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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatcaatgctccatcctcaaacaacacactaatctattcatgtatatgatgttttgattattgaagctatacctatgttaatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGACTTGAGGATTTCAATAAAGATGAAGTTCTCAGAGTCATTCATGTTGCGC

Basic information

species Oryza sativa
transcript LOC_Os08g10320.3
intron # 22
splice site 3'
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|87020846|gb|CI269563.1|CI269563
EST:     CGAACACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGG                         GCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
genomic: CGAACACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGGgtaagttgat ... taatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
EST: gi|29644125|gb|CB649132.1|CB649132
EST:     ACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGG                         GCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
genomic: ACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGGgtaagttgat ... taatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
EST: gi|86851594|gb|CI315172.1|CI315172
EST:     TCTATC-TTTAGAG-GG                         GCCT-GGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
genomic: TCTATCTTTTAGAGTGGgtaagttgat ... taatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
EST: gi|86478974|gb|CI121607.1|CI121607
EST:     AAAGCAAGATCTATCTTTTAGAGTGG                         GCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
genomic: AAAGCAAGATCTATCTTTTAGAGTGGgtaagttgat ... taatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
EST: gi|86889957|gb|CI319946.1|CI319946
EST:     CGAACACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGG                         GCCT-GGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA
genomic: CGAACACTAATAACTCCATCGAGGAAAGCAAGATCTATCTTTTAGAGTGGgtaagttgat ... taatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattcatgtatatgatgttttgattattgaagctatacctatgttaatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGACTTGAGGATTTCAATAAAGATGAAGTTCTCAGAGTCATTCATGTTGCGC
                                          tgttaat  putative branch site (score: 3)
               atgttttgattatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgatcaatgctccatcctcaaacaacacactaatctattcatgtatatgatgttttgattattgaagctatacctatgttaatttacagGCCTGGGACCTGTACGAAAAGGAGCAAGCACAAAGAATCGTTGATCCAAGACTTGAGGATTTCAATAAAGATGAAGTTCTCAGAGTCATTCATGTTGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG