgcatttcaaattcaaaacaaattcaaaacacaccgaccgagattatgctgaattcaaacgcgtttgtgcgcgcaggagggtgtaccagaagtactgcgaggagatgaaggagctgtcgctgacgatcatggaactcctggagctgagcctgggcgtggagcgaggctactacagggagttcttcgcggacagcagctcaatcatgcggtgcaactactacccgccatgcccggagccggagcggacgctcggcacgggcccgcactgcgaccccaccgccctcaccatcctcctccaggacgacgtcggcggcctcgaggtcctcgtcgacggcgaatggcgccccgtcagccccgtccccggcgccatggtcatcaacatcggcgacaccttcatggtaaaccatctcctattctcctctcctctgttctcctctgcttcgaagcaacagaacaagtaattcaagcttttttttctctctcgcgcgaaattgacgagaaaaataagatcgtggtaggggcggggctttcagctgaaagcgggaagaaaccgacctgacgtgatttctctgttccaatcacaaacaatggaatgccccactcctccatgtgttatgatttatctcacatcttatagttaataggagtaagtaacaagctacttttttcatattatagttcgtttgattttttttttttaaagtttttttagttttatccaaatttattgaaaaacttagcaacgtttataataccaaattagtctcatttagtttaatattgtatatattttgataatatatttatgttatattaaaaatattactatatttttctataaacattattaaaagccatttataatataaaatggaaggagtaattaatatggatctcccccgacatgagaatattttccgatggtgtgacgacgccatgtaagcttcggtgggcctggacggccagaggtgccaacagccacgtccaacaacccctgggtccccccctaacactccaaacagtagtgagtagtgtctcgtcgcgttttagtatttgatgacaaacaaagtgtgagttgagttagccaccaccaacttgcacacgagcacatacatttgtgtccattctcgccagtcacttccatctctagtcctaactcctatctagcgatgtaagcggataatttcatcatccgtatataaacctgtttgttatagttaatttcctatataatactataacagtatacattttaaaagaaaacaaaattaggataaacaggccctgctcctatccatccatggcacttggaaggaccagactcggtcatgccatgccaagccaagatatgggttatggaagagtagagaagaggagagatgagagataagcatgcgttctcctcctcgttggatgtgtattttggagggatttgtgtagtagtagcagcggcgccgcggggacggatgcggatggtggcgctttcggtggcgttttcccgggggggttttggtttggcgcttgggggggatggcatggcgcggcgtgcggctgcacgccacacacacgcgcgcgcacgcacgtacgtcgtcgtcgccgcgggcggacggtagcttagggtggtgtgttccgcgcgcgggcgcggattgttccatgccgatcgatttggcgccaccctcgccgcggctcttgtcgcgtcgtgcgcctctctcgcgcggtttgtccttgtcgcgttgctcagccggcgacgggggcacggacattggcgatgtagccctgcacgtgtcggcctctccgttgatgaatgatgatgtatgtatgtatttttttttgtctgaaggaatttgtggggaattgttgtgtgtgcaggcgctgtcgaacgggaggtataagagctgcctgcacagggcggtggtgaaccagcggcgggagcggcggtcgctggcgttcttcctgtgcccgcgggaggacagggtggtgcggccgccgccgagcgccgccacgccgcagcactacccggacttcacctgggccgacctcatgcgcttcacgcagcgccactaccgcgccgacacccgcacgctcgacgccttcacgcgctggctcgcgccgccggccgccgacgccgccgcgacggcgcaggtcgaggcggccagctga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001051549.1 RefSeq:Os01g0883800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os06g0165600

2014-05-22T10:06:01Z

Yimoukong: Undo revision 170736 by Yimoukong (talk)

Os06g0165600

2014-05-22T09:59:08Z

Yimoukong: /* References */

2014-05-22T08:10:28Z

Yimoukong: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The '''''OsDREB1D'''''， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The over-expression of '''''OsDREB1D''''',a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).<ref name="ref1" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. This '''''OsDREB1D''''' gene functions similarly as other DREB transcription factors <ref name="ref1" />.
[[File:Figure 1.Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.png|right|thumb|150px|Figure 1. Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.(from reference <ref name="ref1" />).'']]

===Mutation===
To identify genes involved in the control of rice tillering, Li et al. have screened for mutants with altered tiller numbers from collections derived from spontaneous mutations or g-ray radiation and ethyl methanesulphonate (EMS) mutagenesis, and they found that '''''moc1''''' plants nearly completely lose their tillering ability after a spontaneous '''''moc1''''' mutant, producing only one main culm, in contrast to the multiple tillers in wild-type plants<ref name="ref1" />. They amplified the corresponding ORF from '''''moc1''''' and wild-type plants with polymerase chain reaction (PCR) and sequenced it. DNA sequence comparison revealed a 1.9-kb retrotransposon inserted in this ORF in the '''''moc1''''' mutant. Confirmation of the retrotransposon-interrupted ORF as '''''MOC1''''' was achieved by functional complementation<ref name="ref1" />. Genetic analysis with reciprocal crosses between moc1 and wild-type plants revealed that '''''moc1''''' possesses a recessive mutation in a single nuclear locus<ref name="ref1" />.
We can see the effects of '''''moc1''''' mutant on rice tillering from the following picture 2.
[[File:Moc1 mutant.jpg|right|thumb|150px|''Figure 2． Phenotype and complementation of the moc1 mutant.(from reference <ref name="ref1" />).'']]

===Expression===
The '''''MOC1''''' spatial and temporal expression patterns revealed by RNA in situ hybridization are consistent with the function of '''''MOC1''''' for axillary meristem initiation and tiller bud formation. '''''MOC1''''' expression is detectable in a small number of epidermal or subepidermal cells at the leaf axils before any visible morphological changes at the position where axillary meristems will initiate. Thereafter, '''''MOC1''''' is mainly expressed in the protuberance and axillary meristem and extended to the entire tiller bud including the axillary leaf primordia and young leaves, whereas no signal could be observed in the shoot apical meristem (SAM) <ref name="ref1" />.
Slight overexpression of the '''''MOC1''''' gene can increased tiller number and reduced plant height<ref name="ref1" />.

{| class='wikitable' style="text-align:center"
|-
! | Primer
! | Forward primer
! | Reverse primer
|-
| rowspan="1"|Gene amplication
| | 5’ -TCGTTGTAGTAGCTCT GGTG-3’
| | 5’-CTAACTAGAGATCGAGTAGC-3'<ref name="ref1" />
|-
| rowspan="1"|RT-PCR
| | 5'-AGACGCTCGCCGTGAACT-3'
| | 5'-GCCTTCACCCACTTCAAGA-3'<ref name="ref8" />
|}

===Evolution===
'''''MONOCULM1'''''('''''MOC1''''') genomic regions were sequenced and compared across 14 Oryza genomes by Lu et al, and the result of genomic alignment of the '''''MOC1''''' region in 18 Oryza genomes or subgenomes can be seen from Fig.3<ref name="ref2" />.
[[File:Evolution fig3.jpg|right|thumb|150px|Fig. 3. Genomic alignment of the MOC1 region in 18 Oryza genomes or subgenomes. The species are ordered by genome type. Horizontal light blue bars represent genomic sequence in the MOC1 region. Gene models are shown in black rectangles. Transposons (at least 1 kb) are shown in red and pink for retrotransposons and DNA transposons, respectively. Lines/curves connect orthologous genes with each other and orthologous transposons with each other(from reference<ref name="ref2" />)'']]
 
Sequencing and annotation of the '''''MOC1''''' region of the 14 Oryza species, including 10 diploids and 4 allotetraploids, revealed highly conserved gene colinearity and structure in the '''''MOC1''''' region<ref name="ref2" />. Large and apparently noncoding sequences flanking the '''''MOC1''''' gene were observed to be under strong purifying selection<ref name="ref2" />. '''''MOC1''''' is highly homologous with the tomato Lateral suppressor ('''''Ls''''') gene. Rice '''''MONOCULM1''''' ('''''MOC1''''') and Arabidopsis '''''LATERAL SUPPRESSOR''''' ('''''LAS''''') are orthologs, which play important roles in axillary meristems initiation in rice and Arabidopsis<ref name="ref1" /><ref name="ref9" />.

===Knowledge Extension===
'''''TEOSINTE BRANCHED1''''' ('''''TB1''''') encodes a putative transcription factor of the TCP protein family, and impairment of '''''TB1''''' leading to enhance lateral branching in maize suggests its negative regulatory role in controlling the axillary bud outgrowth<ref name="ref10" /><ref name="ref11" />. The rice ortholog '''''OsTB1'''''/'''''FINE CULM1''''' ('''''FC1''''') shows similar characteristics and therefore also negatively regulates rice tillering <ref name="ref12" />. Consistent with the function of '''''TB1''''' in maize, overexpression of '''''OsTB1''''' reduces rice tillers severely while its loss-of-function mutation in the classical mutant fine culm (fcn1) promotes the outgrowth of rice tillers<ref name="ref7" />. The results reveal that the pivotal role of '''''OsTB1''''' is to control the outgrowth of rice tiller buds rather than the initiation of tiller buds<ref name="ref12" />. D10 also functions as a negative regulator and works independently of '''''OsTB1'''''/'''''FC1''''' in rice<ref name="ref13" />.

===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 = Os06g0165600|
Description = CRT/DRE binding factor (Transcription factor RCBF4)|
Version = NM_001063444.1 GI:115466619 GeneID:4340239|
Length = 904 bp|
Definition = Oryza sativa Japonica Group Os06g0165600, 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 6|Chromosome 6]]|
AP = Chromosome 6:3309920..3310823|
CDS = 3309944..3310705|
GCID = <gbrowseImage1>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtag</cdnaseq>|
AA = <aaseq>MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVR WRGCAGRWVCKVRVPGSRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAW LLHVPRAPVVSGLRPPAARCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAP VLSAKQCEFIFLSSLDCWMLMSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYI ILQMNSMIVLIHELSKYQVFLLLTMITHHLFQWRR</aaseq>|
DNA = <dnaseqindica>25..786#actgcttgagacgtcgcacacgtcatggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtaggcgcggacgccctcgccatcatcgtcgatgtcgccactgatgacgaggtccgcgccgctcaccagctcgcacgcctcgtcgtcgtccatgctcgccacctcggtccagcagctgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063444.1 RefSeq:Os06g0165600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0165600

2014-05-22T08:10:08Z

Yimoukong: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The '''''OsDREB1D'''''， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The over-expression of '''''OsDREB1D''''',a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).<ref name="ref1" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. This '''''OsDREB1D''''' gene functions similarly as other DREB transcription factors <ref name="ref1" />.
[[File:Figure 1.Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.png|right|thumb|150px|Figure 1. Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.png(from reference <ref name="ref1" />).'']]

===Mutation===
To identify genes involved in the control of rice tillering, Li et al. have screened for mutants with altered tiller numbers from collections derived from spontaneous mutations or g-ray radiation and ethyl methanesulphonate (EMS) mutagenesis, and they found that '''''moc1''''' plants nearly completely lose their tillering ability after a spontaneous '''''moc1''''' mutant, producing only one main culm, in contrast to the multiple tillers in wild-type plants<ref name="ref1" />. They amplified the corresponding ORF from '''''moc1''''' and wild-type plants with polymerase chain reaction (PCR) and sequenced it. DNA sequence comparison revealed a 1.9-kb retrotransposon inserted in this ORF in the '''''moc1''''' mutant. Confirmation of the retrotransposon-interrupted ORF as '''''MOC1''''' was achieved by functional complementation<ref name="ref1" />. Genetic analysis with reciprocal crosses between moc1 and wild-type plants revealed that '''''moc1''''' possesses a recessive mutation in a single nuclear locus<ref name="ref1" />.
We can see the effects of '''''moc1''''' mutant on rice tillering from the following picture 2.
[[File:Moc1 mutant.jpg|right|thumb|150px|''Figure 2． Phenotype and complementation of the moc1 mutant.(from reference <ref name="ref1" />).'']]

===Expression===
The '''''MOC1''''' spatial and temporal expression patterns revealed by RNA in situ hybridization are consistent with the function of '''''MOC1''''' for axillary meristem initiation and tiller bud formation. '''''MOC1''''' expression is detectable in a small number of epidermal or subepidermal cells at the leaf axils before any visible morphological changes at the position where axillary meristems will initiate. Thereafter, '''''MOC1''''' is mainly expressed in the protuberance and axillary meristem and extended to the entire tiller bud including the axillary leaf primordia and young leaves, whereas no signal could be observed in the shoot apical meristem (SAM) <ref name="ref1" />.
Slight overexpression of the '''''MOC1''''' gene can increased tiller number and reduced plant height<ref name="ref1" />.

{| class='wikitable' style="text-align:center"
|-
! | Primer
! | Forward primer
! | Reverse primer
|-
| rowspan="1"|Gene amplication
| | 5’ -TCGTTGTAGTAGCTCT GGTG-3’
| | 5’-CTAACTAGAGATCGAGTAGC-3'<ref name="ref1" />
|-
| rowspan="1"|RT-PCR
| | 5'-AGACGCTCGCCGTGAACT-3'
| | 5'-GCCTTCACCCACTTCAAGA-3'<ref name="ref8" />
|}

===Evolution===
'''''MONOCULM1'''''('''''MOC1''''') genomic regions were sequenced and compared across 14 Oryza genomes by Lu et al, and the result of genomic alignment of the '''''MOC1''''' region in 18 Oryza genomes or subgenomes can be seen from Fig.3<ref name="ref2" />.
[[File:Evolution fig3.jpg|right|thumb|150px|Fig. 3. Genomic alignment of the MOC1 region in 18 Oryza genomes or subgenomes. The species are ordered by genome type. Horizontal light blue bars represent genomic sequence in the MOC1 region. Gene models are shown in black rectangles. Transposons (at least 1 kb) are shown in red and pink for retrotransposons and DNA transposons, respectively. Lines/curves connect orthologous genes with each other and orthologous transposons with each other(from reference<ref name="ref2" />)'']]
 
Sequencing and annotation of the '''''MOC1''''' region of the 14 Oryza species, including 10 diploids and 4 allotetraploids, revealed highly conserved gene colinearity and structure in the '''''MOC1''''' region<ref name="ref2" />. Large and apparently noncoding sequences flanking the '''''MOC1''''' gene were observed to be under strong purifying selection<ref name="ref2" />. '''''MOC1''''' is highly homologous with the tomato Lateral suppressor ('''''Ls''''') gene. Rice '''''MONOCULM1''''' ('''''MOC1''''') and Arabidopsis '''''LATERAL SUPPRESSOR''''' ('''''LAS''''') are orthologs, which play important roles in axillary meristems initiation in rice and Arabidopsis<ref name="ref1" /><ref name="ref9" />.

===Knowledge Extension===
'''''TEOSINTE BRANCHED1''''' ('''''TB1''''') encodes a putative transcription factor of the TCP protein family, and impairment of '''''TB1''''' leading to enhance lateral branching in maize suggests its negative regulatory role in controlling the axillary bud outgrowth<ref name="ref10" /><ref name="ref11" />. The rice ortholog '''''OsTB1'''''/'''''FINE CULM1''''' ('''''FC1''''') shows similar characteristics and therefore also negatively regulates rice tillering <ref name="ref12" />. Consistent with the function of '''''TB1''''' in maize, overexpression of '''''OsTB1''''' reduces rice tillers severely while its loss-of-function mutation in the classical mutant fine culm (fcn1) promotes the outgrowth of rice tillers<ref name="ref7" />. The results reveal that the pivotal role of '''''OsTB1''''' is to control the outgrowth of rice tiller buds rather than the initiation of tiller buds<ref name="ref12" />. D10 also functions as a negative regulator and works independently of '''''OsTB1'''''/'''''FC1''''' in rice<ref name="ref13" />.

===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 = Os06g0165600|
Description = CRT/DRE binding factor (Transcription factor RCBF4)|
Version = NM_001063444.1 GI:115466619 GeneID:4340239|
Length = 904 bp|
Definition = Oryza sativa Japonica Group Os06g0165600, 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 6|Chromosome 6]]|
AP = Chromosome 6:3309920..3310823|
CDS = 3309944..3310705|
GCID = <gbrowseImage1>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtag</cdnaseq>|
AA = <aaseq>MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVR WRGCAGRWVCKVRVPGSRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAW LLHVPRAPVVSGLRPPAARCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAP VLSAKQCEFIFLSSLDCWMLMSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYI ILQMNSMIVLIHELSKYQVFLLLTMITHHLFQWRR</aaseq>|
DNA = <dnaseqindica>25..786#actgcttgagacgtcgcacacgtcatggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtaggcgcggacgccctcgccatcatcgtcgatgtcgccactgatgacgaggtccgcgccgctcaccagctcgcacgcctcgtcgtcgtccatgctcgccacctcggtccagcagctgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063444.1 RefSeq:Os06g0165600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0165600

2014-05-22T08:08:46Z

Yimoukong: /* Function */

Please input one-sentence summary here.

==Annotated Information==
===Function===
The '''''OsDREB1D'''''， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The over-expression of '''''OsDREB1D''''',a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).<ref name="ref1" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. This '''''OsDREB1D''''' gene functions similarly as other DREB transcription factors <ref name="ref1" />.
[[File:Figure 1. Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.png|right|thumb|150px|Figure 1. Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.(from reference <ref name="ref1" />).'']]

===Mutation===
To identify genes involved in the control of rice tillering, Li et al. have screened for mutants with altered tiller numbers from collections derived from spontaneous mutations or g-ray radiation and ethyl methanesulphonate (EMS) mutagenesis, and they found that '''''moc1''''' plants nearly completely lose their tillering ability after a spontaneous '''''moc1''''' mutant, producing only one main culm, in contrast to the multiple tillers in wild-type plants<ref name="ref1" />. They amplified the corresponding ORF from '''''moc1''''' and wild-type plants with polymerase chain reaction (PCR) and sequenced it. DNA sequence comparison revealed a 1.9-kb retrotransposon inserted in this ORF in the '''''moc1''''' mutant. Confirmation of the retrotransposon-interrupted ORF as '''''MOC1''''' was achieved by functional complementation<ref name="ref1" />. Genetic analysis with reciprocal crosses between moc1 and wild-type plants revealed that '''''moc1''''' possesses a recessive mutation in a single nuclear locus<ref name="ref1" />.
We can see the effects of '''''moc1''''' mutant on rice tillering from the following picture 2.
[[File:Moc1 mutant.jpg|right|thumb|150px|''Figure 2． Phenotype and complementation of the moc1 mutant.(from reference <ref name="ref1" />).'']]

===Expression===
The '''''MOC1''''' spatial and temporal expression patterns revealed by RNA in situ hybridization are consistent with the function of '''''MOC1''''' for axillary meristem initiation and tiller bud formation. '''''MOC1''''' expression is detectable in a small number of epidermal or subepidermal cells at the leaf axils before any visible morphological changes at the position where axillary meristems will initiate. Thereafter, '''''MOC1''''' is mainly expressed in the protuberance and axillary meristem and extended to the entire tiller bud including the axillary leaf primordia and young leaves, whereas no signal could be observed in the shoot apical meristem (SAM) <ref name="ref1" />.
Slight overexpression of the '''''MOC1''''' gene can increased tiller number and reduced plant height<ref name="ref1" />.

{| class='wikitable' style="text-align:center"
|-
! | Primer
! | Forward primer
! | Reverse primer
|-
| rowspan="1"|Gene amplication
| | 5’ -TCGTTGTAGTAGCTCT GGTG-3’
| | 5’-CTAACTAGAGATCGAGTAGC-3'<ref name="ref1" />
|-
| rowspan="1"|RT-PCR
| | 5'-AGACGCTCGCCGTGAACT-3'
| | 5'-GCCTTCACCCACTTCAAGA-3'<ref name="ref8" />
|}

===Evolution===
'''''MONOCULM1'''''('''''MOC1''''') genomic regions were sequenced and compared across 14 Oryza genomes by Lu et al, and the result of genomic alignment of the '''''MOC1''''' region in 18 Oryza genomes or subgenomes can be seen from Fig.3<ref name="ref2" />.
[[File:Evolution fig3.jpg|right|thumb|150px|Fig. 3. Genomic alignment of the MOC1 region in 18 Oryza genomes or subgenomes. The species are ordered by genome type. Horizontal light blue bars represent genomic sequence in the MOC1 region. Gene models are shown in black rectangles. Transposons (at least 1 kb) are shown in red and pink for retrotransposons and DNA transposons, respectively. Lines/curves connect orthologous genes with each other and orthologous transposons with each other(from reference<ref name="ref2" />)'']]
 
Sequencing and annotation of the '''''MOC1''''' region of the 14 Oryza species, including 10 diploids and 4 allotetraploids, revealed highly conserved gene colinearity and structure in the '''''MOC1''''' region<ref name="ref2" />. Large and apparently noncoding sequences flanking the '''''MOC1''''' gene were observed to be under strong purifying selection<ref name="ref2" />. '''''MOC1''''' is highly homologous with the tomato Lateral suppressor ('''''Ls''''') gene. Rice '''''MONOCULM1''''' ('''''MOC1''''') and Arabidopsis '''''LATERAL SUPPRESSOR''''' ('''''LAS''''') are orthologs, which play important roles in axillary meristems initiation in rice and Arabidopsis<ref name="ref1" /><ref name="ref9" />.

===Knowledge Extension===
'''''TEOSINTE BRANCHED1''''' ('''''TB1''''') encodes a putative transcription factor of the TCP protein family, and impairment of '''''TB1''''' leading to enhance lateral branching in maize suggests its negative regulatory role in controlling the axillary bud outgrowth<ref name="ref10" /><ref name="ref11" />. The rice ortholog '''''OsTB1'''''/'''''FINE CULM1''''' ('''''FC1''''') shows similar characteristics and therefore also negatively regulates rice tillering <ref name="ref12" />. Consistent with the function of '''''TB1''''' in maize, overexpression of '''''OsTB1''''' reduces rice tillers severely while its loss-of-function mutation in the classical mutant fine culm (fcn1) promotes the outgrowth of rice tillers<ref name="ref7" />. The results reveal that the pivotal role of '''''OsTB1''''' is to control the outgrowth of rice tiller buds rather than the initiation of tiller buds<ref name="ref12" />. D10 also functions as a negative regulator and works independently of '''''OsTB1'''''/'''''FC1''''' in rice<ref name="ref13" />.

===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 = Os06g0165600|
Description = CRT/DRE binding factor (Transcription factor RCBF4)|
Version = NM_001063444.1 GI:115466619 GeneID:4340239|
Length = 904 bp|
Definition = Oryza sativa Japonica Group Os06g0165600, 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 6|Chromosome 6]]|
AP = Chromosome 6:3309920..3310823|
CDS = 3309944..3310705|
GCID = <gbrowseImage1>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtag</cdnaseq>|
AA = <aaseq>MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVR WRGCAGRWVCKVRVPGSRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAW LLHVPRAPVVSGLRPPAARCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAP VLSAKQCEFIFLSSLDCWMLMSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYI ILQMNSMIVLIHELSKYQVFLLLTMITHHLFQWRR</aaseq>|
DNA = <dnaseqindica>25..786#actgcttgagacgtcgcacacgtcatggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtaggcgcggacgccctcgccatcatcgtcgatgtcgccactgatgacgaggtccgcgccgctcaccagctcgcacgcctcgtcgtcgtccatgctcgccacctcggtccagcagctgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063444.1 RefSeq:Os06g0165600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

2014-05-22T00:55:10Z

Yimoukong: /* Function */

Please input one-sentence summary here.

==Annotated Information==
OsDREB1D, a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.the over-expression of OsDREB1Dconferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).This OsDREB1D gene functions similarly as other DREB transcription factors.[1]

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

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

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

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

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0165600|
Description = CRT/DRE binding factor (Transcription factor RCBF4)|
Version = NM_001063444.1 GI:115466619 GeneID:4340239|
Length = 904 bp|
Definition = Oryza sativa Japonica Group Os06g0165600, 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 6|Chromosome 6]]|
AP = Chromosome 6:3309920..3310823|
CDS = 3309944..3310705|
GCID = <gbrowseImage1>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:3309920..3310823
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtag</cdnaseq>|
AA = <aaseq>MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVR WRGCAGRWVCKVRVPGSRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAW LLHVPRAPVVSGLRPPAARCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAP VLSAKQCEFIFLSSLDCWMLMSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYI ILQMNSMIVLIHELSKYQVFLLLTMITHHLFQWRR</aaseq>|
DNA = <dnaseqindica>25..786#actgcttgagacgtcgcacacgtcatggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtaggcgcggacgccctcgccatcatcgtcgatgtcgccactgatgacgaggtccgcgccgctcaccagctcgcacgcctcgtcgtcgtccatgctcgccacctcggtccagcagctgaacc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001063444.1 RefSeq:Os06g0165600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]