Difference between revisions of "Os07g0214100"
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===Evolution=== | ===Evolution=== | ||
Please input evolution information here. | Please input evolution information here. | ||
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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, | 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, | ||
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-300 bp element in cereal genes [4, 15]. Especially in glutelin promoter, CTTTCGTGTA has | -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. | 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. | ||
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==Labs working on this gene== | ==Labs working on this gene== | ||
Revision as of 08:30, 5 June 2014
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Contents
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 (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 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 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 [23]. 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~/o 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.
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
Please input evolution information here.
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 [23] and the -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
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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 | |
| Location |
Chromosome 7:6287055..6287694 |
| Sequence Coding Region |
6287180..6287671 |
| Expression | |
| 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) |
