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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttggtatttactttctttgatgtacagaccaaaactccaataatttccggattcttacaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGTGTAAATTATGTTTGTGTCGACCTTCACAGGCTTCAGCTATCCAAGGCAC

Basic information

species Oryza sativa
transcript LOC_Os08g14460.3
intron # 12
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|88964540|gb|CI069888.1|CI069888
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88969032|gb|CI099023.1|CI099023
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88443886|gb|CI552431.1|CI552431
EST:     TGATAAACCAAG                         GAGTTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: TGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86425309|gb|CI070406.1|CI070406
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88968346|gb|CI098588.1|CI098588
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTGTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|87019008|gb|CI259064.1|CI259064
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88958312|gb|CI095831.1|CI095831
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86413437|gb|CI067842.1|CI067842
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86497077|gb|CI139710.1|CI139710
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|58675270|gb|CK063957.1|CK063957
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTCCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86428507|gb|CI075188.1|CI075188
EST:     AAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: AAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88957287|gb|CI095263.1|CI095263
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|33798029|gb|CF324874.1|CF324874
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86433159|gb|CI093502.1|CI093502
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88272469|gb|CI386324.1|CI386324
EST:     GATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|286887|gb|D15694.1|D15694
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|89189153|gb|CI048692.1|CI048692
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|58692085|gb|CK080772.1|CK080772
EST:     CCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: CCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86501879|gb|CI144512.1|CI144512
EST:     ATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: ATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|58587881|gb|CF986189.1|CF986189
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGNTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|86484540|gb|CI127173.1|CI127173
EST:     GCATCCCTCATGTCCAAGCACTGTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
EST: gi|88902915|gb|CI088453.1|CI088453
EST:     GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAG                         GAGGTTGAGTGGATTGGATACTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT
genomic: GCATCCCTCATGTCCAAGCACTTTACGAAGTCTGATAAACCAAGgtaatcttgg ... acaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttgatgtacagaccaaaactccaataatttccggattcttacaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGTGTAAATTATGTTTGTGTCGACCTTCACAGGCTTCAGCTATCCAAGGCAC
                                        ttcttac  putative branch site (score: 2)
                                        ttcttac  CT-rich tract
                           aataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttggtatttactttctttgatgtacagaccaaaactccaataatttccggattcttacaataacagGAGGTTGAGTGGATTGGATGCTGAGCGTGAGGCGGTTGCAGCTCAGGAGGTGTAAATTATGTTTGTGTCGACCTTCACAGGCTTCAGCTATCCAAGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT