Difference between revisions of "Os07g0616800"
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===Haplotype Diversity=== | ===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" />).'']] | ||
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===Recombination=== | ===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="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. | ||
Revision as of 07:32, 24 May 2014
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Contents
characteristic
The current work [1] confirms that six genes comprise the entire rice Sucrose synthase (SUS) gene family.Function
In higher plants sucrose is the major form in which carbohydrate is transported from photosynthetic source tissues to sink tissues, and its subsequent cleavage in the sink tissues is the first step for utilization of the photoassimilate in various metabolic pathways. Sucrose synthase (Sus) plays a major role(s) in sucrose metabolism in a number of different growth processes within a variety of sink tissues. Sus catalyzes a reaction of sucrose and UDP to form fructose and UDPG, the latter being a precursor of complex saccharide biosynthesis. Sus is also proposed to supply UDP-glucose for cellulose synthesis in the cell wall, and in cotton fiber which is supported by experimental evidence from antisense suppression of the enzyme. In addition to these major roles in sink tissue metabolism, Sus gene expression has also been reported to be induced in response to environmental stresses such as hypoxia and cold. Further roles for Sus were proposed in other important metabolic processes including nitrogen fixation in legume nodules and phloem loading and/or unloading. Specially, rice sucrose synthase 3(RSUS3) has its own role in sucrose metabolism. First, Tatsuro Hirose et al [1] and Wang et al [3] suggest that SUS3 play a catalyzed reaction when the RSUS1 which is rich in the phloem and aleurone layers of the seeds, transport sugar into the endosperm cells. Second, RSUS3 is expressed predominantly in rice seed endosperm and is thought to play an important role in starch filling during the milky stage of rice seed ripening [2]. Third, SUS3 and SUS4 were predominantly expressed in the caryopsis, indicating potential roles in carbon allocation within the filling grain and participated in the cleavage of sucrose, taken up by aleurone, thus providing the precursors for starch synthesis. [1]
Expression
Wang et al [3] 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.Nucleotide Polymorphisms
Nucleotide changes and indels at the RSUS3 locus were identified, and the results are summarized in picture 10.Allele Distribution
Puji Lestari [3] 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.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 [3] 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).Recombination
Puji Lestari [2] 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
Sequence analysis revealed that RSUS2 and RSUS3 may have evolved from the same ancestor after the divergence of RSUS1.
Labs working on this gene
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References
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Structured Information
| Gene Name |
Os07g0616800 |
|---|---|
| Description |
Sucrose synthase 3 (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase 3) |
| Version |
NM_001066813.1 GI:115473358 GeneID:4343910 |
| Length |
5494 bp |
| Definition |
Oryza sativa Japonica Group Os07g0616800, 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 7:26089796..26095289 |
| Sequence Coding Region |
26090755..26090864,26091410..26091539,26091635..26091786,26091872..26092064,26092242..26092360 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008400:26089796..26095289 source=RiceChromosome07 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008400:26089796..26095289 source=RiceChromosome07 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atgggggaaactactggagaacgtgccctgacccgtctccacagcatgagggagcgcatcggcgattccctctccgcgcacaccaatgagcttgtggctgtcttctcaaggcttgtgaaccaaggaaagggaatgctacagccccaccagatcattgctgagtacaacgccgcaatccctgagggcgagcgtgagaagctgaaggactctgccttagaggatgtcctgaggggagcacaggaggcgattgtcatccctccatggattgcccttgccattcgcccaaggcctggtgtctgggagtatctgaggatcaatgtaagccagcttggtgttgaggagctgagtgtccctgaatacttgcagttcaaggagcagcttgtggatggaagcacccagaacaactttgtgcttgagctggactttgagccattcaatgcctccttccctcgcccatcgttgtcgaagtctattggcaatggggtgcagttcttgaacaggcacctgtcgtcaaagctgttccatgacaaagagagcatgtaccccctgctcaactttcttcgtgcgcacaactacaaagggatgaccatgatgttgaacgacaggattcgcagtctcgatgctctccaaggtgcattgaggaaggcagaaaaacatcttgcaggcattacagctgacaccccatattcagagttccatcacaggttccaagagcttggtttggagaagggttggggtgactgcgctcagcgagtgcgtgagactattcaccttctcttggaccttcttgaggcccctgagccgtccgccttggagaagttccttggaacaatcccaatggtgttcaatgttgttatcctctccccgcatggttactttgcacaggctaatgtcttggggtaccctgataccggtgggcaggttgtctacattttggatcaagtccgtgctatggagaatgagatgctgctgaggatcaagcaacaaggtctaaacatcacaccaaggattctcattgtgaccaggttgctacctgatgcgcatggcaccacatgtggccagcgccttgagaaggtcctaggcactgagcacactcatatcctgcgtgtgccattccgaacagaaaatgggactgttcgcaaatggatctcgcgttttgaagtctggccttacctggaaacttacaccgatgatgtggcacacgagatttctggagagctgcaggccacccctgacctgatcattgggaactacagtgatggcaaccttgttgcatgtttgctggcacacaagttgggtgtcactcattgtacaatcgcccatgcacttgagaaaaccaagtaccccaactccgacctttactggaagaagtttgaggatcactatcacttctcctgccagttcacagctgacctgattgcaatgaaccatgctgacttcatcatcacaagtaccttccaggagattgctggaaacaaggaaactgtggggcagtatgagtctcacatggcattcacaatgcctggcctttatcgtgttgtccatggtatcgatgtctttgaccccaagttcaacatcgtctctcctggtgctgacatgtccatctacttcccattcaccgaatcacagaagaggctcacctctctccatttagagatagaggagctactcttcagtgatgttgaaaacactgagcacaagtttgttctgaaggacaagaagaagccaatcatcttctcgatggctaggctagaccatgtcaagaatttgactggtctggttgagttgtatggtcggaaccctcgcctgcaagagctagtaaaccttgtggttgtctgtggtgaccatggcaaggaatccaaggacaaagaagagcaggctgagttcaagaagatgtttaatctgatcgagcagtacaatttgaatggccacatccgctggatctccgctcagatgaaccgtgtccgcaatggtgagctctaccgctacatctgcgacatgaggggagcctttgtgcagcccgctctctatgaggcctttgggctaactgtgattgaggccatgacctgtggtcttccaacatttgcaactgcctatggtggtccagccgagatcatcgtgcacggcgtgtctggctaccacattgatccttaccagaacgacaaggcctcggcgctgctcgtggagttctttgagaagtgtcaggaagacccaaaccactggatcaagatctcgcagggtggacttcagcgcatcgaggagaagtacacatggaagctctactctgagaggctgatgactctctccggtgtctacggtttctggaagtatgtcaccaacctcgacaggcgtgagacacgccgctacctggagatgctgtacgccctcaagtaccgcaagatggctaccaccgttccattggccattgagggagaggcctccaccaaatga</cdnaseq> |
| Protein Sequence |
<aaseq>MGETTGERALTRLHSMRERIGDSLSAHTNELVAVFSRLVNQGKG MLQPHQIIAEYNAAIPEGEREKLKDSALEDVLRGAQEAIVIPPWIALAIRPRPGVWEY LRINVSQLGVEELSVPEYLQFKEQLVDGSTQNNFVLELDFEPFNASFPRPSLSKSIGN GVQFLNRHLSSKLFHDKESMYPLLNFLRAHNYKGMTMMLNDRIRSLDALQGALRKAEK HLAGITADTPYSEFHHRFQELGLEKGWGDCAQRVRETIHLLLDLLEAPEPSALEKFLG TIPMVFNVVILSPHGYFAQANVLGYPDTGGQVVYILDQVRAMENEMLLRIKQQGLNIT PRILIVTRLLPDAHGTTCGQRLEKVLGTEHTHILRVPFRTENGTVRKWISRFEVWPYL ETYTDDVAHEISGELQATPDLIIGNYSDGNLVACLLAHKLGVTHCTIAHALEKTKYPN SDLYWKKFEDHYHFSCQFTADLIAMNHADFIITSTFQEIAGNKETVGQYESHMAFTMP GLYRVVHGIDVFDPKFNIVSPGADMSIYFPFTESQKRLTSLHLEIEELLFSDVENTEH KFVLKDKKKPIIFSMARLDHVKNLTGLVELYGRNPRLQELVNLVVVCGDHGKESKDKE EQAEFKKMFNLIEQYNLNGHIRWISAQMNRVRNGELYRYICDMRGAFVQPALYEAFGL TVIEAMTCGLPTFATAYGGPAEIIVHGVSGYHIDPYQNDKASALLVEFFEKCQEDPNH WIKISQGGLQRIEEKYTWKLYSERLMTLSGVYGFWKYVTNLDRRETRRYLEMLYALKY RKMATTVPLAIEGEASTK</aaseq> |
| Gene Sequence |
<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> |
| External Link(s) |
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Cite error: Invalid
<ref>tag; no text was provided for refs namedref1 - ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Cite error: Invalid
<ref>tag; no text was provided for refs namedref4 - ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Cite error: Invalid
<ref>tag; no text was provided for refs namedref3