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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCAATGAAAGAAGGAAGTAATGCCGGTGACATTAATATTGGCCCCAAGGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgctgatagcccgatacgactagtagctcagtccaaactacttatctcgagtcaactgatagattattttgtctttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g42420.3
intron # 6
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|29641164|gb|CB646171.1|CB646171
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29674774|gb|CB671049.1|CB671049
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|33683475|gb|CF311714.1|CF311714
EST:     GCTGAGTCTGTCTCATGTGGNAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GCTGAGTCTGTCTCATGTGG-AGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|7332528|gb|AU085874.1|AU085874
EST:     GCTGAGTCTGTCTCATGTGGAGAAGTTACCAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAAGACGCAAATGCAAAACGTTGTTCG
genomic: GCTGAGTCTGTCTCATGTGGAGAAGTTA-CAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAG-AAAGACGCAAATGCAAAACGTTGTTCG
EST: gi|86827407|gb|CI272815.1|CI272815
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|58695877|gb|CK084564.1|CK084564
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|86478112|gb|CI120745.1|CI120745
EST:     CATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: CATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29645251|gb|CB650258.1|CB650258
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29642943|gb|CB647950.1|CB647950
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|218482069|gb|FG950305.1|FG950305
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|218484262|gb|FG953319.1|FG953319
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29645905|gb|CB650912.1|CB650912
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|86858202|gb|CI271104.1|CI271104
EST:     GTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29639665|gb|CB644674.1|CB644674
EST:     ATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: ATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|25797222|gb|CA753183.1|CA753183
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
EST: gi|29639196|gb|CB644205.1|CB644205
EST:     GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAAT                         GCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT
genomic: GGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgc ... gtctttgcagGCTCATCTGATGGATCAGAGGAGAAAGACGCAAATGCAAAACGTTGTTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCAATGAAAGAAGGAAGTAATGCCGGTGACATTAATATTGGCCCCAAGGCTGAGTCTGTCTCATGTGGAGAAGTTACAGAACGGGAAAGTTCAGAATgtaatggtgctgatagcccgatacgactagtagctcagtccaaactacttatctcgagtcaactgatagattattttgtctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT