RiceWiki - User contributions [en]

Os10g0405500

2014-06-08T15:39:47Z

Syphyll: /* Expression */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.The PAIR3 gene was preferentially expressed in the meiocytes, especially during the male and female meiosis stages. The expression pattern of PAIR3 together with the phenotype observed in the loss-of-function mutants indicated that the PAIR3 protein works in the meiocytes and plays crucial roles in homologous pairing and synapsis. Meanwhile data report that expression of PAIR1, PAIR2, MEL1, OsDMC1 and OsRad21-4 genes are likely to be independent of PAIR3function in controlling chromosome pairing during meiosis. To recover the internal sequence of the transcripts, RT-PCR was performed by using DNase I and SuperScript II (Invitrogen) according to the manufacturer’s instructions. Primers (F78RT1 to F78RT4) were designed according to the sequences within the boundaries defined by the exon ends for PCR amplification of the reverse-transcription products<ref name="ref1" />.The primer sequences of InDel markers were as follows:
*P1 (5’-TACGTGTCCTTGTGCCTGA-3’and 5’-ACAAATGAACTGAGAACGTG-3’)
*P2 (5’-CTTCCGATTAATTTCCTTTC-3’and 5’-GGGTCTAGCTATTTGCTCT-3’)
*P3 (5’-TTCTACGAGCTTCCTACG-3’and 5’-CTTAGACTCATTATAGTAC-3’)
*P4 (5’-CATATAGTGTCATATGCACC-3’and 5’-GTCGTGTGTTTGCCAACAAT-3’)
*P5 (5’-CACTTCAGTGCTGGGTGTGC-3’and 5’-TCAAAGGGCAAGTTAACGAC-3’)
*P6 (5’-GCGCATCCATGCATATCCAA-3’and 5’-GACAAGGTGTTGCCCAAGAA-3’)
*P7 (5’-GTCAATGTGAATGGGAGACC-3’and 5’-AGCAGCTCAAGGCAGCGA-3’)
*P8 (5’-TTTCAGTGGCTCTGTTCGG-3’and 5’-CAAAAGGAAATGAGTGAGGCT-3’)

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.It shows that proteins with poor homology at the amino acid sequence level, but with similar structure, perform similar functions in other model organisms. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. Similarly, the SYCP3/COR1 protein also has a predicted coiled-coil motif in the C-terminal half. In addition, both PAIR3 and SYCP3/COR1 assemble and disassemble in the same time as the SCs and label the AE/LE in a continuous manner. Mutation of either gene results in the defects in pairing, synapsis, and chiasma formation. However, SYCP3 is essential for the formation of LEs, while PAIR3 is not. Several lines of evidence suggest that the AE/LE seen by staining is only a small component of the axial structure by both morphological and functional criteria. In addition, it is likely that axial components may well occur in multiple (partially overlapping) layers. Therefore, it is also possible that PAIR3 is an AE/LE component and localizes on one layer of the AE/LE.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
*2.Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
*3.State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
*4.National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*5. Department of Plant and Resources College of Bioresources, Nihon University, Fujisawa, Kanagawa 252-8510, Japan
*6. Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
<ref name="ref6">
Zhou S R,Wang Y,Li WC. The Plant Cell[J]. Pollen Semi-Sterility1 Encodes a Kinesin-1–Like Protein Important for Male Meiosis, Anther Dehiscence, and Fertility in Rice,2011,23:111-129.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:34:54Z

Syphyll: /* Reference */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.The PAIR3 gene was preferentially expressed in the meiocytes, especially during the male and female meiosis stages. The expression pattern of PAIR3 together with the phenotype observed in the loss-of-function mutants indicated that the PAIR3 protein works in the meiocytes and plays crucial roles in homologous pairing and synapsis. Meanwhile data report that expression of PAIR1, PAIR2, MEL1, OsDMC1 and OsRad21-4 genes are likely to be independent of PAIR3function in controlling chromosome pairing during meiosis. To recover the internal sequence of the transcripts, RT-PCR was performed by using DNase I and SuperScript II (Invitrogen) according to the manufacturer’s instructions. Primers (F78RT1 to F78RT4) were designed according to the sequences within the boundaries defined by the exon ends for PCR amplification of the reverse-transcription products<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.It shows that proteins with poor homology at the amino acid sequence level, but with similar structure, perform similar functions in other model organisms. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. Similarly, the SYCP3/COR1 protein also has a predicted coiled-coil motif in the C-terminal half. In addition, both PAIR3 and SYCP3/COR1 assemble and disassemble in the same time as the SCs and label the AE/LE in a continuous manner. Mutation of either gene results in the defects in pairing, synapsis, and chiasma formation. However, SYCP3 is essential for the formation of LEs, while PAIR3 is not. Several lines of evidence suggest that the AE/LE seen by staining is only a small component of the axial structure by both morphological and functional criteria. In addition, it is likely that axial components may well occur in multiple (partially overlapping) layers. Therefore, it is also possible that PAIR3 is an AE/LE component and localizes on one layer of the AE/LE.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
*2.Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
*3.State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
*4.National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*5. Department of Plant and Resources College of Bioresources, Nihon University, Fujisawa, Kanagawa 252-8510, Japan
*6. Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
<ref name="ref6">
Zhou S R,Wang Y,Li WC. The Plant Cell[J]. Pollen Semi-Sterility1 Encodes a Kinesin-1–Like Protein Important for Male Meiosis, Anther Dehiscence, and Fertility in Rice,2011,23:111-129.</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:30:57Z

Syphyll: /* Labs working on this gene */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.The PAIR3 gene was preferentially expressed in the meiocytes, especially during the male and female meiosis stages. The expression pattern of PAIR3 together with the phenotype observed in the loss-of-function mutants indicated that the PAIR3 protein works in the meiocytes and plays crucial roles in homologous pairing and synapsis. Meanwhile data report that expression of PAIR1, PAIR2, MEL1, OsDMC1 and OsRad21-4 genes are likely to be independent of PAIR3function in controlling chromosome pairing during meiosis. To recover the internal sequence of the transcripts, RT-PCR was performed by using DNase I and SuperScript II (Invitrogen) according to the manufacturer’s instructions. Primers (F78RT1 to F78RT4) were designed according to the sequences within the boundaries defined by the exon ends for PCR amplification of the reverse-transcription products<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.It shows that proteins with poor homology at the amino acid sequence level, but with similar structure, perform similar functions in other model organisms. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. Similarly, the SYCP3/COR1 protein also has a predicted coiled-coil motif in the C-terminal half. In addition, both PAIR3 and SYCP3/COR1 assemble and disassemble in the same time as the SCs and label the AE/LE in a continuous manner. Mutation of either gene results in the defects in pairing, synapsis, and chiasma formation. However, SYCP3 is essential for the formation of LEs, while PAIR3 is not. Several lines of evidence suggest that the AE/LE seen by staining is only a small component of the axial structure by both morphological and functional criteria. In addition, it is likely that axial components may well occur in multiple (partially overlapping) layers. Therefore, it is also possible that PAIR3 is an AE/LE component and localizes on one layer of the AE/LE.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
*2.Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
*3.State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
*4.National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*5. Department of Plant and Resources College of Bioresources, Nihon University, Fujisawa, Kanagawa 252-8510, Japan
*6. Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:28:57Z

Syphyll: /* Evolution */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.The PAIR3 gene was preferentially expressed in the meiocytes, especially during the male and female meiosis stages. The expression pattern of PAIR3 together with the phenotype observed in the loss-of-function mutants indicated that the PAIR3 protein works in the meiocytes and plays crucial roles in homologous pairing and synapsis. Meanwhile data report that expression of PAIR1, PAIR2, MEL1, OsDMC1 and OsRad21-4 genes are likely to be independent of PAIR3function in controlling chromosome pairing during meiosis. To recover the internal sequence of the transcripts, RT-PCR was performed by using DNase I and SuperScript II (Invitrogen) according to the manufacturer’s instructions. Primers (F78RT1 to F78RT4) were designed according to the sequences within the boundaries defined by the exon ends for PCR amplification of the reverse-transcription products<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.It shows that proteins with poor homology at the amino acid sequence level, but with similar structure, perform similar functions in other model organisms. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. The PAIR3 protein contains putative coiled-coil motifs in its Cterminal domain. Similarly, the SYCP3/COR1 protein also has a predicted coiled-coil motif in the C-terminal half. In addition, both PAIR3 and SYCP3/COR1 assemble and disassemble in the same time as the SCs and label the AE/LE in a continuous manner. Mutation of either gene results in the defects in pairing, synapsis, and chiasma formation. However, SYCP3 is essential for the formation of LEs, while PAIR3 is not. Several lines of evidence suggest that the AE/LE seen by staining is only a small component of the axial structure by both morphological and functional criteria. In addition, it is likely that axial components may well occur in multiple (partially overlapping) layers. Therefore, it is also possible that PAIR3 is an AE/LE component and localizes on one layer of the AE/LE.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 
*Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK 
*State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:24:29Z

Syphyll: /* Expression */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.The PAIR3 gene was preferentially expressed in the meiocytes, especially during the male and female meiosis stages. The expression pattern of PAIR3 together with the phenotype observed in the loss-of-function mutants indicated that the PAIR3 protein works in the meiocytes and plays crucial roles in homologous pairing and synapsis. Meanwhile data report that expression of PAIR1, PAIR2, MEL1, OsDMC1 and OsRad21-4 genes are likely to be independent of PAIR3function in controlling chromosome pairing during meiosis. To recover the internal sequence of the transcripts, RT-PCR was performed by using DNase I and SuperScript II (Invitrogen) according to the manufacturer’s instructions. Primers (F78RT1 to F78RT4) were designed according to the sequences within the boundaries defined by the exon ends for PCR amplification of the reverse-transcription products<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 
*Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK 
*State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:20:40Z

Syphyll: /* Wild Type and Mutant */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', A single nucleotide deletion at position 1044 in the coding region was found in the pair3-1 mutant, which resulted in a frame shift mutation. We also obtained one other mutant showing the same defects as pair3-1 from Nipponbare. Immunostaining with an antibody against PAIR3 failed to find any PAIR3 protein in the mutant. Thus, sequencing analysis was carried out and revealed that the mutant also contains a single nucleotide deletion at position 1538 in the coding region, and it was named pair3-2. Both mutations resulted in the loss of predicted coiled-coil motifs. There was no obvious difference in pair3-1 during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.In addition, multiple micronuclei were frequently observed. These results implied that correct chromosome disjunction and cytokinesis were also affected by the mutation in the PAIR3 gene. Such abnormality was also found in the pair3-2 mutants but not in the previously reported pair3 mutants<ref name="ref1" />.We suspected that the mutants identified in the present study contain alleles of pair3 that result in more severe defects<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 
*Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK 
*State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os10g0405500

2014-06-08T15:14:56Z

Syphyll: /* Function */

The rice '''''PAIR3''''' plays a crucial role in homologous chromosome pairing and [http://en.wikipedia.org/wiki/Synapsis synapsis] in [http://en.wikipedia.org/wiki/Meiosis meiosis], which is important for eukaryotic sexual reproduction<ref name="ref1" />.
==Annotated Information==
[[File:Pair3_zhengchang.jpg|right|thumb|275px|'''Figure 1.''' ''Chromosome behavior in Wild type.(from reference) <ref name="ref1" />.'']]
[[File:Pair3_tubian.jpg|right|thumb|275px|'''Figure 2.''' ''Chromosome behavior in Pair3 mutants (from reference) <ref name="ref2" />.'']]
===Function===
Meiosis is essential for eukaryotic sexual reproduction and important for genetic diversity among individuals<ref name="ref1" />. PAIR3(HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 3) localize to the chromosome core during prophase I and associated with both unsynapsed axial elements and synapsed lateral elements <ref name="ref2" />.PAIR3 plays a crucial role in homologous chromosome pairing and synapsis in meiosis<ref name="ref6" />.PAIR3 functions in male meiosis. The cells of the parietal layer including the tapetum appeared to be normal, indicating that PAIR3 did not function in anther wall development and that the male sterile mutant phenotype was not due to defects in anther wall development. This is different from the situation frequently reported in the literature inwhich male sterility is often associated with defects in tapetum development. PAIR3 may not function in tapetal degeneration. If it is mutation during meiosis in rice, rice could not form bivalents and result in sterility in both male and female gametes. PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and synaptonemal complex assembly<ref name="ref2" />.It is required for normal development of the resulting microspores and embryo sac formation<ref name="ref1" />.

===Wild Type VS. Mutant===
The researh by ''Kejian Wang et al.'' described the difference of chromosome behavior between ''PAIR3'' mutants and wild type in 2011:
*'''In the wild type''', chromosomes began to condense and form thin lines at leptotene(Figure 1A). In zygotene, pairing and synapsis occurred between homologous chromosomes(Figure 1B). The synapsis was completed, and 12 fully synapsed chromosomes were clearly visible at pachytene(Figure 1C). With further chromosome condensation occurring in diplotene and diakinesis, SCs were gradually disassembled and the paired homologous chromosomes were held together by chiasmata(Figure 1D). At metaphase I, all bivalents were aligned along the equatorial plate(Figure 1E). Subsequently, homologous chromosomes were separated from each other and moved to the opposite poles of the cell at anaphase I(Figure 1F). The second meiotic division was very similar to mitosis and finally produced tetrad spores(Figure 1, G–I)<ref name="ref2" />.
*'''In the ''PAIR3'' mutant''', there was no obvious difference during leptotene, compared with the wild type(Figure 2A ).However, pairing between homologous chromosomes was not observed from zygotene to pachytene (Figure 2, B and C ). During diakinesis and metaphase I, many randomly distributed univalents were found (Figure 2D ). In telophase I and prophase II, an uneven number of chromosomes could be seen in the two related cells (Figure 2, F and G ). After the second division, tetrads and polyads with different numbers of chromosomes were formed (Figure 2, H–L )<ref name="ref2" />.

===Expression===
RT-PCR analyses by ''Wenya Yuan et al.'' shows that ''PAIR3'' was expressed at a very low level in vegetative organs(root, stem, shoots and leaf). It was preferentially expressed in the meiocytes, especially during the male and female meiosis stages<ref name="ref1" />.

===Evolution===
As ''PAIR3'' shows no strong similarity with known proteins in Arabidopsis and other model organisms, it is likely to be a newly evolved meiotic protein in rice<ref name="ref1" /><ref name="ref2" />. The only motif found in ''PAIR3'' is coiled-coil domain<ref name="ref1" />.

===Knowledge Extension===
How haploid gametes are generated from diploid somatic cells is a interesting question in [http://en.wikipedia.org/wiki/Cytogenetics cytogenetics]. Two important procedures are involed in it: Mitosis and Meiosis. 
*The term mitosis was first introduced by ''Walther Flemming'', who made detailed observations of chromosomes during cell division in ''Salamandra maculosa''<ref name="ref3" />. His results were published in 1878 and then in the seminal book Zellsubstanz, Kern und Zelltheilung (1882; Cell substance, nucleus and cell division)<ref name="ref3" /><ref name="ref4" />.During mitosis, one round of DNA replication is followed by a single round of chromosome segregation, thus generating two genetically identical daughter cells)<ref name="ref3" />.
*The term meiosis was coined by ''Farmer and Moore'' meaning reduction in chromosome number<ref name="ref5" />. It is achieved by one round of DNA replication being followed by two rounds of chromosome segregation with no intervening round of DNA replication<ref name="ref3" />. Fusion of two gametes during sexual reproduction restores the diploid complement of chromosomes in the zygote that gives rise to a new individual<ref name="ref3" />. Meiosis was devided into several stages including Meiosis I, Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis, Synchronous processes, Metaphase I, Anaphase I, Telophase I and Meiosis II<ref name="ref5" />.

==Labs working on this gene==
*National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China 
*Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK 
*State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

==Reference==
<references>
<ref name="ref1">Yuan W, Li X, Chang Y, et al. Mutation of the rice gene ''PAIR3'' results in lack of bivalent formation in meiosis[J]. The Plant Journal, 2009, 59(2): 303-315.</ref>
<ref name="ref2">
Wang K, Wang M, Tang D, et al. ''PAIR3'', an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice[J]. Molecular biology of the cell, 2011, 22(1): 12-19.</ref>
<ref name="ref3">
Petronczki M, Siomos M F, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis[J]. Cell, 2003, 112(4): 423-440.
</ref>
<ref name="ref4">
Flemming W. Zur Kenntnis der Zelle in ihrer Teilung-Erscheinungen[J]. Schriften Naturwiss. Vereins Schl.-Holsk, 1878, 3(1): 26.
</ref>
<ref name="ref5">
Wikipedia term(Meiosis), available at http://en.wikipedia.org/wiki/Meiosis. (Last update: 12 March 2013). </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0405500|
Description = Conserved hypothetical protein|
Version = NM_001071094.2 GI:297610454 GeneID:4348581|
Length = 6865 bp|
Definition = Oryza sativa Japonica Group Os10g0405500, 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 = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:14199602..14206466|
CDS = 14199602..14199622,14200704..14202353,14202462..14202609,14203640..14203780,14203853..14203913 ,14204006..14204155,14204276..14204334,14204853..14204987,14205733..14205824 ,14205915..14205979,14206451..14206466|
GCID = <gbrowseImage1>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:14199602..14206466
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggaattgcatatttgcctcgctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctgggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaaaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagattgtaacgggagctaa</cdnaseq>|
AA = <aaseq>MELHICLATSSDYWSLASNQYPCGKFPKVSVGVTIPRTSSVSRG RDAASTAAFEKNLSQGTDGRSRPPKMDNASLQVSPEAANHGGSAKEVPKPVPAKVSVS QPDDNAIEQTGTFSFGTRREQDSHLDQLDRPPLVSSQGKRQVESADKNKPNSEMLRMK LWEILGGTSQNKEAVASPNPEDIETPCQPKSQIANGPSSGRQKVFTSPVPYNIKTPAQ FNSQTANKPSSDPIESDSDSPQVVEVRPITRSLGRKKEPTGSTHQDKSGSAKKPLSTH RSTPKQKILDNVFAFNDKCTPKTVGKSANGESGSLRNLRSLSRRAKVEPKKAHCSDRI SHKTTQDDMERKVPSKYIPSEKKGEKTNSFSSLSRTGKTAESCSRSPKRERRVNTMAN VGARKMQLSENLLVKTLNDGEHKLSSPQLTSFKSKGKCSSISPQQKENDNTHIPEASD RTAARNSFNSTPSPAANPSPVLRKYSWEHDENPAINGKSGQKDASPLADRFSDMPDDF ASPTFAANIKISPHRSKMLDDDLFSSKYPKGVNRSRSTSFTSDPESEPLDKMEKTNEL PGSESPNSQEERQNRKQPHLSPLSPIESEGAQISIPSFRKGYKSHKWLSDVDSPDKSS IEHLGRKSHLKEGRKGKRQLTSPTHFATSGTQETMSDKEPEKVPENYLTRAFDQLVVV LGRFQTKIKSETRNKSSKILAATGEIIRQHLEGVEGQMQADVDKLVNAGKSKRKRLES TFEEQQEKLRILHEKFKEEVNQQLLGCKNSVEDFEAYHAELKGVADKQKASHKKLLQN AEKTVGAQLSDAETKIAEVQKRARKRMKGLKFVLKELIAETADCNGS</aaseq>|
DNA = <dnaseqindica>1..21#1103..2752#2861..3008#4039..4179#4252..4312#4405..4554#4675..4733#5252..5386#6132..6223#6314..6378#6850..6865#atggaattgcatatttgcctcgttcgtaaacctatcgtgtaggtttccgttggatgattggatcctgaattctgtccgattgtttttgtctctctaaattatggttatctgccgcaagtgttaggctatgttagtgtcgcattccgcagtatttttcacggagttgggttcttctagatagtgagtggagcctggattgtgtattatgtttgtggaagaagatctcttaatgctgagggcacatttaaattgctgatacacaatattggtttgatatgtttgtaatggactgttcctagaatttcactgggggtactaaattgacttgttggacatgcagtctatttaatttgagcctcagtgcagcagtacactgttgcagttatcaatcaaaagcaagttgttagcaatcaaatcatccagcttagaaatttaggtgtggtactgtggttatgtaatgcagctccaccaccactgtagtaatttaaagttgacagttgtagtacaacgatgcagttatttgttactacttttcaatgctagtttcttttccaagcgtgattgcaatattgccatgtgacaatcttttacatgtattgcctgctgaatcaggaaaaagaagtacagatgtatcactaattcacttatgctttggtaggctagttgaggatcagtgtcccttgcccccatgtcaatgcttatttgcggtgttttcgcccttgctgatacagctgtgcttctcacatgtgatggcagatttgaaatttcttcctataaccatgcttgataaagatgtgctttgcaagacctctgtattcatttgctaagcataattttgattctgaaagattgtctcagaccagtagaatcttgtcttatgcagttgtttttctattcaccaggtccaaccttctttagttaatttggtatactattatcccaaaagctgcacctatggaagttgagctgacgaacattcagaaagtgagtagctatttcctctgctaagctgctggatgctttcctttttcatgttatcctttcaccttcagatgttttttcattatagtattaaaaaagttagcatgttatacttttgtaggctacatcaagtgactattggagtttggccagcaatcaatatccatgtggtaaattccctaaggtatcagttggcgtcacaattccaaggacgagttctgtatcaagaggcagagatgctgctagtaccgctgcatttgagaagaacttgtctcagggaactgatggaagatctagacctcccaaaatggataatgcttcacttcaggtctctccagaagcagcaaaccacggcggatctgctaaagaggttcctaaacctgtccctgctaaggtttctgtatcacaacctgatgataatgcaattgagcaaacaggaaccttttcctttggaacaagaagagaacaggacagtcatcttgatcaattagataggccaccacttgtgagttcccaaggaaagcgtcaagtggaatcagctgataaaaacaagcccaacagtgaaatgctcaggatgaaactgtgggagatccttggtggtacttcacaaaacaaggaggctgttgcctcaccaaatcctgaagatattgagacgccatgccaacctaaaagtcaaattgccaatggaccatcttcaggaagacagaaggttttcacttcacctgttccatataatattaagacaccagctcagtttaatagtcaaacagcgaacaaaccatcctctgatccaattgagtcagactccgacagtcctcaagtagttgaagtaagacctattactcgttcgctggggcgcaagaaagaaccaacaggctccacacatcaggataagagcgggagtgcaaagaaaccattgtctactcatcgttctacacccaagcagaaaatattggacaatgtgtttgccttcaacgataaatgcacacctaaaacagtaggaaaatctgcaaatggtgaatctggcagcttgaggaatcttagaagcttgagtaggagggctaaagttgagccaaagaaggcacattgttcggacaggatttctcataagactacacaggatgatatggaaagaaaggtaccttctaaatatataccatcagagaaaaaaggtgagaaaacaaactccttttcttctttatcccgaacaggaaaaactgctgagagttgttctagaagccctaaaagggagagaagggtgaacacgatggctaatgttggggctcgaaagatgcagttatctgaaaatttactggtcaagactctaaatgatggtgaacacaagctctcttctcctcagcttacttcctttaagagcaagggaaaatgttcttctatatcgcctcaacagaaggagaatgataatacccacatccctgaagcttcagacagaacagcagcaagaaatagttttaactccacaccttctcctgctgctaatccatctcctgtactgaggaagtactcatgggaacatgatgagaatcctgcgataaatggtaaatctggacagaaggatgccagtccgttggcagacagattcagcgacatgccagatgattttgcaagtcctacttttgcagcaaacataaaaatatccccccacagaagtaaaatgctagacgatgacctatttagctccaaatatccaaaaggtgtgaacaggtcaagatcaacttcctttacctcggatccagaatcggagccattggtatgcttcaatctctaaagcagattgcaactttagtaaatggttctgtttatactctacgtagcagagcaattttatccgtttgacactaattgttctactgtccaggacaaaatggagaaaaccaacgagttacctggcagtgaatctcctaactctcaggaggaaagacagaacagaaaacaaccacatctttcacccctttctcctattgagagtgaaggggctcaaatttctattccaagctttagaaaaggtcagaacgccatcaatgccaattttctaggctctttattaaaaaggggtagacatgctcctgtcatgtttaatgcttccattctagactcaaaggtagccatgctaacttacagtgcactacccccttattctgcatgtggaccatacttattggacagaaatcttatgtatatgtaattatgtatttcaagcacctcttgaatttatcatttaggtcataggatcaacactggccataatccttataacatttgcataatctgtcagatcaatcctgttagtattggtgttcatgatatgtacacttattttattggtgcaaattttgacatcgttacttttggcctcataaacgctcgaagtttgactatttgaacattgaattctaactatactggcaagcatatttgcagggttgttagtggtgagattgcaaaaaagaaaaaaaatttctgtgtcacccacttcatttacttgacctttttatgacaattacacattttatgtgacatgataaatgagtatttgtgtttgcttttgctgtcattttcgattagtgctgccttactaagccgttagatgtcttccaggtaacctgctattgtaacttgtgttcactggcctgaccgcagaaaatttcctaaattcctttttgtggctgtatagttaggctcttcagattttcagctatgtcttgctgctaggtcacaacatttttttgcaactgaaggatcttgaaacttgaaagtgccaattcatgagagcatgccgtttgtgtgatagctgacaagtggcatagcagcaacaagtggcatattctgccatgtgcaagcatatccttagtttacatatatttcatcagaactgtttaccatgttaaattcgctattagtttagttattcgactgtattattttcagcctttcagaacattaattacttgagctaaagttctcattggagatgcacacatctatctatcttaaagttgcttattcatgccttgtcgctttgtttttcacatgcaggatataaatctcataaatggctttcagatgttgacagccctgataaatcttctattgagcatctgggccgaaaatcacatctaaaagagggtagaaagggcaaaaggcaattaacttcgccaacccattttgccacctctggtaacactgattactttactgttgtgcttgtgcattcatggttttcggtctgaccaatattttttttctcagggacgcaagaaacaatgtcagacaaagaaccagaaaaagtcccagaaaactacctaaccaggtttgacttaggtcattgtggcttaaatagtaggtacaaacatgattgctagtttgctacttggattaatttcatttcttgacttccaccagggcttttgatcagttagtagtggtgctaggaaggttccaaaccaaaatcaagtctgaaacaaggaataaaagttctaagatacttgcagctactggagagataatacgccagcaccttgaaggggttgaggggcagatgcaggctgatgtgtaagatcgagtgccagtgccacttagaaactgcctcttttcttctttatgcacatgcgattgtatataggccagatatgtactgcctctttcatgcatggcatttaactgtgatttcagggacaagctggtcaatgcaggaaaatctaaaaggaaacgtctagagtcaacatttgaaggtaaaactctaatcatgtcgatgcaaccattcataatgcaattaatctatgagggcatgatgtggcaatattttttatccaactattgtttgttgtaactgtaacattttttattctacgtatttggattattcatctcatgtaacacaaactcttaaatcttgattcatcaatacagagtcatgtttgaactctagatagaatgtttgaagtctactacaggataacaatgtaatctgcctgttcccttggtttggttggctagaatgacaagtaatttgaaatggagggaacattagtttgagaaaatctcatgcagtatttgtcttattctgcctgcaatcatctgatgtggcttggacgcttggtctttatctacttcgttattttgatctcgtattatatactgagttaaatctcaatatgcaactgtatataatgttacaacttctttttccttcatgccttgtttttcttggatgattttaactattcaactgatgtcttctggtttgcagagcaacaagaaaagttaaggattcttcacgagaagttcaaggaggaggtcaaccagcagttgctcggttgcaagaactctgttgaggattttgaggcttaccatgcagaacttaagggagttgctgacaagcaaagtaagttaaacttaatacatacactatctttatgaatgggactgaagcaattaaagatttcttaccaatgtacacctgaaaatcccataaaaataatgtacacctgaaaaaagtctctaaggttgcaaagccatgttaacattctatatactgagcctgatgaactattccctccatctcacaacctaggaggcaccaagtaagaaccaataaatgttgagatgaccataaatatgcctactaaatgacatgctagacacactctacctgttttacagctttaaattagggtataatagaaaagggtggaatatttacattaattatgaaaagaatgtatcccgaaaaggacgggcagtttttgtgaaatgtaggaagtatggttataagcatttccattggaattctctacttacaaattggtaacactacatgttatccagtcatttgtacttcaactctttcttagtatagttaaaatcacacgtttagttttcgtgaaaaaacctaacgaatttagttgaaaagaatgacagcccaatcttcgtatgaagtgagttttctgagaggttcgccggttcccctgcaatggcatacttgtccagtgacataactccagctttgatcctctcttagcactattaggatgcaagttatggtgtggttaacaggacaaccacttcaaggattctatttatactaccgttcactgacccatggtgtgtgctaatatttgcatcaacagaagcctcacacaagaagctccttcaaaatgctgagaagacagtcggcgctcagctgagcgacgcggaaaccaaaatcgctgaggtccagaaggtgagccaatgcaacttttaaaccatcctgataagtgataaccatatatctaccaaatgctcaatctgtttttgacacgttgcttttcagagggcacggaagaggatgaagggcctcaaatttgtgctcaaggagctcattgcagaaactgcagagtaacccaaccaaagttggttcactctgcacaagtacatagcaaaggtgtattgaccaggacgtacagtttcacttacaaataggctactgtttcatttacaaagggttaaaggagaatttacaaaagggtacaggagaatagtgtcagaatgcatataggtttcttaccagatgaacttttcacagcatacattcaaggattctattctttccattagcatacattcttcgcctagctatcagatagacatgcattgttaccggcgtgccagtttgaataatttacattcctgagaaccgacacattttctgtgtactgtaatcgtattttatgaaaattgaaaattcataagttggaacatctactgcaaagttgcgatgcaaatgctcattgtacttggtttggtggcaatgttctctccattatttcagctgtgaagaatgtgtaatgtgtacatatgtttctgcagttgtaacgggagctaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071094.2 RefSeq:Os10g0405500]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os07g0422100

2014-06-08T09:22:28Z

Syphyll: /* Expression */

Please input one-sentence summary here.

==Annotated Information==
===Function===
Please input function information here.

===Expression===
Please input expression information here.
Os07g0422100 whose expression is induced by drought stress, was identified using drought-treated rice plants at the flowering stage, and was found expressing specifically in rice panicle after drought treatment. Os07g0422100 might contain a drought-inducible promoter which makes the gene specifically express in drought stressed rice panicle. When the reporter gene GUS was driven by the promoter of Os07g0422100, the reporter gene can be efficiently induced after drought treatment, therefore affording a method to assess the degree of drought stress.

===Evolution===
Please input evolution information here.

You can also add sub-section(s) at will.

==Labs working on this gene==
Please input related labs here.

==References==
Please input cited references here.

==Structured Information==
{{JaponicaGene|
GeneName = Os07g0422100|
Description = AWPM-19-like family protein|
Version = NM_001066020.1 GI:115471772 GeneID:4343047|
Length = 1000 bp|
Definition = Oryza sativa Japonica Group Os07g0422100, 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 = [[:category:Japonica Chromosome 7|Chromosome 7]]|
AP = Chromosome 7:14268003..14269002|
CDS = 14268074..14268200,14268296..14268690|
GCID = <gbrowseImage1>
name=NC_008400:14268003..14269002
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:14268003..14269002
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggccggagtcgggaggaacatgctggcgccgctcttggtgctcaacctcatcatgtacctcatcgtcatcggcttcgcgagctggaacctcaaccacttcatcaatggccagaccaactacccaggcgtggcgggcaacggcgcgacgttctacttcctggtgttcgccatcctggccggggtggtgggcgcggcgtccaagctggcgggcgtccaccacgtgcgcgcgtggcgccacgacagcctcgccaccaacgcggcctcctccctcatcgcgtgggccatcaccgcgctcgccttcggcctcgcctgcaaggagatccacatcggcggccaccgcgggtggcgcctccgcgtgctcgaggctttcgtcatcatcctcgccttcacgcagctgctctacgtgctcatgctccacacgggcctcttcggtggcggcgacggcgcctaccgggaccacgactacggcgttggcgccggtgctgccgccggcgagcccaaggggacagcgagggtctga</cdnaseq>|
AA = <aaseq>MAGVGRNMLAPLLVLNLIMYLIVIGFASWNLNHFINGQTNYPGV AGNGATFYFLVFAILAGVVGAASKLAGVHHVRAWRHDSLATNAASSLIAWAITALAFG LACKEIHIGGHRGWRLRVLEAFVIILAFTQLLYVLMLHTGLFGGGDGAYRDHDYGVGA GAAAGEPKGTARV</aaseq>|
DNA = <dnaseqindica>72..198#294..688#tctcgatcgatctcttcttcgtcttctgcgtcgtcgtcgtcgtccagcggtgagctatcagggtagcagccatggccggagtcgggaggaacatgctggcgccgctcttggtgctcaacctcatcatgtacctcatcgtcatcggcttcgcgagctggaacctcaaccacttcatcaatggccagaccaactacccaggtacgacatcgatctgcatatctctgattcttgaaataaaagtgcatgcgacgtactgatatacaatgcgctcgaacacacgtacgtgcgtgcaggcgtggcgggcaacggcgcgacgttctacttcctggtgttcgccatcctggccggggtggtgggcgcggcgtccaagctggcgggcgtccaccacgtgcgcgcgtggcgccacgacagcctcgccaccaacgcggcctcctccctcatcgcgtgggccatcaccgcgctcgccttcggcctcgcctgcaaggagatccacatcggcggccaccgcgggtggcgcctccgcgtgctcgaggctttcgtcatcatcctcgccttcacgcagctgctctacgtgctcatgctccacacgggcctcttcggtggcggcgacggcgcctaccgggaccacgactacggcgttggcgccggtgctgccgccggcgagcccaaggggacagcgagggtctgatcgatgatctccccgacacggggtcacgcaagaataaacgataatacatacttgatggtcattttgtgtgtgtgacagtgtgactgtgaggctctgcctctgtgtgcagcagtgcagtgtaagctctgtgctctcgcctttaattacactactagttgtttagcgttgtgtgttgggtttgtgtagcttgtacatgtgtgtatgtgaccgtacctagtacgtactttgatcgtagtagctaggtgtgcacgtcatggcctgtattttgctcgcatggaagtgccgtcctcaattaattactccttgtcaccg</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001066020.1 RefSeq:Os07g0422100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]