Difference between revisions of "Os12g0102400"
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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. | 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. | ||
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| + | Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556. | ||
| + | |||
| + | Wang, X., et al., 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946. | ||
==Structured Information== | ==Structured Information== | ||
Revision as of 08:39, 1 June 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
It is a gene encoding RING-C2 type protein in rice, called OsRINGC2-2 located on chromosome 12. RING (Really Interesting New Gene) finger proteins are believed to play a critical role in mediating the transfer of ubiquitin to heterogeneous substrate(s). While the two canonical types, RING-H2 and RING-HC, have been well-characterized, the molecular functions of the modified types, particularly the RING-C2 types, remain elusive. We isolated two rice genes harboring the RING-C2 domain on the distal parts of rice chromosomes 11 and 12, termed OsRINGC2-1 and OsRINGC2-2, respectively. A comparison of sequence divergences between 10 duplicate pairs on the distal parts of rice chromosomes 11 and 12 and randomly selected duplicate pairs suggested that OsRINGC2-1 and OsRINGC2-2 have evolved in concert via gene conversion. An in vitro ubiquitination assay revealed that both proteins possess E3 ligase activity, suggesting that the innate functions of these RING domains have not been affected by their modifications during evolution. Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution. These results shed light on the molecular functions of OsRINGC2-1 and OsRINGC2-2 and provide insight into their molecular evolution.
Expression
It is a gene encoding RING-C2 type protein in rice. Two RING-C2 types are the modified types of canonical types RING-H2 and RING-HC. Some modified types of RINGs including RING-v, RING-D, RINGS/T, RING-G, and RING-C2 exist in various plant genomes. Interestingly, only two RING-C2 types exist in the rice genome, whereas 10 occur in Arabidopsis and 10 in apple, respectively. Functions of the modified RING domains remain largely unidentified.
Subcellular localizations were strikingly different; OsRINGC2-1 was found only in the cytoplasm with many punctate complexes, whereas OsRINGC2-2 was observed in both the nucleus and cytoplasm. The expression patterns of both genes showed striking differences in response to salt stress, whereas plants heterogeneous for both genes mediated salt tolerance in Arabidopsis, supporting the notion of concerted evolution.
Evolution
Complete genome sequences and bioinformatics provide new insights into the evolutionary history of plant genomes. In particular, the Poaceae genome, which includes major food crops such as rice, wheat, corn, and sorghum, is believed to have undergone a pregrass whole-genome duplication event with a common ancestor 70–90 million years ago (Mya)(Paterson et al., 2009; Salse et al., 2008, 2009; Wang et al., 2005) followed by independent gene loss during speciation.
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).
Labs working on this gene
Please input related labs here.
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
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.
Paterson, A.H., et al., 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551–556.
Wang, X., et al., 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946.
Structured Information
| Gene Name |
Os12g0102400 |
|---|---|
| Description |
Zinc finger, RING-type domain containing protein |
| Version |
NM_001071769.1 GI:115486859 GeneID:4351244 |
| Length |
6708 bp |
| Definition |
Oryza sativa Japonica Group Os12g0102400, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 12:104922..111629 |
| Sequence Coding Region |
105119..105120,105421..105520,105598..105725,105939..106101,106198..106310 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008405:104922..111629 source=RiceChromosome12 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008405:104922..111629 source=RiceChromosome12 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgatgaccatgagcgacgatggagaccgcacctgcccgctctgtgctgaggacatggacatcactgaccagcagctcaagccctgcaaatgcggctatgagatttgtgtctggtgctggcaccacatcattgatatggctgagaaagaggacactgagggccgctgccccgcatgccgcactcgctatgacaaagataggattgtcaagatggctgccacttgtgacaggacggtagtggagaaaaatgtggacaagaaacagaagacccaaaaggtcaagtcaaaggccgcggtaactgtggaagctaagaaacatcttgctagcgtcagggttatccagagaaacctcgtgtacataattggactacctgcaaatttatgcaacgaaagcatacttgagcgcagggaatactttggtcagtatggcaaggttctgaaagtttcagtttctcggccgactggggctccttcccagcaggcaccaacaaacaacagtatcagcgtatatattacatatgccaaagaagaagaggccatcaggtgtattcaagctgtacacaattttgttttggaagggaaagtgttaagagcgtgctttggtactacaaagtattgccatgcatggctgcggaacatgacctgtggaaatccagattgtctctatttacatgatgtaggaagccaggaagatagtttcactaaagatgagataatctcagcatatacaaggagtagggttccccaaatggcgtctaatgtttctcaaagacgcgcagggactgtattacctcctccagcagaagatttctcatatagtgcagtggttgcagctaaacatccaatcaagaatggaataactaatactgcaaatcaatccaggctttcgcctccaaacagtagttctgggagatccacacttccaccagctgcttcatgggggcatcgcgatttgaataccaggacaacagcaactggggtggcatcgtcacaatctcttactaaatcaaaagcagatcctcaaagtaattcattctcgagttcttcgactgtttcaagtacaaaactaccttcttcatggaatgatgacacaagcacagttccgaaaatgacggaaggacgagatagtttgtctaaaaccttgaagccatataagcctggtattgcaaaggaaacccaagctgtaacatcactggagtcatcgcttgacatagacttctctaccataccttcagcttggaacgatgatgatgtcacatcagatggcatgtcaaaaggaagtgacgagaagcaggttgtaaatgacaatggaaagtttgaatgttcagtttcttcaaagccagctgaatcagggcatcttacatcgaagtcaacgacatcaccaaagaaagacatcgcagtaaacagtaccaggcaaagtcctctaaattgtgtatcaagtccatcggtttctaaatcagaagtaaaggatggtgatggtgattaccaagtaaccaacatggcttctaaaacatctactttggtaattagaaaggaccaatctaatcaagcagctattgacacagcaaccgaagatactagatctgagagcacggatattgataggctttctgttggagtatcttcagtaacattaagcagaaaagatggggttcaaagtattgccgaaaaccaacaaccggatgcaatcctaagtacttcagttgtggtgccctttagtcagaatttgaaacttgctgagtgtaatgattctacatgtcagcctagttcagataagcatcgtgattggtgttcagatatccagagtagtgtgtctcctcagttaaatgacatagaaagttatgcagtagccactgataaatctcatggtagagtgctggatgctgctgatcaagcttcgtcttcaccatatgtccatttccctaacactgctcctatttcactgtggaatggtaaagagattaaccatacatcaacaagtgatagaacttccacaatgatgcaacctgggctgttatcttcagttgacagcacttctaccatgttaaatggacatcaagaagggctagggactatatatgcacctggtaaggtttctgaacatcctagaatgaaaaaccatcagcctggagcagttggtgcagtgagaattgataacataggcagttttgacaaggctgtaagtgtaaataaggatgagagcagcataattgctgatattttgtctttggagtttgatccatgggatgagtcgtattcaacggctaacaattttgctaagatgcttagtgcatctgaaaagaacgatgtgctttttgatgcacgttcatggaaaacaaaaaccagcaatagtgagtctagattttcatttgctagacaagataatcaaggaagcctcctagattcatctatgagaaattataaaagtgagcagaatttcagtttgccatcccagaattctcatggaaacatttatcagagtggcattgcatttcaatctcctgaggaaggtttctcaaagagcaactctcttactatgttggatatgctagctaccggcacatcaaagcctaaagtatccgcgcctcctggattttcagcaccagcaagagttcctactgggttttcttctggattttcatcccatgaggggttgaatccacctccaggattttcatctcataatgggcctaatccccctcctggattttcttctcagggtgggtctaatcagatctatggttcggcatactcagaaactcgcccatttgatgatcttttgggtataaatactagccattatcaaccacagttagctagacaaacaagtgatatagaatttgttgatcctgctatattggctgtgggtaaagggcggatgcctggaataagtgattcagggttggagatgaaaacttcccatacttttccttcgcagttgcaaacatcaaatgatccaaggtttcaattacttatgcagcagaacatgccttcccatcaaaatgttggatttgcagaacatgttcaagatgcattcaaccctatgaatgataattatcttgcatcccgacttatacctcagaaccatggttctctatcctcttacacacagatgtcactccaacaacctagaagctcacatcttacaaatggtcattgggatggctggggtgatttgagacaagggaataatgtttccatgcctgacatgtcaaggatgttatatccaactgaagcaaacaacttccacatgctgggttcaaatgatctgtataacagagcttttggactgtga</cdnaseq> |
| Protein Sequence |
<aaseq>MMTMSDDGDRTCPLCAEDMDITDQQLKPCKCGYEICVWCWHHII DMAEKEDTEGRCPACRTRYDKDRIVKMAATCDRTVVEKNVDKKQKTQKVKSKAAVTVE AKKHLASVRVIQRNLVYIIGLPANLCNESILERREYFGQYGKVLKVSVSRPTGAPSQQ APTNNSISVYITYAKEEEAIRCIQAVHNFVLEGKVLRACFGTTKYCHAWLRNMTCGNP DCLYLHDVGSQEDSFTKDEIISAYTRSRVPQMASNVSQRRAGTVLPPPAEDFSYSAVV AAKHPIKNGITNTANQSRLSPPNSSSGRSTLPPAASWGHRDLNTRTTATGVASSQSLT KSKADPQSNSFSSSSTVSSTKLPSSWNDDTSTVPKMTEGRDSLSKTLKPYKPGIAKET QAVTSLESSLDIDFSTIPSAWNDDDVTSDGMSKGSDEKQVVNDNGKFECSVSSKPAES GHLTSKSTTSPKKDIAVNSTRQSPLNCVSSPSVSKSEVKDGDGDYQVTNMASKTSTLV IRKDQSNQAAIDTATEDTRSESTDIDRLSVGVSSVTLSRKDGVQSIAENQQPDAILST SVVVPFSQNLKLAECNDSTCQPSSDKHRDWCSDIQSSVSPQLNDIESYAVATDKSHGR VLDAADQASSSPYVHFPNTAPISLWNGKEINHTSTSDRTSTMMQPGLLSSVDSTSTML NGHQEGLGTIYAPGKVSEHPRMKNHQPGAVGAVRIDNIGSFDKAVSVNKDESSIIADI LSLEFDPWDESYSTANNFAKMLSASEKNDVLFDARSWKTKTSNSESRFSFARQDNQGS LLDSSMRNYKSEQNFSLPSQNSHGNIYQSGIAFQSPEEGFSKSNSLTMLDMLATGTSK PKVSAPPGFSAPARVPTGFSSGFSSHEGLNPPPGFSSHNGPNPPPGFSSQGGSNQIYG SAYSETRPFDDLLGINTSHYQPQLARQTSDIEFVDPAILAVGKGRMPGISDSGLEMKT SHTFPSQLQTSNDPRFQLLMQQNMPSHQNVGFAEHVQDAFNPMNDNYLASRLIPQNHG SLSSYTQMSLQQPRSSHLTNGHWDGWGDLRQGNNVSMPDMSRMLYPTEANNFHMLGSN DLYNRAFGL</aaseq> |
| Gene Sequence |
<dnaseqindica>198..199#500..599#677..804#1018..1180#1277..1389#2105..2188#2272..2320#2410..2501#2759..2888#2985..3061#3137..4755#5103..5300#5366..5904#acgcgaacacgacgacaccagccagcaagcagcggaggagagagagagagagagagagactccatagacggccatcgatcgtacgcgactccccccatccatccatccacccgccggcgccccctccctctcatcgatcgatcgattcccaccgccgcccccgttttgaccacctacctagggtttcccccatcggaatgtgagtacttcaccctctctgatcccccccttttcttttctgattgttgctccaatccacttgggagcataatagactctttggattggatcctcgatttgaaggatcagcccctgcgcttgcccccccacccctcactttctcgtttattcgatttgatgataggaagcttctctctcttattagggattgattgattacaccgtgttactacagattgttattcccacaaacaaacaatctcatgtactactaataatattatctttcatgtctcctgccgctgaattgctcccgaaggatgaccatgagcgacgatggagaccgcacctgcccgctctgtgctgaggacatggacatcactgaccagcagctcaagccctgcaaatgcggctatgaggtttcttcccttccctccccaccactctactctccacaccccccttccattcacctcccttttgcatctcactgcagatttgtgtctggtgctggcaccacatcattgatatggctgagaaagaggacactgagggccgctgccccgcatgccgcactcgctatgacaaagataggattgtcaagatggctgccacttgtgacaggtccctccatctcaaaccgtcttttttcctttcacctcactaactgcactgacatgcgaagatggccgcacaagagcttagggtcttcagttcaacaaaacgaaacatcacccagttgtcgtgaattgtggtttgcaaagcgccataagcaacttcttttacctgtctatcgcatcggaaattttgtacttatgcttcttttaatggaaacaggacggtagtggagaaaaatgtggacaagaaacagaagacccaaaaggtcaagtcaaaggccgcggtaactgtggaagctaagaaacatcttgctagcgtcagggttatccagagaaacctcgtgtacataattggactacctgcaaatttatgcaacgaaagcgtgagtaccatattgtgcacagacagattcttttcaactgagtaatgtgtatattttgtttctcaccttggcaacacaattcattttttatttcagatacttgagcgcagggaatactttggtcagtatggcaaggttctgaaagtttcagtttctcggccgactggggctccttcccagcaggcaccaacaaacaacagtatcagcgtgtatgtttatgtgaatctcatgccacatgtttatgatgtttctctcatggataaacatgacctattatttcaagtgattagatatatcttaccgtatgtacaagtggtgttttcaagttatgctctcctgtactttccaagcctagagcatttaagcataggtgatttattgttgagaaattatatgcttaaatatagatgaaaatgatggctaattcaaatatgatatgtccatgttcttgcaattaatttcagatttatattacctacttaacagtatgatttgactaaggatcatgaatttccatatccatttgtgaatcagtgaatgccacacctagcagcctagtagccaaagcaaaagatgtagatttctagtgttgaataatcagataaatgcaaacgtgactgcttcagtcatatcatgatcattatattaactatggtatgtactaattgtatgtttacatcataagtctgattgagctcagaacctttgcatatgcagatgtcaggtatttcatagaatttacctcaaggattatcaaaattttcctgtctgagcactttgtagttctttgaatgcagctccatctttctcttaggaatcctcagcatcgactggatccatgtagattccaaaatgtgaaacttagattgtatatagaatgcactgtgtgtgttgaaaatgggctcattattgtgatgttttcagatatattacatatgccaaagaagaagaggccatcaggtgtattcaagctgtacacaattttgttttggaagggaaagtgttaaggtcaccctctatgctttgtagccttattgcagcagttttttttacataacgcagttagcctaatcgttaatggtttgttgcagagcgtgctttggtactacaaagtattgccatgcatggctgcggaacatggtatactcgttgcttcatcctggcagctttatttaccattactctacctactgccatccttctgagggcttttatcttctcttttttagacctgtggaaatccagattgtctctatttacatgatgtaggaagccaggaagatagtttcactaaagatgagataatctcagcatatacaaggtaagctgagctcgttgaacatatgtgtggaaagttccactgttccttattatggcactgtgccagtcctagccatatgtactttttcccctgccaagcctactgctactgttactatataatgctcttctgttctgagaatttgtagtctatcaacttttccctatactatgcatgaattattatgctttgctaaatgctaagattttcagtagttctgattggtgctttcgactcatcatctctcgttcctacaggagtagggttccccaaatggcgtctaatgtttctcaaagacgcgcagggactgtattacctcctccagcagaagatttctcatatagtgcagtggttgcagctaaacatccaatcaagaatggaataactgtatgttttttatactgaaaaatccattgggacactggacatgttcatttctgtttgatttcatgctgctacattaactggtcttattttgtacagaatactgcaaatcaatccaggctttcgcctccaaacagtagttctgggagatccacacttccaccagctgcttcatggtatgatgctgcttagggtctcatgatatgttttaaaatgtgaatttgttgctaaaatttttttggtatgagcagggggcatcgcgatttgaataccaggacaacagcaactggggtggcatcgtcacaatctcttactaaatcaaaagcagatcctcaaagtaattcattctcgagttcttcgactgtttcaagtacaaaactaccttcttcatggaatgatgacacaagcacagttccgaaaatgacggaaggacgagatagtttgtctaaaaccttgaagccatataagcctggtattgcaaaggaaacccaagctgtaacatcactggagtcatcgcttgacatagacttctctaccataccttcagcttggaacgatgatgatgtcacatcagatggcatgtcaaaaggaagtgacgagaagcaggttgtaaatgacaatggaaagtttgaatgttcagtttcttcaaagccagctgaatcagggcatcttacatcgaagtcaacgacatcaccaaagaaagacatcgcagtaaacagtaccaggcaaagtcctctaaattgtgtatcaagtccatcggtttctaaatcagaagtaaaggatggtgatggtgattaccaagtaaccaacatggcttctaaaacatctactttggtaattagaaaggaccaatctaatcaagcagctattgacacagcaaccgaagatactagatctgagagcacggatattgataggctttctgttggagtatcttcagtaacattaagcagaaaagatggggttcaaagtattgccgaaaaccaacaaccggatgcaatcctaagtacttcagttgtggtgccctttagtcagaatttgaaacttgctgagtgtaatgattctacatgtcagcctagttcagataagcatcgtgattggtgttcagatatccagagtagtgtgtctcctcagttaaatgacatagaaagttatgcagtagccactgataaatctcatggtagagtgctggatgctgctgatcaagcttcgtcttcaccatatgtccatttccctaacactgctcctatttcactgtggaatggtaaagagattaaccatacatcaacaagtgatagaacttccacaatgatgcaacctgggctgttatcttcagttgacagcacttctaccatgttaaatggacatcaagaagggctagggactatatatgcacctggtaaggtttctgaacatcctagaatgaaaaaccatcagcctggagcagttggtgcagtgagaattgataacataggcagttttgacaaggctgtaagtgtaaataaggatgagagcagcataattgctgatattttgtctttggagtttgatccatgggatgagtcgtattcaacggctaacaattttgctaagatgcttagtgcatctgaaaagaacgatgtgctttttgatgcacgttcatggaaaacaaaaaccagcaatagtgagtctagattttcatttgctagacaagataatcaaggaagcctcctagattcatctatgagaaattataaaagtgagcagaatttcagtttgccatcccagaattctcatggaaacatttatcagagtggcattgcatttcaatctcctgaggaaggtttctcaaagagcaactctcttactatgttggatatgctagctaccggtgagtagtatgaagttatattacgctgcttgtttattaaattcttaatgaacagtgagatgcagtactgcagttaatgtttttattttaatatttattttatatatttgaggtaatattaatgtgtcacaaaacaaatagatatattcgctaggatacagaagggatccaatgtttgtgcacccattcccctcttttaattcaatgttggcaatcttgtaacatatgtgattgggttgtggagctattaagtataaaatgcactgtgtttttatgttgaagcattttagtaactgatgttttcaccatggtacttctatgtacttacaaaaaaaatgctttttcaggcacatcaaagcctaaagtatccgcgcctcctggattttcagcaccagcaagagttcctactgggttttcttctggattttcatcccatgaggggttgaatccacctccaggattttcatctcataatgggcctaatccccctcctggattttcttctcagggtgggtctaatcagatctatggttcggcatactcaggttctctctctctctgcttctcctaaaacaatttcagtttctaataagtttgcaatgttttgcagaaactcgcccatttgatgatcttttgggtataaatactagccattatcaaccacagttagctagacaaacaagtgatatagaatttgttgatcctgctatattggctgtgggtaaagggcggatgcctggaataagtgattcagggttggagatgaaaacttcccatacttttccttcgcagttgcaaacatcaaatgatccaaggtttcaattacttatgcagcagaacatgccttcccatcaaaatgttggatttgcagaacatgttcaagatgcattcaaccctatgaatgataattatcttgcatcccgacttatacctcagaaccatggttctctatcctcttacacacagatgtcactccaacaacctagaagctcacatcttacaaatggtcattgggatggctggggtgatttgagacaagggaataatgtttccatgcctgacatgtcaaggatgttatatccaactgaagcaaacaacttccacatgctgggttcaaatgatctgtataacagagcttttggactgtgattatctttgggagatgcgacttgacctatcacccagctaacttgcacatttctcagttcttgaaattgattggttgcacaggctcaacttggtgattgttgagcttgtggattggcgcatgagtgtttattgaaaggcattggattcaagtggaccagcatgaaactgggtgtgtaaccagacgtttcaagcaccaggtttgtgtttcaccattctattcacatctttttttactatattatatgcatggcttgctaccccttgtcctggataggtggtgtgagttatcttcttattgcattggttagtactgtttgtgcttggtctcttccattttattctggaatttgttgctgtgtttgttctggaatttgctggcaagttactcaccatttgcctcgtttggtcatcaggttctgttttgggcgaaaggatatatatatcaaagatgcatccatgaggttgtccttcaagtttatatatacttgtggtggaagcagactcgagaatatataaaccgtttagcatttgcttctttcttctttttttgccgtcatgtggaaatattttcttggttttggcatagtaaaagcgtcattttgtacatgatacgttactcgttgctagtagcttttgtggtgcacatgagattattttgttgatgggtttgctgaaccaaacgtaaatggctatatggtaccaggccagccagcttatgctgaattgggtgttgtttggtgttgaatcaaaaacaaggtcgaggagtacttcggtgtgctgttgttaataatatcaattcatgac</dnaseqindica> |
| External Link(s) |
