Os07g0214100 - Revision history

Xysj2012: /* Structured Information */

2015-06-12T08:36:58Z

‎Structured Information

Wangyitong: /* Structured Information */

2014-06-06T04:46:57Z

‎Structured Information

Wangyitong: /* Structured Information */

2014-06-06T02:53:28Z

‎Structured Information

Wangyitong: /* References */

2014-06-06T02:45:28Z

‎References

Wangyitong: /* Structured Information */

2014-06-06T02:24:12Z

‎Structured Information

Wangyitong: /* Labs working on this gene */

2014-06-06T02:23:35Z

‎Labs working on this gene

Wangyitong: /* Evolution */

2014-06-06T02:23:05Z

‎Evolution

Wangyitong: /* Function */

2014-06-06T02:21:05Z

‎Function

Wangyitong: /* Function */

2014-06-06T01:52:26Z

‎Function

Wangyitong: /* Evolution */

2014-06-05T08:30:24Z

‎Evolution

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 least four members, though genomic clones for the two cDNA clones, RA5 and RA14, have not
 yet been obtained.
 Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|

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              Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
              clade; Ehrhartoideae; Oryzeae; Oryza.
-|1. Adachi T, Yamagata H, Tsukagoshi N, Udaka S: Multipleand tandemly arranged promoters of the cell wall protein gene operon in Bacillus brevis 47. J Bact 171:
-!0-1016 (1989).
+possessed an insert of about 16 kb in length. DNA inserts from the genomic clone 24 digested
-. Barber D, Sanchez-Monge R, Gomez L, Carpizo J, Armentia A, Lopez-Otin C, Juan F, Salcedo G: A barley flour of insect a-amylase is a major allergen associated with baker's asthma disease. FEBS Lett 248:119-122 (1989).
+with restriction enzymes. Its restriction map was constructed as shown in Fig. 2. Barn HI-Sal I and
-. Cagampang GB, Cruz LJ, Espiritu SG, Santiago RG, Juliano BO: Studies on the extraction and composition of rice proteins. Cereal Chem 43:145-155 (1966).
+Bam HI-Hind III fragments (bars under the restriction map in Fig. 2) hybridized with the RA
-. Color V, Robert LS, Kavanagh TA, Bevan MW, Thompson RD: Localization of sequences in wheat endosperm protein genes which confer tissue-specific expression in tobacco. EMBO J 6:3559-3564 (1987).
+cDNA probe, and were subcloned onto pUC118, termed pRAG1 and pRAG2, respectively, and
-. Forde BG, Heyworth A, Pywell J, Kreis M: Nucleotide sequence of a B 1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. Nucl Acids Res 13:7327-7339 (1985).
+were used for nucleotide sequencing. Their nucleotide sequences are shown in Fig. 3. From the
-. Forde BG, Kreis M, Williamson MS, Fry RP, Pywell J, Shewry PR, Bunce N, Miflin B J: Short tandem repeats shared by B- and C-hordein cDNAs suggest a common evolutionary origin for two groups of cereal storage protein genes. EMBO J 4:9-15 (1985).
+nucleotide sequence, it was deduced that pRAG2 has a complete coding region for RA without intron, whereas pRAG 1 has approximately a half of the RA gene corresponding to 5' region. The nucleotide sequence of the truncated clone, RAG1, however shows complete agreement with the
-. Garcia-Olmedo F, Salcedo G, Sanchez-Monge R, Gomez L, Royo J, Carbonero P: Plant, proteinaceous inhibitors of proteinases and c~-amylases. Oxford Surv Plant Mol Cell Biol 4:275-334 (1987).
+cDNA clone, RA17, suggesting that cDNA clone RA17 is derived from RAG1 gene transcripts. On the other hand, RAG2 displays strong homology (97.2 ~o identity) with another eDNA clone, RA 14 (Table 1). Two RA genes are located divergently at a distance of 4 kb. The 5' region of RAG1 gene has relatively long direct repeat units (about 170 bp), three 22 bp direct repeat units, and two 12 bp direct repeat units (Fig. 3). In addition, six and two 8 bp direct repeat units (ATGCAAAA) overlined in Fig. 3 exist in RAG 1 and RAG2 promoters, respectively (Table 2). DNA blotting analysis of completely digested rice genomic DNA was performed as described
-. Gomez L, Martin E, Hernandez D, Sanchez-Monge R, Barber D, Pozo V, Andres B, Armentia A, Lahoz C, Salcedo G, Palomino P: Members of the a-amylase inhibitors family from wheat endosperm are major allergens associated with baker's asthma. FEBS Lett 261:85-88 (1990).
+in Materials and methods using the Nco I-Eco RI eDNA (RA17) probe encoding a complete mature RA. Three hybridizing bands were observed in lanes 2 and 3 (Fig. 4). About 6 kb fragment in the Eco RI/Bam HI digest (lane 4 in Fig. 4) would correspond to the Eco RI/Bam HI fragment containing RAG2 in the isolated genomic clone, 24. Besides two cloned RA genes, several other RA genes would still exist. The present study confirms that the RA gene family is composed of at
-. Izumi H, Adachi T, Fujii N, Matsuda T, Nakamura R, Tanaka K, Urisu A, Kurosawa Y: Nucleotide sequence of a cDNA clone encoding a major allergenic protein in rice seeds - Homology of the deduced amino acid sequence with members of a-amylase/trypsin inhibitor family. FEBS Lett 302:213-216 (1992).
+least four members, though genomic clones for the two cDNA clones, RA5 and RA14, have not
-. Joshi CP: An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucl Acids Res 16:6643-6653 (1987).
+yet been obtained.
 Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|

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 ==References==
 Please input cited references here.
 ==Structured Information==

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              Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
              clade; Ehrhartoideae; Oryzeae; Oryza.
+|1. Adachi T, Yamagata H, Tsukagoshi N, Udaka S: Multipleand tandemly arranged promoters of the cell wall protein gene operon in Bacillus brevis 47. J Bact 171:
 Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|
 AP = Chromosome 7:6287055..6287694|

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

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 You can also add sub-section(s) at will.
-Recently many promoters of the plant genes have been characterized, and many transcription factors and cis-elements have already been identified.Several motifs already identified in the plant
+Recently many promoters of the plant genes have been characterized, and many transcription factors and cis-elements have already been identified.Several motifs already identified in the plant genes also exist in the 5'-flanking region of RA genes. RAG 1 and RAG2 have eight and two octamer direct repeats (Fig. 3 and Table 2), respectively.This consensus sequence, ATGCAAAA, reminisces the heptamer sequence, TGCAAAA, identified in rice glutelin genes  and the -300 bp element in cereal genes . Especially in glutelin promoter, CTTTCGTGTA has been identified as the recognition site of DNAbinding protein . This is similar to the sequences, CTTTGGTCTT and CTTTAGTCTT (nucleotide numbers -91 to -82 and -103 to -94 in Fig. 3) in RAG1 and RAG2 promoter regions, respectively. The accumulation pattern of RA mRNA is also similar to that of glutelin mRNA (Gtl)  and thus it is conceived that the regulations of two genes presumably resemble each other. In addition, the 5' region of RAG1 gene has a motif (CATC, nucleotide number from -198 to -195 in Fig. 3) specific for cereal prolamine genes . It is supposed that some common feature of the transcriptional machinery might be shared among prolamine, glutelin and RA genes. Several putative cis elements exist in RA promoter as described above, but it is still unknown whether they are functional or not. Further study on identification of cis elements and their roles is in progress.
 ==Labs working on this gene==

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   Seed allergenic protein
 RAG1 shows complete agreement with the cDNA clone, RA17, suggesting that cDNA clone RA17 is derived from RAG1 gene transcripts. On
-the other hand, RAG2 displays strong homology (97.2 ~o identity) with another eDNA clone, RA 14 (Table 1). Two RA genes are located divergently at a distance of 4 kb. The 5' region of RAG1 gene has relatively long direct repeat units (about 170 bp), three 22 bp direct repeat units, and two 12 bp direct repeat units (Fig. 3). In addition, six and two 8 bp direct repeat units (ATGCAAAA)
+the other hand, RAG2 displays strong homology  with another eDNA clone, RA 14 (Table 1). Two RA genes are located divergently at a distance of 4 kb. The 5' region of RAG1 gene has relatively long direct repeat units (about 170 bp), three 22 bp direct repeat units, and two 12 bp direct repeat units (Fig. 3). In addition, six and two 8 bp direct repeat units (ATGCAAAA) overlined in Fig. 3 exist in RAG 1 and RAG2 promoters, respectively (Table 2). DNA blotting analysis of completely digested rice genomic DNA was performed as described in Materials and methods using the Nco I-Eco RI eDNA (RA17) probe encoding a complete mature RA. Three hybridizing bands were observed in lanes 2 and 3 (Fig. 4). About 6 kb fragment in The synthetic oligonucleotide primer is complementary to 17 nucleotide sequence (numbered 62 to 78 in Fig. 3) that corresponds to the potential signal sequence of the clone, RAG1. Total RNA prepared from rice seed at 20 DAF was analyzed by using the synthetic oligonucleotide primer. The result of primer extension analysis is shown in Fig. 5. Primer-extended products detected here would be derived mainly from RAG1 gene tran-scripts because the population of its cDNA, RA17, is dominant in the cDNA library. The 5' end of RA gene transcripts was expected to be at the position of A (numbered -26 in Fig. 3), though other minor bands were also detected, suggesting that the transcriptional initiation site of RAG1 is 26 bp upstream of the translational initiation codon, ATG. The distance between the transcriptional initiation site and the translational initiation site of RAG 1 gene complies with that of most plant genes . In the 5' region, the putative TATA box and CAAT box exists about 45 bp and 147 bp upstream of the transcriptional initiation site, respectively. The transcriptional initiation site of RAG2 gene might be the same as that of RAG1 gene since the nucleotide sequence around comparable region resembles each other. The size of RA gene family is relatively small compared with that of the prolamine genes, which
-overlined in Fig. 3 exist in RAG 1 and RAG2 promoters, respectively (Table 2). DNA blotting analysis of completely digested rice genomic DNA was performed as described in Materials and methods using the Nco I-Eco RI eDNA (RA17) probe encoding a complete mature RA. Three hybridizing bands were observed in lanes 2 and 3 (Fig. 4). About 6 kb fragment in The synthetic oligonucleotide primer is complementary to 17 nucleotide sequence (numbered 62 to 78 in Fig. 3) that corresponds to the potential signal sequence of the clone, RAG1. Total RNA prepared from rice seed at 20 DAF was analyzed by using the synthetic oligonucleotide primer. The result of primer extension analysis is shown in Fig. 5. Primer-extended products detected here would be derived mainly from RAG1 gene tran-scripts because the population of its cDNA, RA17, is dominant in the cDNA library. The 5' end of RA gene transcripts was expected to be at the position of A (numbered -26 in Fig. 3), though other minor bands were also detected, suggesting that the transcriptional initiation site of RAG1 is 26 bp upstream of the translational initiation codon, ATG. The distance between the transcriptional initiation site and the translational initiation site of RAG 1 gene complies with that of most plant genes [10]. In the 5' region, the putative TATA box and CAAT box exists about 45 bp and 147 bp upstream of the transcriptional initiation site, respectively. The transcriptional
+encode the predominant protein fraction of the major cereals though glutelin is predominant in rice seed. Rice glutelin genes were reported to be encoded by about 15 to 24 copies based on DNA blotting analysis . However, the size difference of their multigene families is not consistent with the relative abundances of their gene products. This difference might occur depending on the control of their transcription or translation level. Comparison of two genes, RAG1 and RAG2, showed that though RAG1 was truncated, coding regions displayed 80 identity, and the 5'- flanking regions (from -1000 to + 1 in Fig. 3) revealed 57~o identity. The 5' region of RAG1 (numbered -1000 to -935) showed significant divergence from the comparable sequence of RAG2. However, two regions were highly conserved between the two genes (nucleotide number from -933 through -804 and from -297 through -3 of RAG1 and from -927 through -795 and from -297 through -3 of RAG2, respectively). The one conserved region arranged downstream was found to be located around TATA box, hence this region might play an important role for transcriptional initiation. Moreover, one 169 bp direct- repeat unit (underlined in Fig. 3), of the clone, RAG1, was involved in the conserved region. RAG1, RAG2 (recombination activating gene): These are closely linked (11p13) and encode the proteins of lymphocyte-specific recombination of the V(D)J sequences of immunoglobulin genes. The functional part of RAG1 is the core sequence whereas other tracts can be deleted without affecting recombination. Mutation in RAG results in the inability to form functional antigen receptors on B and T cells and antibodies. The recombinational cleavage takes place between the coding sequence of the immunoglobulin genes and the so-called recombinational signal sequence (RSS) nucleotides. Recombination usually occurs between the original coding sequences or it may take place by the rejoining of one coding end, the signal sequence, which originally belonged to the other coding end (hybrid joint) or the same codingand signal sequence end can be reunited (open-andshut joint). Besides RAGs, the joining reaction requires the double-strand repair protein XRCC4, a DNA-dependent protein kinase and the Ku protein(- s). For recombination, an accessory protein HMG1 or HMG2 is also required. Nucleotides may be added or deleted in each type of joining. RAG1 and RAG2 are actually transposons but after the joining of the V(D)J ends, normally following the formation of the antibody genes, RAGs are inactivated. RAG proteins seem homologous to the Tc1 transposon of Caenorhabditis. The V(D)J recombinase shows a sequence similarity to retroviral integrase superfamily (Zhu L et al 2004 Nature [Lond] 432:995). RAG1 and RAG2 genes are coordinately regulated by cell-type specific elements upstream of RAG2. The 5′ promoter upstream sequences in RAG2 regulate B and T cells differently. For T cells there are four T cell receptors (TCR) and for the B cell to recombine there are threeimmunoglobulin loci. ▶antibody, ▶immunoglobulins, ▶junctional diversification, ▶NHEJ, ▶combinatorial diversification, ▶RSS, ▶V(J)D recombinase, ▶XRCC4, ▶Ku, ▶DNA-PK, ▶TCR, ▶hybrid dysgenesis, ▶reticulosis familial histiocytic, ▶integrase;
 ===Expression===

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 ===Evolution===
 Please input evolution information here.
 Recently many promoters of the plant genes have been characterized, and many transcription factors and cis-elements have already been identified.Several motifs already identified in the plant
 genes also exist in the 5'-flanking region of RA genes. RAG 1 and RAG2 have eight and two octamer direct repeats (Fig. 3 and Table 2), respectively.This consensus sequence, ATGCAAAA,
@@ Line 35: / Line 37: @@
 -300 bp element in cereal genes [4, 15]. Especially in glutelin promoter, CTTTCGTGTA has
 been identified as the recognition site of DNAbinding protein [35]. This is similar to the sequences, CTTTGGTCTT and CTTTAGTCTT (nucleotide numbers -91 to -82 and -103 to -94 in Fig. 3) in RAG1 and RAG2 promoter regions, respectively. The accumulation pattern of RA mRNA is also similar to that of glutelin mRNA (Gtl) [23] and thus it is conceived that the regulations of two genes presumably resemble each other. In addition, the 5' region of RAG1 gene has a motif (CATC, nucleotide number from -198 to -195 in Fig. 3) specific for cereal prolamine genes [5]. It is supposed that some common feature of the transcriptional machinery might be shared among prolamine, glutelin and RA genes. Several putative cis elements exist in RA promoter as described above, but it is still unknown whether they are functional or not. Further study on identification of cis elements and their roles is in progress.
 ==Labs working on this gene==