Os07g0616800 - Revision history

Xysj1981 at 06:29, 8 March 2017

2017-03-08T06:29:28Z

Xysj1981 at 06:28, 8 March 2017

2017-03-08T06:28:31Z

Xysj2012: /* Structured Information */

2015-06-12T08:47:57Z

‎Structured Information

Chenlizhao at 08:52, 8 June 2014

2014-06-08T08:52:32Z

Chenlizhao: /* References */

2014-06-08T08:39:03Z

‎References

Chenlizhao at 08:30, 8 June 2014

2014-06-08T08:30:10Z

Chenlizhao at 08:26, 8 June 2014

2014-06-08T08:26:55Z

Chenlizhao at 08:14, 8 June 2014

2014-06-08T08:14:40Z

Chenlizhao: /* Recombination */

2014-05-24T08:46:44Z

‎Recombination

Chenlizhao: /* Haplotype Diversity */

2014-05-24T08:46:27Z

‎Haplotype Diversity

@@ Line 14: / Line 14: @@
 ===Nucleotide Polymorphisms===
-Nucleotide changes and indels at the RSUS3 locus were identified, and the results are summarized in picture 10. [[File: picture 10. Summary of the frequency of polymorphisms.jpg|right|thumb|150px|''picture10. Summary of the frequency of polymorphisms (from reference <ref name="ref3" />).'']] Puji Lestari <ref name="ref3" /> analyzed the full sequence of RSUS3 from 43 rice varieties consisting of 13 indica varieties, 22 japonica varieties, and 8 wild rice accessions( Oryza rufipogon) to examine the distribution of DNA polymorphisms, revealed allelic diversity at the RSUS3 locus. Sequence polymorphisms were detected across the length of 7733 bp, which covers a 1652 bp upstream region, a 2815 bp coding region, a 2724 bp noncoding region, and a 542 bp downstream region. No triallelic SNPs were found in any of the defined regions. The frequency of SNPs/indels was highest in the promoter region. The 3’ NTR contained abundant nucleotide and length polymorphisms (frequency of total variants 50.041). However, the overall indel frequency in the transcribed region was higher than the nucleotide substitution frequency in the region. The SNP frequency in the coding region was less than the average of SNP frequency in the entire transcribed region; one SNP occurred every 216.5 bp in the coding region. The frequency of nucleotide substitutions was about 1.6 times higher in the noncoding region than in the coding region, and both nucleotide changes and indels were more frequent in the noncoding region than in the coding region. The differences in the distribution of the differences in the lengths of the indels in all regions varied in size from 1 to 32 bp, with an average indel length of 2.87 bp. The distribution of SNP and indel sites was not significantly different (when degrees of freedom =2, SNPs χ2=0.228; indels χ2=0.377) across the entire region excluding intron (5’ NTR-transcript-3’ NTR).
+Nucleotide changes and indels at the RSUS3 locus were identified, and the results are summarized in picture 10.Puji Lestari <ref name="ref3" /> analyzed the full sequence of RSUS3 from 43 rice varieties consisting of 13 indica varieties, 22 japonica varieties, and 8 wild rice accessions( Oryza rufipogon) to examine the distribution of DNA polymorphisms, revealed allelic diversity at the RSUS3 locus. Sequence polymorphisms were detected across the length of 7733 bp, which covers a 1652 bp upstream region, a 2815 bp coding region, a 2724 bp noncoding region, and a 542 bp downstream region. No triallelic SNPs were found in any of the defined regions. The frequency of SNPs/indels was highest in the promoter region. The 3’ NTR contained abundant nucleotide and length polymorphisms (frequency of total variants 50.041). However, the overall indel frequency in the transcribed region was higher than the nucleotide substitution frequency in the region. The SNP frequency in the coding region was less than the average of SNP frequency in the entire transcribed region; one SNP occurred every 216.5 bp in the coding region. The frequency of nucleotide substitutions was about 1.6 times higher in the noncoding region than in the coding region, and both nucleotide changes and indels were more frequent in the noncoding region than in the coding region. The differences in the distribution of the differences in the lengths of the indels in all regions varied in size from 1 to 32 bp, with an average indel length of 2.87 bp. The distribution of SNP and indel sites was not significantly different (when degrees of freedom =2, SNPs χ2=0.228; indels χ2=0.377) across the entire region excluding intron (5’ NTR-transcript-3’ NTR).
 ===Allele Distribution===
-Puji Lestari <ref name="ref3" /> adopted Tajima’s D test and Fu and Li’s D* and F* tests to evaluate the allele distribution in the germplasm used in this study and assess the neutrality of the mutations. The frequency spectrum of polymorphic sites for the total length was skewed toward a deficit of low-frequency alleles relative to expectations based on a positive outcome by Tajima’s D test (0.923). The Tajima’s D value for the total region of RSUS3 excluding intron was lower than that for the entire length. Separate Tajima’s D tests for each region (upstream, coding, and noncoding region) revealed positive and nonsignificant departures from the neutral expectation, with the exception of the 3’ downstream NTR, which had a negative Tajima’s D value (D = -0.326). Using the coalescent process to test the neutrality of the mutations in the entire gene sequence, similar positive values were obtained, but significant deviation from the neutral expectation (P <0.02) occurred with the Fu and Li D* (1.959) and F* (1.894) tests. A summary of this neutrality test is presented in picture 11. [[File: picture 11. Nucleotide diversity and divergence in each region of the RSUS3 gene.jpg|right|thumb|150px|''picture11. Nucleotide diversity and divergence in each region of theRSUS3gene (from reference <ref name="ref3" />).'']]
+Puji Lestari <ref name="ref3" /> adopted Tajima’s D test and Fu and Li’s D* and F* tests to evaluate the allele distribution in the germplasm used in this study and assess the neutrality of the mutations. The frequency spectrum of polymorphic sites for the total length was skewed toward a deficit of low-frequency alleles relative to expectations based on a positive outcome by Tajima’s D test (0.923). The Tajima’s D value for the total region of RSUS3 excluding intron was lower than that for the entire length. Separate Tajima’s D tests for each region (upstream, coding, and noncoding region) revealed positive and nonsignificant departures from the neutral expectation, with the exception of the 3’ downstream NTR, which had a negative Tajima’s D value (D = -0.326). Using the coalescent process to test the neutrality of the mutations in the entire gene sequence, similar positive values were obtained, but significant deviation from the neutral expectation (P <0.02) occurred with the Fu and Li D* (1.959) and F* (1.894) tests. A summary of this neutrality test is presented in picture 11.
 ===Recombination===

@@ Line 11: / Line 11: @@
 ===Expression===
 Wang et al <ref name="ref2" /> used the mono-specific antibodies for three RSuS isoforms and found differentially and developmentally regulated expression of three rice sucroce synthase genes. The expression of RSuS3 could only be detected in the seeds in etiolated seedlings.[[File:picture. 4 Distribution of RSuS isozymes in various rice tissues.jpg|right|thumb|150px|''picture 4. Distribution of RSuS isozymes in various rice tissues (from reference <ref name="ref2" />).'']] However, researchers found temporal expression of RSus3 genes in developing seeds. RSuS3 was barely detectable before 3 DAP and reached a plateau from 6 to 12 DAP, or the milky stage in which the starch filling in the endosperm was the most active.[[File:picture.5 Temporal expression of RSuS in seeds at various maturation stages.jpg|right|thumb|150px|''picture 5. Temporal expression of RSuS in seeds at various maturation stages (from reference <ref name="ref2" />).'']]
-Tatsuro Hirose et al <ref name="ref1" /> used Real-time RT-PCR to determine the expression profile for each member of the Sus gene family in various tissues of rice and found tissue-specific expression of each member of the Sus gene family. The transcript of SUS3 was most abundant in either the panicles at the grain filling stage of development or dry seeds respectively, and was absent from or expressed only at very low levels in the other tissues examined.[[File:picture.6A The transcript levels of the SUS genes in various rice tissues.jpg|right|thumb|150px|''picture 6A. The transcript levels of the SUS genes in various rice tissues (from reference <ref name="ref1" />).'']] [[File:picture.6B The transcript levels of the SUS genes in various rice tissues.jpg|right|thumb|150px|''picture 6B. The transcript levels of the SUS genes in various rice tissues (from reference <ref name="ref1" />).'']] Expression of SUS3 in elongating internodes was either negligible or not detected.[[File:picture.7 Profiles of transcript levels for SUS and Ces genes in elongating internodes.jpg|right|thumb|150px|''picture 7.Profiles of transcript levels for SUS and Ces genes in elongating internodes (from reference <ref name="ref1" />).'']] However, during the grain filling period in caryopses, the gene expression level of the SUS3 was very low at 1 and 2 DAF, and increased rapidly to a peak at 5 DAF before decreasing there after.[[File:picture.8 Sus gene expression and activity in developing caryopsis.jpg|right|thumb|150px|''picture 8.Sus gene expression and activity in developing caryopsis <ref name="ref1" />).'']] Furthermore, to investigate the response of the SUS genes to submergence, their transcript levels were determined in the shoots of seedlings, germinated under submerged conditions, during a developmental time-course from 3 to 7 days after imbibition (DAI). The SUS3 transcript was not detectable in both control and submerged samples.[[File:picture.9 Sus activity and transcript levels of four of the rice SUS genes in germinating shoots in response to submergence.jpg|right|thumb|150px|''picture 9.Sus activity and transcript levels of four of the rice SUS genes in germinating shoots in response to submergence <ref name="ref1" />).'']]
+Tatsuro Hirose et al <ref name="ref1" /> used Real-time RT-PCR to determine the expression profile for each member of the Sus gene family in various tissues of rice and found tissue-specific expression of each member of the Sus gene family. The transcript of SUS3 was most abundant in either the panicles at the grain filling stage of development or dry seeds respectively, and was absent from or expressed only at very low levels in the other tissues examined.[[File:picture.6A The transcript levels of the SUS genes in various rice tissues.jpg|right|thumb|150px|''picture 6A. The transcript levels of the SUS genes in various rice tissues (from reference <ref name="ref1" />).'']] Furthermore, to investigate the response of the SUS genes to submergence, their transcript levels were determined in the shoots of seedlings, germinated under submerged conditions, during a developmental time-course from 3 to 7 days after imbibition (DAI). The SUS3 transcript was not detectable in both control and submerged samples.[[File:picture.9 Sus activity and transcript levels of four of the rice SUS genes in germinating shoots in response to submergence.jpg|right|thumb|150px|''picture 9.Sus activity and transcript levels of four of the rice SUS genes in germinating shoots in response to submergence <ref name="ref1" />).'']]
 ===Nucleotide Polymorphisms===

@@ Line 48: / Line 48: @@
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

@@ Line 40: / Line 40: @@
 <references>
 * <ref name="ref1">
-Hirose T, Scofield GN, Terao T. An expression analysis profile for the entire sucrose synthase gene family in rice[J]. Plant Sci, 2008, 174:534–543.
+Hirose T, Scofield GN, Terao T. An expression analysis profile for the entire sucrose synthase gene family in rice[J]. Plant Sci, 2008, 174:534–543.</ref>
 * <ref name="ref2">
-Puji Lestari, Gian Lee, Tae-Ho Ham, Reflinur, Mi-Ok Woo, Rihua Piao, Wemzhu Jiang, Sang Ho Chu, Joohyun Lee, Hee-Jong Koh. Single Nucleotide Polymorphisms and Haplotype Diversity in RiceSucrose Synthase 3[J]. Journal of Heredity, 2011, 102:735-746.
+Puji Lestari, Gian Lee, Tae-Ho Ham, Reflinur, Mi-Ok Woo, Rihua Piao, Wemzhu Jiang, Sang Ho Chu, Joohyun Lee, Hee-Jong Koh. Single Nucleotide Polymorphisms and Haplotype Diversity in RiceSucrose Synthase 3[J]. Journal of Heredity, 2011, 102:735-746.</ref>
 * <ref name="ref3">
-Ai-Yu <Wang, Mau-Han Kao, Wei-Horng Yang, Yiyang Sayion, Li-fei Liu, Ping-Du Lee, Jong-Ching Su. Differentially and developmentally regulated expression of three rice sucrose synthase genes[J]. Plant Cell Phyisol, 1999, 40:800–807.
+Ai-Yu <Wang, Mau-Han Kao, Wei-Horng Yang, Yiyang Sayion, Li-fei Liu, Ping-Du Lee, Jong-Ching Su. Differentially and developmentally regulated expression of three rice sucrose synthase genes[J]. Plant Cell Phyisol, 1999, 40:800–807.</ref>
 </references>

@@ Line 44: / Line 44: @@
 * <ref name="ref2">
 Puji Lestari, Gian Lee, Tae-Ho Ham, Reflinur, Mi-Ok Woo, Rihua Piao, Wemzhu Jiang, Sang Ho Chu, Joohyun Lee, Hee-Jong Koh. Single Nucleotide Polymorphisms and Haplotype Diversity in RiceSucrose Synthase 3[J]. Journal of Heredity, 2011, 102:735-746.
 /ref>
 * <ref name="ref3">
 Ai-Yu <Wang, Mau-Han Kao, Wei-Horng Yang, Yiyang Sayion, Li-fei Liu, Ping-Du Lee, Jong-Ching Su. Differentially and developmentally regulated expression of three rice sucrose synthase genes[J]. Plant Cell Phyisol, 1999, 40:800–807.
 </references>
 ==Structured Information==

@@ Line 64: / Line 64: @@
 Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|
 AP = Chromosome 7:26089796..26095289|
 name=NC_008400:26089796..26095289
 source=RiceChromosome07
@@ Line 75: / Line 73: @@
 preset=GeneLocation
 </gbrowseImage2>|
-CDNA=<cdnaseq>atgggggaaactactggagaacgtgccctgacccgtctccacagcatgagggagcgcatcggcgattccctctccgcgcacaccaatgagcttgtggctgtcttctcaaggcttgtgaaccaaggaaagggaatgctacagccccaccagatcattgctgagtacaacgccgcaatccctgagggcgagcgtgagaagctgaaggactctgccttagaggatgtcctgaggggagcacaggaggcgattgtcatccctccatggattgcccttgccattcgcccaaggcctggtgtctgggagtatctgaggatcaatgtaagccagcttggtgttgaggagctgagtgtccctgaatacttgcagttcaaggagcagcttgtggatggaagcacccagaacaactttgtgcttgagctggactttgagccattcaatgcctccttccctcgcccatcgttgtcgaagtctattggcaatggggtgcagttcttgaacaggcacctgtcgtcaaagctgttccatgacaaagagagcatgtaccccctgctcaactttcttcgtgcgcacaactacaaagggatgaccatgatgttgaacgacaggattcgcagtctcgatgctctccaaggtgcattgaggaaggcagaaaaacatcttgcaggcattacagctgacaccccatattcagagttccatcacaggttccaagagcttggtttggagaagggttggggtgactgcgctcagcgagtgcgtgagactattcaccttctcttggaccttcttgaggcccctgagccgtccgccttggagaagttccttggaacaatcccaatggtgttcaatgttgttatcctctccccgcatggttactttgcacaggctaatgtcttggggtaccctgataccggtgggcaggttgtctacattttggatcaagtccgtgctatggagaatgagatgctgctgaggatcaagcaacaaggtctaaacatcacaccaaggattctcattgtgaccaggttgctacctgatgcgcatggcaccacatgtggccagcgccttgagaaggtcctaggcactgagcacactcatatcctgcgtgtgccattccgaacagaaaatgggactgttcgcaaatggatctcgcgttttgaagtctggccttacctggaaacttacaccgatgatgtggcacacgagatttctggagagctgcaggccacccctgacctgatcattgggaactacagtgatggcaaccttgttgcatgtttgctggcacacaagttgggtgtcactcattgtacaatcgcccatgcacttgagaaaaccaagtaccccaactccgacctttactggaagaagtttgaggatcactatcacttctcctgccagttcacagctgacctgattgcaatgaaccatgctgacttcatcatcacaagtaccttccaggagattgctggaaacaaggaaactgtggggcagtatgagtctcacatggcattcacaatgcctggcctttatcgtgttgtccatggtatcgatgtctttgaccccaagttcaacatcgtctctcctggtgctgacatgtccatctacttcccattcaccgaatcacagaagaggctcacctctctccatttagagatagaggagctactcttcagtgatgttgaaaacactgagcacaagtttgttctgaaggacaagaagaagccaatcatcttctcgatggctaggctagaccatgtcaagaatttgactggtctggttgagttgtatggtcggaaccctcgcctgcaagagctagtaaaccttgtggttgtctgtggtgaccatggcaaggaatccaaggacaaagaagagcaggctgagttcaagaagatgtttaatctgatcgagcagtacaatttgaatggccacatccgctggatctccgctcagatgaaccgtgtccgcaatggtgagctctaccgctacatctgcgacatgaggggagcctttgtgcagcccgctctctatgaggcctttgggctaactgtgattgaggccatgacctgtggtcttccaacatttgcaactgcctatggtggtccagccgagatcatcgtgcacggcgtgtctggctaccacattgatccttaccagaacgacaaggcctcggcgctgctcgtggagttctttgagaagtgtcaggaagacccaaaccactggatcaagatctcgcagggtggacttcagcgcatcgaggagaagtacacatggaagctctactctgagaggctgatgactctctccggtgtctacggtttctggaagtatgtcaccaacctcgacaggcgtgagacacgccgctacctggagatgctgtacgccctcaagtaccgcaagatggctaccaccgttccattggccattgagggagaggcctccaccaaatga</cdnaseq>|
+CDNA=<cdnaseq>atggggga aactactgga gaacgtgccc
-AA=<aaseq>MGETTGERALTRLHSMRERIGDSLSAHTNELVAVFSRLVNQGKGMLQPHQIIAEYNAAIPEGEREKLKDSALEDVLRGAQEAIVIPPWIALAIRPRPGVWEYLRINVSQLGVEELSVPEYLQFKEQLVDGSTQNNFVLELDFEPFNASFPRPSLSKSIGNGVQFLNRHLSSKLFHDKESMYPLLNFLRAHNYKGMTMMLNDRIRSLDALQGALRKAEKHLAGITADTPYSEFHHRFQELGLEKGWGDCAQRVRETIHLLLDLLEAPEPSALEKFLGTIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRAMENEMLLRIKQQGLNITPRILIVTRLLPDAHGTTCGQRLEKVLGTEHTHILRVPFRTENGTVRKWISRFEVWPYLETYTDDVAHEISGELQATPDLIIGNYSDGNLVACLLAHKLGVTHCTIAHALEKTKYPNSDLYWKKFEDHYHFSCQFTADLIAMNHADFIITSTFQEIAGNKETVGQYESHMAFTMPGLYRVVHGIDVFDPKFNIVSPGADMSIYFPFTESQKRLTSLHLEIEELLFSDVENTEHKFVLKDKKKPIIFSMARLDHVKNLTGLVELYGRNPRLQELVNLVVVCGDHGKESKDKEEQAEFKKMFNLIEQYNLNGHIRWISAQMNRVRNGELYRYICDMRGAFVQPALYEAFGLTVIEAMTCGLPTFATAYGGPAEIIVHGVSGYHIDPYQNDKASALLVEFFEKCQEDPNHWIKISQGGLQRIEEKYTWKLYSERLMTLSGVYGFWKYVTNLDRRETRRYLEMLYALKYRKMATTVPLAIEGEASTK</aaseq>|
+tgacccgtct ccacagcatg agggagcgca tcggcgattc cctctccgcg cacaccaatg
 DNA = <dnaseqindica> 1 gagcatccat cggttctctg ctctgttcat ccatagagtt tcctcctctt ctcctttagt
 gcaaggcttg aggatccatc tagaagatag caatggggga aactactgga gaacgtgccc

@@ Line 52: / Line 52: @@
 GeneName = Os07g0616800|
 Description = Sucrose synthase 3 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 3)|
-Version = NM_001066813.1 GI:115473358 GeneID:4343910|
+Version = AK100306.1 GI:32985515|
-Length = 5494 bp|
+Length = 2771 bp|
-Definition = Oryza sativa Japonica Group Os07g0616800, complete gene.|
+Definition = Oryza sativa Japonica Group cDNA clone:J023078G01, full insert sequence.|
-Source = Oryza sativa Japonica Group
+Source = Oryza sativa Japonica Group (Japanese rice)
    ORGANISM  Oryza sativa Japonica Group
@@ Line 75: / Line 75: @@
 preset=GeneLocation
 </gbrowseImage2>|
-CDNA = <cdnaseq>atgggggaaactactggagaacgtgccctgacccgtctccacagcatgagggagcgcatcggcgattccctctccgcgcacaccaatgagcttgtggctgtcttctcaaggcttgtgaaccaaggaaagggaatgctacagccccaccagatcattgctgagtacaacgccgcaatccctgagggcgagcgtgagaagctgaaggactctgccttagaggatgtcctgaggggagcacaggaggcgattgtcatccctccatggattgcccttgccattcgcccaaggcctggtgtctgggagtatctgaggatcaatgtaagccagcttggtgttgaggagctgagtgtccctgaatacttgcagttcaaggagcagcttgtggatggaagcacccagaacaactttgtgcttgagctggactttgagccattcaatgcctccttccctcgcccatcgttgtcgaagtctattggcaatggggtgcagttcttgaacaggcacctgtcgtcaaagctgttccatgacaaagagagcatgtaccccctgctcaactttcttcgtgcgcacaactacaaagggatgaccatgatgttgaacgacaggattcgcagtctcgatgctctccaaggtgcattgaggaaggcagaaaaacatcttgcaggcattacagctgacaccccatattcagagttccatcacaggttccaagagcttggtttggagaagggttggggtgactgcgctcagcgagtgcgtgagactattcaccttctcttggaccttcttgaggcccctgagccgtccgccttggagaagttccttggaacaatcccaatggtgttcaatgttgttatcctctccccgcatggttactttgcacaggctaatgtcttggggtaccctgataccggtgggcaggttgtctacattttggatcaagtccgtgctatggagaatgagatgctgctgaggatcaagcaacaaggtctaaacatcacaccaaggattctcattgtgaccaggttgctacctgatgcgcatggcaccacatgtggccagcgccttgagaaggtcctaggcactgagcacactcatatcctgcgtgtgccattccgaacagaaaatgggactgttcgcaaatggatctcgcgttttgaagtctggccttacctggaaacttacaccgatgatgtggcacacgagatttctggagagctgcaggccacccctgacctgatcattgggaactacagtgatggcaaccttgttgcatgtttgctggcacacaagttgggtgtcactcattgtacaatcgcccatgcacttgagaaaaccaagtaccccaactccgacctttactggaagaagtttgaggatcactatcacttctcctgccagttcacagctgacctgattgcaatgaaccatgctgacttcatcatcacaagtaccttccaggagattgctggaaacaaggaaactgtggggcagtatgagtctcacatggcattcacaatgcctggcctttatcgtgttgtccatggtatcgatgtctttgaccccaagttcaacatcgtctctcctggtgctgacatgtccatctacttcccattcaccgaatcacagaagaggctcacctctctccatttagagatagaggagctactcttcagtgatgttgaaaacactgagcacaagtttgttctgaaggacaagaagaagccaatcatcttctcgatggctaggctagaccatgtcaagaatttgactggtctggttgagttgtatggtcggaaccctcgcctgcaagagctagtaaaccttgtggttgtctgtggtgaccatggcaaggaatccaaggacaaagaagagcaggctgagttcaagaagatgtttaatctgatcgagcagtacaatttgaatggccacatccgctggatctccgctcagatgaaccgtgtccgcaatggtgagctctaccgctacatctgcgacatgaggggagcctttgtgcagcccgctctctatgaggcctttgggctaactgtgattgaggccatgacctgtggtcttccaacatttgcaactgcctatggtggtccagccgagatcatcgtgcacggcgtgtctggctaccacattgatccttaccagaacgacaaggcctcggcgctgctcgtggagttctttgagaagtgtcaggaagacccaaaccactggatcaagatctcgcagggtggacttcagcgcatcgaggagaagtacacatggaagctctactctgagaggctgatgactctctccggtgtctacggtttctggaagtatgtcaccaacctcgacaggcgtgagacacgccgctacctggagatgctgtacgccctcaagtaccgcaagatggctaccaccgttccattggccattgagggagaggcctccaccaaatga</cdnaseq>|
+CDNA=<cdnaseq>atgggggaaactactggagaacgtgccctgacccgtctccacagcatgagggagcgcatcggcgattccctctccgcgcacaccaatgagcttgtggctgtcttctcaaggcttgtgaaccaaggaaagggaatgctacagccccaccagatcattgctgagtacaacgccgcaatccctgagggcgagcgtgagaagctgaaggactctgccttagaggatgtcctgaggggagcacaggaggcgattgtcatccctccatggattgcccttgccattcgcccaaggcctggtgtctgggagtatctgaggatcaatgtaagccagcttggtgttgaggagctgagtgtccctgaatacttgcagttcaaggagcagcttgtggatggaagcacccagaacaactttgtgcttgagctggactttgagccattcaatgcctccttccctcgcccatcgttgtcgaagtctattggcaatggggtgcagttcttgaacaggcacctgtcgtcaaagctgttccatgacaaagagagcatgtaccccctgctcaactttcttcgtgcgcacaactacaaagggatgaccatgatgttgaacgacaggattcgcagtctcgatgctctccaaggtgcattgaggaaggcagaaaaacatcttgcaggcattacagctgacaccccatattcagagttccatcacaggttccaagagcttggtttggagaagggttggggtgactgcgctcagcgagtgcgtgagactattcaccttctcttggaccttcttgaggcccctgagccgtccgccttggagaagttccttggaacaatcccaatggtgttcaatgttgttatcctctccccgcatggttactttgcacaggctaatgtcttggggtaccctgataccggtgggcaggttgtctacattttggatcaagtccgtgctatggagaatgagatgctgctgaggatcaagcaacaaggtctaaacatcacaccaaggattctcattgtgaccaggttgctacctgatgcgcatggcaccacatgtggccagcgccttgagaaggtcctaggcactgagcacactcatatcctgcgtgtgccattccgaacagaaaatgggactgttcgcaaatggatctcgcgttttgaagtctggccttacctggaaacttacaccgatgatgtggcacacgagatttctggagagctgcaggccacccctgacctgatcattgggaactacagtgatggcaaccttgttgcatgtttgctggcacacaagttgggtgtcactcattgtacaatcgcccatgcacttgagaaaaccaagtaccccaactccgacctttactggaagaagtttgaggatcactatcacttctcctgccagttcacagctgacctgattgcaatgaaccatgctgacttcatcatcacaagtaccttccaggagattgctggaaacaaggaaactgtggggcagtatgagtctcacatggcattcacaatgcctggcctttatcgtgttgtccatggtatcgatgtctttgaccccaagttcaacatcgtctctcctggtgctgacatgtccatctacttcccattcaccgaatcacagaagaggctcacctctctccatttagagatagaggagctactcttcagtgatgttgaaaacactgagcacaagtttgttctgaaggacaagaagaagccaatcatcttctcgatggctaggctagaccatgtcaagaatttgactggtctggttgagttgtatggtcggaaccctcgcctgcaagagctagtaaaccttgtggttgtctgtggtgaccatggcaaggaatccaaggacaaagaagagcaggctgagttcaagaagatgtttaatctgatcgagcagtacaatttgaatggccacatccgctggatctccgctcagatgaaccgtgtccgcaatggtgagctctaccgctacatctgcgacatgaggggagcctttgtgcagcccgctctctatgaggcctttgggctaactgtgattgaggccatgacctgtggtcttccaacatttgcaactgcctatggtggtccagccgagatcatcgtgcacggcgtgtctggctaccacattgatccttaccagaacgacaaggcctcggcgctgctcgtggagttctttgagaagtgtcaggaagacccaaaccactggatcaagatctcgcagggtggacttcagcgcatcgaggagaagtacacatggaagctctactctgagaggctgatgactctctccggtgtctacggtttctggaagtatgtcaccaacctcgacaggcgtgagacacgccgctacctggagatgctgtacgccctcaagtaccgcaagatggctaccaccgttccattggccattgagggagaggcctccaccaaatga</cdnaseq>|
-AA = <aaseq>MGETTGERALTRLHSMRERIGDSLSAHTNELVAVFSRLVNQGKG                     MLQPHQIIAEYNAAIPEGEREKLKDSALEDVLRGAQEAIVIPPWIALAIRPRPGVWEY                     LRINVSQLGVEELSVPEYLQFKEQLVDGSTQNNFVLELDFEPFNASFPRPSLSKSIGN                     GVQFLNRHLSSKLFHDKESMYPLLNFLRAHNYKGMTMMLNDRIRSLDALQGALRKAEK                     HLAGITADTPYSEFHHRFQELGLEKGWGDCAQRVRETIHLLLDLLEAPEPSALEKFLG                     TIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRAMENEMLLRIKQQGLNIT                     PRILIVTRLLPDAHGTTCGQRLEKVLGTEHTHILRVPFRTENGTVRKWISRFEVWPYL                     ETYTDDVAHEISGELQATPDLIIGNYSDGNLVACLLAHKLGVTHCTIAHALEKTKYPN                     SDLYWKKFEDHYHFSCQFTADLIAMNHADFIITSTFQEIAGNKETVGQYESHMAFTMP                     GLYRVVHGIDVFDPKFNIVSPGADMSIYFPFTESQKRLTSLHLEIEELLFSDVENTEH                     KFVLKDKKKPIIFSMARLDHVKNLTGLVELYGRNPRLQELVNLVVVCGDHGKESKDKE                     EQAEFKKMFNLIEQYNLNGHIRWISAQMNRVRNGELYRYICDMRGAFVQPALYEAFGL                     TVIEAMTCGLPTFATAYGGPAEIIVHGVSGYHIDPYQNDKASALLVEFFEKCQEDPNH                     WIKISQGGLQRIEEKYTWKLYSERLMTLSGVYGFWKYVTNLDRRETRRYLEMLYALKY                     RKMATTVPLAIEGEASTK</aaseq>|
+AA=<aaseq>MGETTGERALTRLHSMRERIGDSLSAHTNELVAVFSRLVNQGKGMLQPHQIIAEYNAAIPEGEREKLKDSALEDVLRGAQEAIVIPPWIALAIRPRPGVWEYLRINVSQLGVEELSVPEYLQFKEQLVDGSTQNNFVLELDFEPFNASFPRPSLSKSIGNGVQFLNRHLSSKLFHDKESMYPLLNFLRAHNYKGMTMMLNDRIRSLDALQGALRKAEKHLAGITADTPYSEFHHRFQELGLEKGWGDCAQRVRETIHLLLDLLEAPEPSALEKFLGTIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRAMENEMLLRIKQQGLNITPRILIVTRLLPDAHGTTCGQRLEKVLGTEHTHILRVPFRTENGTVRKWISRFEVWPYLETYTDDVAHEISGELQATPDLIIGNYSDGNLVACLLAHKLGVTHCTIAHALEKTKYPNSDLYWKKFEDHYHFSCQFTADLIAMNHADFIITSTFQEIAGNKETVGQYESHMAFTMPGLYRVVHGIDVFDPKFNIVSPGADMSIYFPFTESQKRLTSLHLEIEELLFSDVENTEHKFVLKDKKKPIIFSMARLDHVKNLTGLVELYGRNPRLQELVNLVVVCGDHGKESKDKEEQAEFKKMFNLIEQYNLNGHIRWISAQMNRVRNGELYRYICDMRGAFVQPALYEAFGLTVIEAMTCGLPTFATAYGGPAEIIVHGVSGYHIDPYQNDKASALLVEFFEKCQEDPNHWIKISQGGLQRIEEKYTWKLYSERLMTLSGVYGFWKYVTNLDRRETRRYLEMLYALKYRKMATTVPLAIEGEASTK</aaseq>|
-DNA = <dnaseqindica>960..1069#1615..1744#1840..1991#2077..2269#2447..2565#2653..2869#2980..3075#3191..3364#3472..3588#3684..3850#3929..4153#4241..4559#4645..4889#4984..5122#5219..5266#agcatccatcggttctctgctctgttcatccatagagtttcctcctcttctcctttagtgcaaggtagagaagagcatgtgtgtgtgtgtgtgtgtgtgaactgtgaagtgcagagtgcttctgtagttctgtgttatgtccatagtgatcttgttaggattgttgctatggatgcatgatgttatggttgatctctgaattacagtagggacttttctgagatctctggattagtggggggtgctaaatttttttctggttgcatcagcttgggtttctggtattggtgtgggttcttgctctgaattttggttcagaatgtcgatttgtttgtgtttgttctctgaagttgagagtagctatgatccatccagcacagaactgcaggtcctgcctgccggctgcatatacaggacatgccattttgcaagctctgggcttatggtttctcttttggagttcttcttcttgcatgatctgtgttctctaacaaaggaagcaagatttagcaactttattcagagacaagaaaaggatctggcaaccttttgtttctgttttatcctactcgtaaagattgttatttaagcaaaaatttcccaaaagttttaaatataatttccatgatgtgccactctcatgtccttgaacctggcactcattatgggctcctcagaagtgctgtagctaatgtcactaatcttttgtatctttgttcatagtcttgtattttatgatgcttatccctttgtgctttccatgtttgatgtccaaatgtcatggcaatgtttttgacttctagtaggggttttagtacctttttgttagataagtacatccaaattctgtttatttattcaaaaatcattctgtttattcactgaaaacatttgtccattcaatggactcataaactgtctgtgtttttcaggcttgaggatccatctagaagatagcaatgggggaaactactggagaacgtgccctgacccgtctccacagcatgagggagcgcatcggcgattccctctccgcgcacaccaatgagcttgtggctgtcttctcaaggtttgcacttaaatccttctcattttaatttgtattgatctacaagtacaaagatctagttcaaatgatgcatattgattgctttgtttatctcaaagttatgctgatgttagctggataaagagtgcatttactacatgcccaatacaaccatgatcttagctgtaaattgttaagtctgatgatcaccccagaatatatctgctattatccattccgtcgtttctataatatcctttggtaactctcagtagaagtgcttttaatttttcagttggagagaacaatttctgacggtgatctgttttaattgttctgtatagtgtcaagaaatattcctgtatttccaatatagtgctttttacagttccatcatatcaatggattaacatatggaacaaaaaaaatatttaaatcggttctgtttgtttaaaaaaaaggaaaaaagtttttgttcattcccacaaaacaatacattttcgaatttcaagtaatacaaagttggtaaatctaaaataactgttgttatgcaattttctgttcaggcttgtgaaccaaggaaagggaatgctacagccccaccagatcattgctgagtacaacgccgcaatccctgagggcgagcgtgagaagctgaaggactctgccttagaggatgtcctgaggggagcacaggtttgcatcagcagaactcactgcactatcatgctgaatggtactcccaaatgttcagctctgatgtaaaaaaatgttgctggtttgttgtgcaggaggcgattgtcatccctccatggattgcccttgccattcgcccaaggcctggtgtctgggagtatctgaggatcaatgtaagccagcttggtgttgaggagctgagtgtccctgaatacttgcagttcaaggagcagcttgtggatggaaggtatctggagctgtgattttaaccaataccatgcttaaagttataccttagattcctgatttgacaatcatgtgattgttttcagcacccagaacaactttgtgcttgagctggactttgagccattcaatgcctccttccctcgcccatcgttgtcgaagtctattggcaatggggtgcagttcttgaacaggcacctgtcgtcaaagctgttccatgacaaagagagcatgtaccccctgctcaactttcttcgtgcgcacaactacaaagggatggtaggttacactttccgatttcttgatttgattaaccgatccatatatttactatgatttataaactagtgtgttgtctgaatccttgtattcattgcctttgccatgacaactggaactactactcattgctgaatcaagcggagtttgcaataacttatgtccgtcctttttcagaccatgatgttgaacgacaggattcgcagtctcgatgctctccaaggtgcattgaggaaggcagaaaaacatcttgcaggcattacagctgacaccccatattcagagttccatcacaggtactgcacaatcgtcatgcaatgtctgaccaaatagaagttactatcaatgcatatctgacaatgttctttcatcaataaatttaggttccaagagcttggtttggagaagggttggggtgactgcgctcagcgagtgcgtgagactattcaccttctcttggaccttcttgaggcccctgagccgtccgccttggagaagttccttggaacaatcccaatggtgttcaatgttgttatcctctccccgcatggttactttgcacaggctaatgtcttggggtaccctgataccggtgggcaggtaatatactatccagttctacgagctggaatgttacctctttatataattgaaaccaccaagagtccaagactgatgccccagttttcttatgtgatggcaacttacaggttgtctacattttggatcaagtccgtgctatggagaatgagatgctgctgaggatcaagcaacaaggtctaaacatcacaccaaggattctcattgtaagttttttatttgaacgtaaattctcattgtaagttcaatacccaataaggtcaattacaaccttgcactttaattgattccaaataatgaggcctttttggtattacataggtgaccaggttgctacctgatgcgcatggcaccacatgtggccagcgccttgagaaggtcctaggcactgagcacactcatatcctgcgtgtgccattccgaacagaaaatgggactgttcgcaaatggatctcgcgttttgaagtctggccttacctggaaacttacaccgatgtatgtctcatcttccaacaagtttattgtcatcgtttcatcaaaataatcaacttaggttccttaaaaaaaatgatcaacttatcattcttttctgttgctttcaggatgtggcacacgagatttctggagagctgcaggccacccctgacctgatcattgggaactacagtgatggcaaccttgttgcatgtttgctggcacacaagttgggtgtcactcatgtacgaattctagcaccttattcaatacaattttttttatgataagcatagtatttcaattattcactgtagtattcttgttccatcatgtgcagtgtacaatcgcccatgcacttgagaaaaccaagtaccccaactccgacctttactggaagaagtttgaggatcactatcacttctcctgccagttcacagctgacctgattgcaatgaaccatgctgacttcatcatcacaagtaccttccaggagattgctggaaagtaagattttccttttacaaactttctggatatttgtaaatggcataagctgatcttacatcatcatccaattttcagcaaggaaactgtggggcagtatgagtctcacatggcattcacaatgcctggcctttatcgtgttgtccatggtatcgatgtctttgaccccaagttcaacatcgtctctcctggtgctgacatgtccatctacttcccattcaccgaatcacagaagaggctcacctctctccatttagagatagaggagctactcttcagtgatgttgaaaacactgagcacaagtgagtattgtataatcttttaccagtttgagttgtaactcaacatatgcatatcatgcctgttatcttactggactacctctgtaggtttgttctgaaggacaagaagaagccaatcatcttctcgatggctaggctagaccatgtcaagaatttgactggtctggttgagttgtatggtcggaaccctcgcctgcaagagctagtaaaccttgtggttgtctgtggtgaccatggcaaggaatccaaggacaaagaagagcaggctgagttcaagaagatgtttaatctgatcgagcagtacaatttgaatggccacatccgctggatctccgctcagatgaaccgtgtccgcaatggtgagctctaccgctacatctgcgacatgaggggagcctttgtgcaggtgatgaacactgtcaagctatgagctctccaacaaatttgtagtgttagctagttctgattttctcttttctttttgcaaccagcccgctctctatgaggcctttgggctaactgtgattgaggccatgacctgtggtcttccaacatttgcaactgcctatggtggtccagccgagatcatcgtgcacggcgtgtctggctaccacattgatccttaccagaacgacaaggcctcggcgctgctcgtggagttctttgagaagtgtcaggaagacccaaaccactggatcaagatctcgcagggtggacttcagcgcatcgaggagaagtatgcaaaattctcgtcttaccatgttaccatatgatgaagatgaacactatctaggatctaactgagatgttgccacttgatatcgatgcaggtacacatggaagctctactctgagaggctgatgactctctccggtgtctacggtttctggaagtatgtcaccaacctcgacaggcgtgagacacgccgctacctggagatgctgtacgccctcaagtaccgcaagatggtatgcgcaacattatcgcactttccttcatccatttcatctcagcctatagcctttgtgcttattcttgtactgttgctttgtgttcttgtgcaggctaccaccgttccattggccattgagggagaggcctccaccaaatgatctggccttacccggtgaaaagaatgggcaatgggtgctccattgttgcagtgctgatccaggggtgaagaaaaacagaaatcgaggaacgaatgcatccatttagtttctaagggtttagttgatttcagggccagttcttgtggggttttcaatggaagaaattgatgtaatgctctggccttttcatggatactatgaatgaaataaatgaataacaagattctc</dnaseqindica>|
+DNA = <dnaseqindica> 1 gagcatccat cggttctctg ctctgttcat ccatagagtt tcctcctctt ctcctttagt
 Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001066813.1 RefSeq:Os07g0616800]|
 }}

@@ Line 23: / Line 23: @@
 ===Recombination===
-Puji Lestari <ref name="ref4" /> used the algorithm of Hudson and Kaplan to determine that at least 11 recombination events were responsible for the polymorphism pattern identified in the RSUS3 gene. The recombinations were detected in the informative sites of the 3 regions: a minimum of 3 recombinations in the 5’ NTR (-1639 to -1630, -1594 to -1588, and -679 to -600), 4 in the transcribed region (1072–2734, 2734–3305, 4117–4148, and 4148–4572), 1 in the position between the transcribed region and the downstream region (4572–5627), and 3 in the 3’ NTR (5627–5923, 6041–6050, and 6050–6055). A total of 48 polymorphic sites in the entire region without intron were analyzed for evidence of recombination.
+Puji Lestari <ref name="ref3" /> used the algorithm of Hudson and Kaplan to determine that at least 11 recombination events were responsible for the polymorphism pattern identified in the RSUS3 gene. The recombinations were detected in the informative sites of the 3 regions: a minimum of 3 recombinations in the 5’ NTR (-1639 to -1630, -1594 to -1588, and -679 to -600), 4 in the transcribed region (1072–2734, 2734–3305, 4117–4148, and 4148–4572), 1 in the position between the transcribed region and the downstream region (4572–5627), and 3 in the 3’ NTR (5627–5923, 6041–6050, and 6050–6055). A total of 48 polymorphic sites in the entire region without intron were analyzed for evidence of recombination.
 ===Evolution===

@@ Line 20: / Line 20: @@
 ===Haplotype Diversity===
-Some researchers predicted initially the number of haplotypes of RSUS3 using the coalescent theory. The predicted haplotype numbers for each functional part of the promoter, transcript, and downstream region were 17, 12, and 12, respectively. The highest haplotype diversity (Hd: 0.866) was observed in the promoter region, and the lowest Hd (0.828) was observed in the downstream region. Puji Lestari <ref name="ref3" /> analyzed the entire region excluding intron revealed that the nucleotide diversity ranged from 1.645 to 1.801, and the estimated haplotype number was from 10 to 22. Finally, using bootstrap analysis, the genealogy of the sequences containing 11 major highly differentiated haplotypes groups across the region of 5’ NTR-transcript-3’ NTR was successfully assembled. They constructed a neighbor joining tree to illustrate the phylogenetic branching order between the 5’ NTR transcript-3’ NTR and to elucidate the evolutionary history(picture 12).[[File:picture 12 Neighbor joining tree representing the RSUS3 haplotype relationships based on the entire region excluding intron (upstream, transcript, and 3' downstream NTR sequence).jpg|right|thumb|150px|''picture 12. Neighbor joining tree representing the RSUS3 haplotype relationships based on the entire region excluding intron (upstream, transcript, and 3' downstream NTR sequence) (from reference <ref name="ref4" />).'']]
+Some researchers predicted initially the number of haplotypes of RSUS3 using the coalescent theory. The predicted haplotype numbers for each functional part of the promoter, transcript, and downstream region were 17, 12, and 12, respectively. The highest haplotype diversity (Hd: 0.866) was observed in the promoter region, and the lowest Hd (0.828) was observed in the downstream region. Puji Lestari <ref name="ref3" /> analyzed the entire region excluding intron revealed that the nucleotide diversity ranged from 1.645 to 1.801, and the estimated haplotype number was from 10 to 22. Finally, using bootstrap analysis, the genealogy of the sequences containing 11 major highly differentiated haplotypes groups across the region of 5’ NTR-transcript-3’ NTR was successfully assembled. They constructed a neighbor joining tree to illustrate the phylogenetic branching order between the 5’ NTR transcript-3’ NTR and to elucidate the evolutionary history(picture 12).[[File:picture 12 Neighbor joining tree representing the RSUS3 haplotype relationships based on the entire region excluding intron (upstream, transcript, and 3' downstream NTR sequence).jpg|right|thumb|150px|''picture 12. Neighbor joining tree representing the RSUS3 haplotype relationships based on the entire region excluding intron (upstream, transcript, and 3' downstream NTR sequence) (from reference <ref name="ref3" />).'']]
 ===Recombination===