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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAGCCTTGATATCATGATTTTATCATTATAAAATATTCTATGCCGCCTTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgcttttccatcctagtttcattttcatgtagtgtcagcataatctgaaagtacatgctgtgctcatcag

Basic information

species Oryza sativa
transcript LOC_Os03g62640.5
intron # 10
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29689015|gb|CB685290.1|CB685290
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGCCCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29681221|gb|CB677496.1|CB677496
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29674745|gb|CB671020.1|CB671020
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29621719|gb|CB626730.1|CB626730
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|87008593|gb|CI315051.1|CI315051
EST:     AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29625503|gb|CB630514.1|CB630514
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29627006|gb|CB632017.1|CB632017
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29656041|gb|CB652316.1|CB652316
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGAAAGGAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88842454|gb|CI081710.1|CI081710
EST:     AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: AGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29678407|gb|CB674682.1|CB674682
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29666282|gb|CB662557.1|CB662557
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29623141|gb|CB628152.1|CB628152
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29639322|gb|CB644331.1|CB644331
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|18385491|gb|BM418690.1|BM418690
EST:     TTCCAGGAGTAGAGAAGTAAAAGAAGGAAGCCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAGGGACCGCCAATGGTCAGGCATCCAGGGATAGAG
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCG-CAATGGTCAGGCATCCAGGGATAGAG
EST: gi|29617713|gb|CB622725.1|CB622725
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88223512|gb|CI223361.1|CI223361
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29674494|gb|CB670769.1|CB670769
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29687899|gb|CB684174.1|CB684174
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|88841254|gb|CI080708.1|CI080708
EST:     CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: CAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29623912|gb|CB628923.1|CB628923
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|58680707|gb|CK069394.1|CK069394
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29626367|gb|CB631378.1|CB631378
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29639320|gb|CB644329.1|CB644329
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATAGG-CAGGCATCCAGGGATAGAG
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAAT-GGTCAGGCATCCAGGGATAGAG
EST: gi|15852100|gb|BI804896.1|BI804896
EST:     CCAGGAGGAGAGAAGTAAAAGAAGGAA-GCCCCTGAAGATGACACGGCG                         ATCAAGAGAATACAGC-AGGACC-CAATGGTCA-GCATCCAGGGATAGAG
genomic: CCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACA-GGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAG
EST: gi|86886570|gb|CI322802.1|CI322802
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAACATGACAGGCG                         ATCAATAGAATACAGCAAGGACCGCAAT-GTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29672227|gb|CB668502.1|CB668502
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29681846|gb|CB678121.1|CB678121
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|29633032|gb|CB638041.1|CB638041
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGGCCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
EST: gi|86256324|gb|CI012614.1|CI012614
EST:     TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCG                         ATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA
genomic: TTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgctt ... tgctcatcagATCAAGAGAATACAGCAAGGACCGCAATGGTCAGGCATCCAGGGATAGAGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGAGCCTTGATATCATGATTTTATCATTATAAAATATTCTATGCCGCCTTCCAGGAGGAGAGAAGTAAAAGAAGGAAGGCACCTGAAGATGACAGGCGgtatgtgcttttccatcctagtttcattttcatgtagtgtcagcataatctgaaagtacatgctgtgctcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG