We have
implemented a large scale EST project as a part of rice gene
network discovery plan on rice (Oryza Sativa) with a
bioinformatics database established since 10 October 2000. The
database has 25170 rice ESTs and was constructed after 3'-end
single pass sequencing, containing 3 sub-datasets with 13316,
9369 and 2485 Poly(A+) ESTs from leaf, endosperm and
stem respectively．Leaf ,endosperm and stem dataset was obtained
from cDNA libraries of leave induced by Magnaporthe grisea，
stem in the 3- to 5-leaf stage and endosperm 10 days after anthesis,
respectively. These clones represent an estimated 5633，3004
and 1903 mRNA transcripts (Tentative Unique Transcripts,
TUTs).
| Basic
statistic of General dataset |
| Clones |
28324 |
Total
bases (Mb) |
11.78 |
| Poly(A+)
EST |
25170 |
Poly(A+)
EST percent (%) |
88.9 |
| Longest
(nt) |
1060 |
Average
(nt) |
482 |
| Singleton |
5818 |
Contig |
3503 |
| TUTs |
9321 |
TUTs
percent (%) |
37 |
| A:
identified TUT |
1388 |
Percent
of A (%) |
14.9 |
| B:
mapped TUTs |
2702 |
Percent
of B (%) |
29 |
| A∩B |
428 |
TUTs
only found |
1787 |
3'end
sequencing was selected for that the 3'Untranslated Region
(3'UTR) in each 3'EST gene is transcript specific region,
it might be true that there are polymorphism occurred for
mature mRNA 3'UTR because of the fact of mRNA splicing and
post-transcription modification. There are different percentage
of sequences with ploy(A+) in above 3 datasets, tissue specificity
differences might be one of the main reasons to cause the
differences of tentative unique transcripts(TUT) percentage
among the 3 sub-datasets, highest percentage of TUT(76.6%)
in the stem sub-dataset was found. The distribution of mapped
TUTs varied from chromosome to chromosome. Many TUT(s) were
mapped on more than one chromosome, which indicated the common
existence of multi-copies of those TUT(s) or its homologies
on chromosomes. Notable portion of the TUTs was found as new
ones. A few genes were expressed with high redundancy in respective
library. There are obvious differences of gene expressed(s)
in the three libraries, even of the redundancy of co-expressed
gene(s), the gene expression profile specificity was due to
that the three libraries were from distinct tissue and biological
process.
Experiment
and results:
3'end sequencing analysis results
Supply data:
3'end sequence data
More information
on experiment and analysis results:
Introduction: Reviews on related field
Navigation: Browse the data and related analysis results
This project
was supported by the Ministry of Science and Technology, P.R.China
and the People's government of Zhejiang Province,
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