Os12g0102400 - Revision history

Rice2012: /* Reference */

2015-06-13T09:13:52Z

‎Reference

Rice2012: /* Reference */

2015-06-13T09:13:27Z

‎Reference

Rice2012 at 09:12, 13 June 2015

2015-06-13T09:12:02Z

Rice2012: /* Reference */

2015-06-13T09:11:21Z

‎Reference

Rice2012: /* Reference */

2015-06-13T09:10:41Z

‎Reference

Lmw2015: /* Structured Information */

2015-06-12T04:30:07Z

‎Structured Information

Liucaixia1214: /* Evolution */

2014-06-10T13:30:21Z

‎Evolution

Liucaixia1214: /* Evolution */

2014-06-10T13:28:07Z

‎Evolution

Liucaixia1214: /* Evolution */

2014-06-10T13:23:42Z

‎Evolution

Liucaixia1214: /* Evolution */

2014-06-10T13:20:19Z

‎Evolution

@@ Line 32: / Line 32: @@
 ==Reference==
-<references>
-<ref name="ref1">
+Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060
-Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060</ref>
 Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.

@@ Line 32: / Line 32: @@
 ==Reference==
+<references>
-Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060
+<ref name="ref1">
+Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060</ref>
 Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.

← Older revision		Revision as of 09:12, 13 June 2015
Line 9:		Line 9:


−	[[File: liu-Os12g0102400-Fig1.jpg\|right\|thumb\|200px\|''Gene identification via enzyme digestion. A: Schematic diagram of the pBIN35S-RINGC2 constructs. Restriction enzyme sites are indicated. B: Restriction profiles of each genes.~~. (from reference <ref name="Jung" />)~~.'']]	+	[[File: liu-Os12g0102400-Fig1.jpg\|right\|thumb\|200px\|''Gene identification via enzyme digestion. A: Schematic diagram of the pBIN35S-RINGC2 constructs. Restriction enzyme sites are indicated. B: Restriction profiles of each genes..'']]

	===Expression===		===Expression===

@@ Line 32: / Line 32: @@
 ==Reference==
-<ref name="ref2">Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.</ref>
+Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060
-<ref name="ref3">Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.</ref>
+Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.
 [[Category:Genes]]
 [[Category:Japonica mRNA]]
@@ Line 47: / Line 47: @@
 [[Category:Japonica Chromosome 12]]
 [[Category:Chromosome 12]]
 == Structured Information ==

@@ Line 32: / Line 32: @@
 ==Reference==
-Jung, Chang Gyo, Lim, Sung Don, Hwang, Sun-Goo, & Jang, Cheol Seong. (2012). Molecular characterization and concerted evolution of two genes encoding RING-C2 type proteins in rice. Gene, 505(1), 9-18. doi: http://dx.doi.org/10.1016/j.gene.2012.05.060
+<references>
-Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.
+<ref name="ref2">Lim, S.D., et al., 2010. A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes. Plant Mol. Biol. 72, 369–380.</ref>
-Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.
+<ref name="ref3">Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.</ref>
 [[Category:Genes]]
 [[Category:Japonica mRNA]]
@@ Line 46: / Line 47: @@
 [[Category:Japonica Chromosome 12]]
 [[Category:Chromosome 12]]

@@ Line 22: / Line 22: @@
 Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).
-The finding that the distal regions of rice chromosomes 11 and 12 diverged 70–90 Mya and may have undergone frequent illegitimate recombination such as gene conversion (Paterson et al., 2009; Wang et al., 2011) raises the question regarding the evolutionary fate of OsRINGC2-1 and OsRINGC2-2 located on the distal parts of these chromosomes.We attempted to choose each of 10 OsRINGC2-1 and OsRINGC2-2 neighboring genes, respectively, and 100 randomly selected duplicate genes, which were generated by whole-genome duplication elsewhere in the genome. Strikingly low Ka, Ks, and dsm values were observed between duplicate genes (but not all) located on the distal parts of chromosomes 11 and 12 as compared to those of random sets (Fig 3).
+The finding that the distal regions of rice chromosomes 11 and 12 diverged 70–90 Mya and may have undergone frequent illegitimate recombination such as gene conversion  raises the question regarding the evolutionary fate of OsRINGC2-1 and OsRINGC2-2 located on the distal parts of these chromosomes.We attempted to choose each of 10 OsRINGC2-1 and OsRINGC2-2 neighboring genes, respectively, and 100 randomly selected duplicate genes, which were generated by whole-genome duplication elsewhere in the genome. Strikingly low Ka, Ks, and dsm values were observed between duplicate genes (but not all) located on the distal parts of chromosomes 11 and 12 as compared to those of random sets (Fig 3).
 [[File: liu-Os12g0102400-Fig2.jpg|right|thumb|200px|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values.  Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]

← Older revision		Revision as of 13:28, 10 June 2014
Line 21:		Line 21:

	Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).		Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).
		+
		+	The finding that the distal regions of rice chromosomes 11 and 12 diverged 70–90 Mya and may have undergone frequent illegitimate recombination such as gene conversion (Paterson et al., 2009; Wang et al., 2011) raises the question regarding the evolutionary fate of OsRINGC2-1 and OsRINGC2-2 located on the distal parts of these chromosomes.We attempted to choose each of 10 OsRINGC2-1 and OsRINGC2-2 neighboring genes, respectively, and 100 randomly selected duplicate genes, which were generated by whole-genome duplication elsewhere in the genome. Strikingly low Ka, Ks, and dsm values were observed between duplicate genes (but not all) located on the distal parts of chromosomes 11 and 12 as compared to those of random sets (Fig 3).

	[[File: liu-Os12g0102400-Fig2.jpg\|right\|thumb\|200px\|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]		[[File: liu-Os12g0102400-Fig2.jpg\|right\|thumb\|200px\|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]

← Older revision		Revision as of 13:23, 10 June 2014
Line 23:		Line 23:

	[[File: liu-Os12g0102400-Fig2.jpg\|right\|thumb\|200px\|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]		[[File: liu-Os12g0102400-Fig2.jpg\|right\|thumb\|200px\|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]
		+
		+	[[File: liu-Os12g0102400-Fig3.jpg\|right\|thumb\|200px\|''Sequence divergence of duplicated genes pairs in upstream and downstream of Os11g01190 and Os12g01190.. (from reference <ref name="Jung" />).'']]

	==Labs working on this gene==		==Labs working on this gene==

← Older revision		Revision as of 13:20, 10 June 2014
Line 21:		Line 21:

	Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).		Investigation on the dynamic expansion and genomic localization of rice RING finger protein genes over evolution revealed only two RING-C2 type protein genes located on the distal part on each of rice chromosomes 11 and 12 (Lim et al., 2010).
		+
		+	[[File: liu-Os12g0102400-Fig2.jpg\|right\|thumb\|200px\|''A phylogenic tree of RING-C2 type genes in Viridiplantae. The numbers on the left side indicate percent bootstrap values. Solid circles indicate OsRINGC2-1 and OsRINGC2-2. The species abbreviations are listed as follows; At, Arabidopsis thaliana; Al, Arabidopsis lyrata; Cp, Carica papaya; Cs, Cucumis sativus; Rc, Ricinus communis; Me, Manihot esculenta; Gm, Glycine max; Mt, Medicago truncatula; Bd, Brachypodium distachyon; Zm, Zea mays; Os, Oryza sativa, Sb, Sorghum bicolor; Si, Setaria italica; Ac, Aquilegia coerulea; Pp, Prunus persica; Pt, Populus trichocarpa; Mg, Mimulus guttatus; Sm, Selaginella moellendorffii; Vv, Vitis vinifera. (from reference <ref name="Jung" />).'']]

	==Labs working on this gene==		==Labs working on this gene==