http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=LiyisongRiceWiki - User contributions [en]2026-08-27T17:48:41ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=182643Os07g01247002014-06-09T13:43:48Z<p>Liyisong: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:treelyss.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
3. CRL5 shares significant sequence similarity with AINTEGUMENTA (ANT) containing 2 AP2 domains in Arabidopsis.<ref name="ref4" /><ref name="ref2" /><br />
<br />
5. Seven AINTEGUMENTA-like (AIL)/PLETHORA (PLT) proteins were reported to share high sequence similarity with ANT.<ref name="ref5" /><ref name="ref2" /><br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
4. It has been reported that a reduction of crown root number commonly occurs in auxin-related mutants in rice<ref name="ref6" /><ref name="ref7" /><ref name="ref8" /><ref name="ref9" />.An abnormality in gravitropic response is also a characteristic auxin-related phenotype in both rice and Arabidopsis<ref name="ref10" /><ref name="ref11" />.Thus,we examined the root gravitropic response in crl5 by measuring root curvature after gravistimulation at 90° for 24 h, followed by a return to vertical growth. In general, wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl5 roots was clearly impaired. Comparing the root tip angles, all wild-type roots had root tip angles of over 35°(average 51.1± 2.6°), whereas all crl5 roots had angles of below 55° (average 31.1 ± 2.9°) (Figure 1i). The gravitropic response was therefore defective in crl5, which suggests that CRL5 has an auxin-related function.<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
<br />
<ref name="ref4">Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth.Plant Cell 1996; 8:155-68; PMID:8742707; DOI:10.1105/tpc.8.2.155.</ref><br />
<br />
<ref name="ref5">Nole-Wilson S, Tranby TL, Krizek BA.AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or divisioncompetent<br />
states. Plant Mol Biol 2005; 57:613-28; PMID:15988559; DOI:10.1007/s11103-005-0955-6.</ref><br />
<br />
<ref name="ref6">Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., Shibata, Y., Gomi, K., Umemura, I., Hasegawa, Y., Ashikari, M., Kitano, H. and Matsuoka, M. (2005)<br />
Crown Rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin Signaling. Plant Cell, 17, 1387–1396.</ref><br />
<br />
<ref name="ref7">Liu, H., Wang, S., Yu, X., Yu, J., He, X., Zhang, S., Shou, H. and Wu, P. (2005) ARL1, a LOB domain protein required for adventitious root ormation in rice. Plant J. 43, 47–56.</ref><br />
<br />
<ref name="ref8">Kitomi, Y., Ogawa, A., Kitano, H. and Inukai, Y. (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root, 2, 19–28.</ref><br />
<br />
<ref name="ref9">Liu, S., Wang, J., Wang, L., Wang, X., Xue, Y., Wu, P. and Shou, H. (2009) Adventitious root formation in rice requires OsGNOM1 and is mediated by<br />
the OsPINs family. Cell Res. 19, 1110–1119.</ref><br />
<br />
<ref name="ref10">Leyser, H.M., Pickett, F.B., Dharmasiri, S. and Estelle, M. (1996) Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR-AC1 promoter. Plant J. 10, 403–413.</ref><br />
<br />
<ref name="ref11">Tian, Q. and Reed, J.W. (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development, 126, 711–721.</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=182640Os07g01247002014-06-09T13:42:15Z<p>Liyisong: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:treelyss.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
3. CRL5 shares significant sequence similarity with AINTEGUMENTA (ANT) containing 2 AP2 domains in Arabidopsis.<ref name="ref4" /><ref name="ref2" /><br />
<br />
5. Seven AINTEGUMENTA-like (AIL)/PLETHORA (PLT) proteins were reported to share high sequence similarity with ANT.<ref name="ref5" /><ref name="ref2" /><br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
4. It has been reported that a reduction of crown root number commonly occurs in auxin-related mutants in rice<ref name="ref6" /><ref name="ref7" /><ref name="ref8" /><ref name="ref9" />.An abnormality in gravitropic response is also a characteristic auxin-related phenotype in both rice and Arabidopsis<ref name="ref10" /><ref name="ref11" />.Thus,we examined the root gravitropic response in crl5 by measuring root curvature after gravistimulation at 90° for 24 h, followed by a return to vertical growth. In general, wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl5 roots was clearly impaired. Comparing the root tip angles, all wild-type roots had root tip angles of over 35°(average 51.1± 2.6°), whereas all crl5 roots had angles of below 55° (average 31.1 ± 2.9°) (Figure 1i). The gravitropic response was therefore defective in crl5, which suggests that CRL5 has an auxin-related function.<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
<br />
<ref name="ref4">Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth.Plant Cell 1996; 8:155-68; PMID:8742707; DOI:10.1105/tpc.8.2.155.</ref><br />
<br />
<ref name="ref5">Nole-Wilson S, Tranby TL, Krizek BA.AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or divisioncompetent<br />
states. Plant Mol Biol 2005; 57:613-28; PMID:15988559; DOI:10.1007/s11103-005-0955-6.<br />
<br />
<ref name="ref6">Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., Shibata, Y., Gomi, K., Umemura, I., Hasegawa, Y., Ashikari, M., Kitano, H. and Matsuoka, M. (2005)<br />
Crown Rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin Signaling. Plant Cell, 17, 1387–1396.<br />
<br />
<ref name="ref7">Liu, H., Wang, S., Yu, X., Yu, J., He, X., Zhang, S., Shou, H. and Wu, P. (2005) ARL1, a LOB domain protein required for adventitious root ormation in rice. Plant J. 43, 47–56.<br />
<br />
<ref name="ref8">Kitomi, Y., Ogawa, A., Kitano, H. and Inukai, Y. (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root, 2, 19–28.<br />
<br />
<ref name="ref9">Liu, S., Wang, J., Wang, L., Wang, X., Xue, Y., Wu, P. and Shou, H. (2009) Adventitious root formation in rice requires OsGNOM1 and is mediated by<br />
the OsPINs family. Cell Res. 19, 1110–1119.<br />
<br />
<ref name="ref10">Leyser, H.M., Pickett, F.B., Dharmasiri, S. and Estelle, M. (1996) Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR-AC1 promoter. Plant J. 10, 403–413.<br />
<br />
<ref name="ref11">Tian, Q. and Reed, J.W. (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development, 126, 711–721.<br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=182634Os07g01247002014-06-09T13:39:34Z<p>Liyisong: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:treelyss.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
3. CRL5 shares significant sequence similarity with AINTEGUMENTA (ANT) containing 2 AP2 domains in Arabidopsis.<ref name="ref4" /><ref name="ref2" /><br />
<br />
5. Seven AINTEGUMENTA-like (AIL)/PLETHORA (PLT) proteins were reported to share high sequence similarity with ANT.<ref name="ref5" /><ref name="ref2" /><br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
4. It has been reported that a reduction of crown root number commonly occurs in auxin-related mutants in rice<ref name="ref6" /><ref name="ref7" /><ref name="ref8" /><ref name="ref9" />.An abnormality in gravitropic response is also a characteristic auxin-related phenotype in both rice and Arabidopsis<ref name="ref10" /><ref name="ref11" />.Thus,we examined the root gravitropic response in crl5 by measuring root curvature (h in Figure 1j) after gravistimulation at 90� for 24 h, followed by a return to vertical growth. In general, wild-type roots responded sharply to the change in the gravity vector, whereas the response of crl5 roots was clearly impaired (Figure 1i). Comparing the root tip angles, all wild-type roots had root tip angles of over 35� (average 51.1 � 2.6�), whereas all crl5 roots had angles of below 55� (average 31.1 � 2.9�) (Figure 1i). The gravitropic response was therefore defective in crl5, which suggests that CRL5 has an auxin-related function.<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
<br />
<ref name="ref4">Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth.Plant Cell 1996; 8:155-68; PMID:8742707; DOI:10.1105/tpc.8.2.155.</ref><br />
<br />
<ref name="ref5">Nole-Wilson S, Tranby TL, Krizek BA.AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or divisioncompetent<br />
states. Plant Mol Biol 2005; 57:613-28; PMID:15988559; DOI:10.1007/s11103-005-0955-6.<br />
<br />
<ref name="ref6">Inukai, Y., Sakamoto, T., Ueguchi-Tanaka, M., Shibata, Y., Gomi, K., Umemura, I., Hasegawa, Y., Ashikari, M., Kitano, H. and Matsuoka, M. (2005)<br />
Crown Rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin Signaling. Plant Cell, 17, 1387–1396.<br />
<br />
<ref name="ref7">Liu, H., Wang, S., Yu, X., Yu, J., He, X., Zhang, S., Shou, H. and Wu, P. (2005) ARL1, a LOB domain protein required for adventitious root ormation in rice. Plant J. 43, 47–56.<br />
<br />
<ref name="ref8">Kitomi, Y., Ogawa, A., Kitano, H. and Inukai, Y. (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root, 2, 19–28.<br />
<br />
<ref name="ref9">Liu, S., Wang, J., Wang, L., Wang, X., Xue, Y., Wu, P. and Shou, H. (2009) Adventitious root formation in rice requires OsGNOM1 and is mediated by<br />
the OsPINs family. Cell Res. 19, 1110–1119.<br />
<br />
<ref name="ref10">Leyser, H.M., Pickett, F.B., Dharmasiri, S. and Estelle, M. (1996) Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR-AC1 promoter. Plant J. 10, 403–413.<br />
<br />
<ref name="ref11">Tian, Q. and Reed, J.W. (1999) Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene. Development, 126, 711–721.<br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=179780Os07g01247002014-06-07T05:05:49Z<p>Liyisong: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:treelyss.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
3. CRL5 shares significant sequence similarity with AINTEGUMENTA (ANT) containing 2 AP2 domains in Arabidopsis.<ref name="ref4" /><ref name="ref2" /><br />
<br />
5. Seven AINTEGUMENTA-like (AIL)/PLETHORA (PLT) proteins were reported to share high sequence similarity with ANT.<ref name="ref5" /><ref name="ref2" /><br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
<br />
<ref name="ref4">Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth.Plant Cell 1996; 8:155-68; PMID:8742707; DOI:10.1105/tpc.8.2.155.</ref><br />
<br />
<ref name="ref5">Nole-Wilson S, Tranby TL, Krizek BA.AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or divisioncompetent<br />
states. Plant Mol Biol 2005; 57:613-28; PMID:15988559; DOI:10.1007/s11103-005-0955-6.<br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Treelyss.png&diff=179778File:Treelyss.png2014-06-07T05:05:18Z<p>Liyisong: new</p>
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<div> new</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Tree.png&diff=179776File:Tree.png2014-06-07T05:02:05Z<p>Liyisong: uploaded a new version of &quot;File:Tree.png&quot;: Reverted to version as of 14:22, 1 June 2014</p>
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<div></div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=176291Os07g01247002014-06-02T14:26:03Z<p>Liyisong: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
3. CRL5 shares significant sequence similarity with AINTEGUMENTA (ANT) containing 2 AP2 domains in Arabidopsis.<ref name="ref4" /><ref name="ref2" /><br />
<br />
5. Seven AINTEGUMENTA-like (AIL)/PLETHORA (PLT) proteins were reported to share high sequence similarity with ANT.<ref name="ref5" /><ref name="ref2" /><br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
<br />
<ref name="ref4">Elliott RC, Betzner AS, Huttner E, Oakes MP, Tucker WQ, Gerentes D, et al. AINTEGUMENTA, an APETALA2-like gene of Arabidopsis with pleiotropic roles in ovule development and floral organ growth.Plant Cell 1996; 8:155-68; PMID:8742707; DOI:10.1105/tpc.8.2.155.</ref><br />
<br />
<ref name="ref5">Nole-Wilson S, Tranby TL, Krizek BA.AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or divisioncompetent<br />
states. Plant Mol Biol 2005; 57:613-28; PMID:15988559; DOI:10.1007/s11103-005-0955-6.<br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175993Os07g01247002014-06-02T04:58:12Z<p>Liyisong: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<ref name="ref1" /><br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<ref name="ref1" /><br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<ref name="ref1" /><br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175991Os07g01247002014-06-02T04:57:39Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <ref name="ref1" /><br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <ref name="ref1" /><br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<ref name="ref1" /><br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175961Os07g01247002014-06-02T04:34:55Z<p>Liyisong: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==Labs working on this gene==<br />
1. Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175954Os07g01247002014-06-02T04:21:24Z<p>Liyisong: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
<br />
<ref name="ref3"> Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175953Os07g01247002014-06-02T04:20:24Z<p>Liyisong: /* Proposed Gene Regulatory Pathways */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
1. The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
2. However, we found that CRL5 is not a master switch for crown root initiation: upon exogenous application, auxin can increase crown roots in rice seedlings.<ref name="ref3" /><br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175949Os07g01247002014-06-02T04:04:15Z<p>Liyisong: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<ref name="ref1" /><br />
<br />
[[File:d.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:D.png&diff=175948File:D.png2014-06-02T04:03:40Z<p>Liyisong: </p>
<hr />
<div></div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175947Os07g01247002014-06-02T04:03:17Z<p>Liyisong: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
1. Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
2. Comparison of the amino acid sequences of two AP2 domains and the conserved intervening linker region in CRL5, CRL5-like1 and CRL5-like2 from rice, and ANT, PLT1 and PLT2 from Arabidopsis.<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175940Os07g01247002014-06-02T03:44:40Z<p>Liyisong: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2"> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175938Os07g01247002014-06-02T03:44:16Z<p>Liyisong: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2" /> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175937Os07g01247002014-06-02T03:43:48Z<p>Liyisong: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<ref name="ref1" /><br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<ref name="ref1" /><br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2" /> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175935Os07g01247002014-06-02T03:42:21Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<ref name="ref2" /><br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2" /> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175934Os07g01247002014-06-02T03:41:37Z<p>Liyisong: /* References */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
<ref name="ref2" /> Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175933Os07g01247002014-06-02T03:41:07Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1" /><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175932Os07g01247002014-06-02T03:40:15Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175930Os07g01247002014-06-02T03:40:04Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"><br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175929Os07g01247002014-06-02T03:39:23Z<p>Liyisong: /* Annotated Information */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175928Os07g01247002014-06-02T03:38:58Z<p>Liyisong: Undo revision 175926 by Liyisong (talk)</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175926Os07g01247002014-06-02T03:37:39Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175924Os07g01247002014-06-02T03:37:03Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175921Os07g01247002014-06-02T03:34:46Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
<references><br />
1.<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175920Os07g01247002014-06-02T03:33:21Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
1.<ref name="ref1"> Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.</ref><br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175918Os07g01247002014-06-02T03:31:41Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<ref name="ref1"> <br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5. Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175905Os07g01247002014-06-02T03:04:33Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 Mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175903Os07g01247002014-06-02T03:03:34Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175902Os07g01247002014-06-02T03:03:13Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175901Os07g01247002014-06-02T03:02:31Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).[[File:hg.png|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175900Os07g01247002014-06-02T03:02:11Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).[[File:hg.png|central|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175897Os07g01247002014-06-02T03:01:49Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).[[File:hg.png|left|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175896Os07g01247002014-06-02T03:01:25Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).[[File:hg.png|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175894Os07g01247002014-06-02T03:00:42Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).[[File:hg.png|right|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175893Os07g01247002014-06-02T03:00:18Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png|right|thumb|400px|]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175891Os07g01247002014-06-02T02:58:22Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175890Os07g01247002014-06-02T02:58:12Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)[[File:func.png|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175888Os07g01247002014-06-02T02:57:49Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)[[File:func.png|right|thumb|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175887Os07g01247002014-06-02T02:57:19Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|left|thumb|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175886Os07g01247002014-06-02T02:56:57Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|right|thumb|500px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175885Os07g01247002014-06-02T02:56:09Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[File:func.png|right|thumb|200px|]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175876Os07g01247002014-06-02T02:42:19Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown(finger.g)<br />
<br />
[[file:func.png]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175874Os07g01247002014-06-02T02:41:53Z<p>Liyisong: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
<br />
1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
<br />
2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
<br />
3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
<br />
4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
<br />
5.Schematic diagram of the de novo root initiation. CRL5 may function in de-differentiated cells (highlighted) to promote root initiation, not in the de-differentiation process. The factor inducing the de-differentiation is unknown.<br />
<br />
[[file:func.png]]<br />
<br />
===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
<br />
[[File:tree.png]]<br />
<br />
===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
<br />
2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
<br />
3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
<br />
[[File:ae.png]]<br />
<br />
[[File:ig.png]]<br />
<br />
==Proposed Gene Regulatory Pathways ==<br />
<br />
The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
<br />
[[File:pathway.png]]<br />
<br />
==Characterization of the crl5 mutant ==<br />
<br />
1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
<br />
[[File:mutate.png]]<br />
<br />
2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
<br />
3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
<br />
[[File:hg.png]]<br />
<br />
==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
<br />
2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Func.png&diff=175871File:Func.png2014-06-02T02:40:53Z<p>Liyisong: </p>
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<div></div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os07g0124700&diff=175866Os07g01247002014-06-02T02:35:40Z<p>Liyisong: /* Characterization of the crl5 mutant */</p>
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<div>Please input one-sentence summary here.<br />
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==Annotated Information==<br />
===Function===<br />
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1. CRL5 encodes a member of the APETALA2 (AP2)/EHYLENE RESPONSIVE FACTOR (ERF) transcription factor family.<br />
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2. CRL5 functions downstream of the AUXIN (AUX)/INDOLE-3-ACETIC ACID (IAA) and AUXIN RESPONSE FACTOR (ARF)-mediated auxin signaling pathways involved in crown root initiation. <br />
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3. Further analysis revealed that CRL5 upregulates a type-A response regulator(RR) of cytokinin signaling, OsRR1. <br />
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4. It indicated that auxin-induced CRL5 functions as a positive regulator of crown root initiation through repression of cytokinin signaling.<br />
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===Evolution===<br />
Through a BLAST search using the amino acid sequence of CRL5, there are two homologous genes in rice, CRL5-like1 and CRL5-like2, which shared 57 and 49% amino acid identity,respectively, with CRL5.<br />
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[[File:tree.png]]<br />
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===Expression===<br />
1. CRL5 expression in various organs of wild-type rice as determined by semi-quantitative RT-PCR using ACT1 as a control(Figure 3a).CRL5 was expressed in nodes where crown roots were produced. High levels of CRL5 transcripts were observed in floral organs, but as differentiation progressed, CRL5 expression in floral organs was clearly downregulated (Figure 3a).<br />
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2. Localized GFP signal of ProCRL5:GFP in a crown root tip (b), crown root with emerging lateral roots (c), lateral root primordium (d) and stem base of the plant(Figure 3b-e).<br />
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3. In situ hybridization with cross sections through the nodes in a 7-day-old wild-type plant. Localization of CRL5 in the regions where crown root initiation occurs<br />
(the identical region shown in fb and g), as determined using the antisense (i) and sense probes (j). No signal was detected with the sense probe of CRL5. The red<br />
arrowhead indicates the peripheral cylinder of vascular bundles. Scale bars = 200 lm.(Figure 3i,j).<br />
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[[File:ae.png]]<br />
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[[File:ig.png]]<br />
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==Proposed Gene Regulatory Pathways ==<br />
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The proposed gene regulatory pathways controlling crown root initiation in rice.<br />
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[[File:pathway.png]]<br />
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==Characterization of the crl5 mutant ==<br />
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1. Although wild-type plants (cv. Kinmaze) formed many crown roots by the seedling stage, the number of crown roots produced by crl5 was significantly reduced at the identical stage of development (Figure a,f).<br />
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[[File:mutate.png]]<br />
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2. Comparison of lateral root number between wild-type and crl5. ns, not significant(Figure g).<br />
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3. Comparison of a seminal root length between wild-type and crl5. *, Statistically significant difference from wild-type (P < 0.05)(Figure h).<br />
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[[File:hg.png]]<br />
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==References==<br />
1. Kitomi Y, Ito H, Hobo T, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type‐A response regulator of cytokinin signaling[J]. The Plant Journal, 2011, 67(3): 472-484.<br />
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2. Kitomi Y, Kitano H, Inukai Y. Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice[J]. Plant signaling & behavior, 2011, 6(9): 1276.<br />
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==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os07g0124700|<br />
Description = Similar to PLETHORA1|<br />
Version = NM_001065341.1 GI:115470414 GeneID:4342308|<br />
Length = 4702 bp|<br />
Definition = Oryza sativa Japonica Group Os07g0124700, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|<br />
AP = Chromosome 7:1298598..1303299|<br />
CDS = 1298600..1298630,1298781..1298789,1298901..1298989,1299091..1299164,1300196..1300246<br>,1300439..1300515,1302199..1302863|<br />
GCID = <gbrowseImage1><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008400:1298598..1303299<br />
source=RiceChromosome07<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>aaggaaggccagaccaggaaagggaggcaagtttatctcggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccgctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaa</cdnaseq>|<br />
AA = <aaseq>KEGQTRKGRQVYLGGYDMEEKAARAYDLAALKYWGPSTHINFPL EDYQEELEEMKNMTRQEYVAHLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVSGN KDLYLGTFSTQEEAAEAYDVAAIKFRGLNAVTNFDITRYDVDKIMASNTLLPADLARR NAATTTSKDDHSAAGAGAIVSVHSAADIAVADTLWKATTAPRQQQQHHDDVVLSGADQ AAFSVLHDLVAVDAAAAHQQQQQQQHMSMSAASSLVTSLSNSREGSPDRGGGLSMLFA KPSPAVAASAQQQASTKLMAAPLPLGSWVSSPPASARPPAVSIAHMPLFAAWTDA</aaseq>|<br />
DNA = <dnaseqindica>3..33#184..192#304..392#494..567#1599..1649#1842..1918#3602..4266#agaaggaaggccagaccaggaaagggaggcaaggtaattaattaatcaccttttcttattcaccatcattagcatcattttaatcgtaattactgcctaactaatcactcacaagcttgctcctgttcttcgcttctggttttgtgtgtactactgctgatattgctgcgcctccctgatcagtttatctcggtaagtgttattacattcctcatgtggtaactttacatggtaaaaatgttctcgtggtaaaaagtaaaaataaataaaaaaagttcttttactttggttgggggtgattaggtgggtatgacatggaggagaaagcggcgagagcgtatgacctggcggcgctcaagtattggggcccttccacacacatcaacttcccggtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagctggaggactaccaggaggagctggaggagatgaagaacatgacaaggcaggagtatgtggctcacttaaggaggtaattcataaaaacagattgttcttgttgccaaaatgctgaataaattaatcacttaatctgcactcttcagaaaaatgactagacaaatggatgtatatatacctgcatcatacatagttaatgtcatgcttgcacaaagtcaactaaatgggtaacaccacagcatgtacagtgtcatccgcaccacaatgtaggacacattttagacactttcaaagccattcatggaatatctggatttatgttttaatattgatatgcaataagaaatgatgagctgtacattgtgaaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatatatatatagtaaccaataatcaaaatgatgaataatacatggattatagttatggacaaattagctagtgctatatttaagatagagagtgacgagtgcataatgagaatatgtacttgtttgaagagatgcacataaaactacgagaagtggatttttatctattgaggggatatcatcccctagttttctttataccattcaaatgtcatcaaaatattttttttatatgataaatcaatattaggtatgtcacttcattaacatacaagtttatatttgactacgaatagtatgcactatgtgattaagtacaaacaaatttgactcaatgtgtaatatacatattgttgaactattattcgtgtactaattaattaaggagatcttcctctaatttgggataatggttaataacaacaatataatgatgcaaactttaaaagtatttgttacttgtggtaacgtgcaagttcctataaatatatgcatgtgaatgtgcagagaatggtagtagtatagtactactatagttaacgttcctaccggccagtgtctgaactctgaagaagtctgaacatgtgtgtttgttttggtgtgtggatgcaggaaaagtagcggtttctcacggggagcttccatgtaccgtggtgtcacaaggtaacaatacatacacacacacacatcgatctatcgatcgatcggtacatttgtttatgtactgcacatttccttactgaaaagtacacattttgcattggtgagaaagatatacgtacgtaaattcagaagaagaagagaaaattcagaataaaaatttgtacatgtgttttttggtttgcttatatgcaggcatcatcagcacggacggtggcaggcacgcatcggccgagtctccggcaacaaggacctctacctcggcactttcagtacgaatcattatatcgatcctaattaaattagccttaattattttttctagctctgaataataattctgcaaacacgtacatacatatagtagacgacgacgacgacgtctgcaatgcatgcatgcatggtcgatcgatcgattgatcgtcttttgcatgcatgcctgcctccatgcatgcatgatgagtactatctagtaccaattcatcatgatgcagattcatagcttaattagatcctacacatacatgcttcctccgtcttaaaaaaatcaacttcttgctacgataaatctgaacgtaacctatgtttagatttagtcagaaatatgtttttttctgggaaggagtgcatagatatacaattagagcaggtacaatagcacactataagtcagctataaatacatttatatgagataaaagataagagagaagaccatcacggattccaagatacaatgtatttatgataagtaggaccagatattaatagtgtagtatatgtttataggtaactattatatgaattggctattaaatttactatatactacctccatattttaatgtatggcgccgttgactttttatccaatatttgaccatttgtcttattcaaaaatttatgtaattattatttattttattgtgacttgatttatcatcaaatgttctttaagcatgacataaatattttcatatttgcacaaaaattttgaataaaacgaatggtcaaacgtttatcaaaaagtcaacggcgtcatatattaaaatacggagggagtatgatttaaagctattaattggctataatattaaacttcctcttatgtttatatggatgcaatgtgagagacgatgagaggttgcgtgggcattgcgtttgcatgcggaggctgtcatgctccaggggcacaaccccgtcctgtcacaatgatcattagcatgtcacataattttgcatatactataatactccatttcatacctccatccatcgatcgcatgcaacgcaacgcaaaagctggctatctcttctctctctctctagatcgtctaaagcttacatgtgcatcatgcctccctgccaaagaatgtttctctctctctacactaatcttagagagagagagagagagagatagagagagagagaatgagagagatgaatgtgtgtatgggcctgtgcgtgcagctgcgattctctcacttttgcataaggctgaccgacctagtttgcaaatgcatgcattccctgggcctgcatctgcatatcctttctagtttttacactgtccagccatcgcacgcgcctgcttgctttcttccctgctttctttgaccattttttacgtaacatatgcattgcatattttgcggttatctcagggatcttcctgctaacttcacaaggtcgtgggttaattagatgatctggattcgaaacctcaccccttctaattatttgatattaggtcatttctaatattcgtgtctttttgcattgcttatcgtagcgcatcacattttttaaatgtaaaattaaatattttgcttatcgtagcacatcacatttttagtgtaaaattaaatattttcgattgtaggtataaaattttatagtgtaaaattcagatatctcgaaggatggtaaaatttgtggatggatggatgcaggcacgcaggaggaggcggcggaggcgtacgacgtggcggcgatcaagttccgggggctcaacgccgtcaccaacttcgacatcacccgctacgacgtcgacaagatcatggccagcaacaccctcctccccgccgacctcgcccgccgcaacgccgccaccaccacctccaaggacgaccactccgccgccggcgccggcgccattgtctcggtgcactccgccgccgacatcgccgtcgccgacaccctctggaaggccaccactgccccgaggcagcagcagcagcaccacgacgacgtcgtgctgtccggcgccgaccaggccgcattctccgtcctccacgacctcgtcgccgtcgacgccgcggcggcgcaccagcagcagcagcagcagcagcacatgtccatgtcggcggcgtcgtcgctggtgacgagcctgagcaactcgcgcgaggggagccccgaccgcggcggcggcctctccatgctcttcgccaagccgtcgcccgccgtggcggcgtcggcgcagcagcaggcgtcgaccaagctcatggcggcgccgctgccgctcggctcctgggtctcctcgccgccggcgtctgccaggccgcccgccgtctccatcgcccacatgcccctcttcgccgcctggaccgacgcctaatcaccctcgccgccatggctcaccggagtagtaattagctagctatagctagagctaggcaacgacgacgacgacactagcttaattagctcgtgtttagttggttaatttagggttcttggttgctcggcgacatgattagctaagctagcgatgtagtagtagcactagcagctagttggagtattaattagtatcactcaaggcgaggaaaccgacgcacgccatggccgcggcctctcccccacctttccttcttctccggcgacggccggccgccatgtatcagagagctcgatcggcgccggagaagaagggtttttgtaacacggaggccggagatctatcgaggcggtgcttctcctccaaaatccaaaactatatatcttatattaattaattaattaattatagcctcaccaaattaatttctcaa</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065341.1 RefSeq:Os07g0124700]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 7]]<br />
[[Category:Chromosome 7]]</div>Liyisonghttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Hg.png&diff=175865File:Hg.png2014-06-02T02:35:11Z<p>Liyisong: </p>
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<div></div>Liyisong