Os07g0214100

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Annotated Information

Function

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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 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 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

Please input expression information here. Stage- and tissue-specific expression of RA gene To investigate the expression of RA genes, total RNA and protein were prepared from rice seeds at different stages of maturation (5, 10, 15, 20, 25, and 30 DAF), and from other tissues. RNA and protein preparations were used for RNA blotting and immunoblotting analyses, respectively. The mRNA of RA was detected only in ripening seed (lane 4 in Fig. 6A) but not in leaves, stalks, and roots (lanes 1, 2, and 3, respectively, in Fig. 6A). RA mRNA accumulated from 10 DAF and reached its maximum level at 15 to 20 DAF (lanes 3 and 4 in Fig. 6B). Immunoblotting analysis showed that the protein synthesis was consistent with the accumulation of RA mRNAs (data not shown). In conclusion, RA gene expression is controlled in transcription level.

Evolution

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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 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

Please input related labs here. Department of Food Science and Technology, School of Agriculture, Nagoya University, Chikusa, Nagoya 464-01, Japan; 2Department of Biochemistry, College of Agricultural Chemistry, Kyoto Prefectural University, Shimogamo, Kyoto 606, Japan

References

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Structured Information

Gene Name	Os07g0214100
Description	Seed allergenic protein RA17 precursor
Version	NM_001065719.1 GI:115471170 GeneID:4342722
Length	640 bp
Definition	Oryza sativa Japonica Group Os07g0214100, 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	Chromosome 7
Location	Chromosome 7:6287055..6287694
Sequence Coding Region	6287180..6287671
Expression	GEO Profiles:Os07g0214100
Genome Context	<gbrowseImage1> name=NC_008400:6287055..6287694 source=RiceChromosome07 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008400:6287055..6287694 source=RiceChromosome07 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atggcttccaacaaggtagtgttctcggtattgctcctcgtcgttctctccgtgctcgcggcggcgatggcgaccatggcggaccaccaccaagtctacagccccggtgagcaatgtcggccaggaataagctatccgacatactcactcccgcaatgtcgaacattggtgaggcgccaatgcgttggccgtggcgcggccagcgccgcggacgagcaagtctggcaagactgctgccggcagctcgccgccgtcgacgacggctggtgcaggtgcggggcgctcgatcacatgctgtcaggcatctacagggagctcggcgccaccgaggccgggcaccccatggccgaggtgttccccggctgccggagaggggacttggagcgcgcggcggcgagcctcccggcgttctgcaacgtggacatccccaatgggcctggtggtgtctgctactggcttgggtatcctaggaccccaagaaccggtcactag</cdnaseq>
Protein Sequence	<aaseq>MASNKVVFSVLLLVVLSVLAAAMATMADHHQVYSPGEQCRPGIS YPTYSLPQCRTLVRRQCVGRGAASAADEQVWQDCCRQLAAVDDGWCRCGALDHMLSGI YRELGATEAGHPMAEVFPGCRRGDLERAAASLPAFCNVDIPNGPGGVCYWLGYPRTPR TGH</aaseq>
Gene Sequence	<dnaseqindica>24..515#atttttcacaaactaagcaaaatatggcttccaacaaggtagtgttctcggtattgctcctcgtcgttctctccgtgctcgcggcggcgatggcgaccatggcggaccaccaccaagtctacagccccggtgagcaatgtcggccaggaataagctatccgacatactcactcccgcaatgtcgaacattggtgaggcgccaatgcgttggccgtggcgcggccagcgccgcggacgagcaagtctggcaagactgctgccggcagctcgccgccgtcgacgacggctggtgcaggtgcggggcgctcgatcacatgctgtcaggcatctacagggagctcggcgccaccgaggccgggcaccccatggccgaggtgttccccggctgccggagaggggacttggagcgcgcggcggcgagcctcccggcgttctgcaacgtggacatccccaatgggcctggtggtgtctgctactggcttgggtatcctaggaccccaagaaccggtcactaggctactatagttagctgtgtgtgtgtgactatgtggggttgctaaataattagtgctttcttttgtcaggaagcatctatttatatatatgtggtgaataaatgatgaacttcaatgttcttctg</dnaseqindica>
External Link(s)	NCBI Gene:Os07g0214100, RefSeq:Os07g0214100