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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggacctgttctataattttgttctcaagtgaatacgcaaaacatgatcatcttgcttacgtctttttaattgtcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAGGCGGAGCATGCTTTCTACTTGGACTGGGCTGTTCACTCCTTCAGAATCA

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
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|29623204|gb|CB628215.1|CB628215
EST:     CGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|218478602|gb|FG965538.1|FG965538
EST:     CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCA
genomic: CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCA
EST: gi|218486860|gb|FG950334.1|FG950334
EST:     CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|428194|gb|D24342.1|D24342
EST:     CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|29615680|gb|CB620692.1|CB620692
EST:     ATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: ATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|29620903|gb|CB625914.1|CB625914
EST:     ATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: ATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|396941330|gb|HO188539.1|HO188539
EST:     TCTTGCCATC-AGAAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: TCTTGCCATCAAG-AAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|29657688|gb|CB653963.1|CB653963
EST:     CAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|10930997|gb|AU161271.1|AU161271
EST:     CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
EST: gi|218501245|gb|FG948195.1|FG948195
EST:     CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAG                         GTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG
genomic: CTCTTGCCATCAAGAAGGAGGTCGAGGACCTTGAGGCTGGTGGTATACAGgttggacctg ... tcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatacgcaaaacatgatcatcttgcttacgtctttttaattgtcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAGGCGGAGCATGCTTTCTACTTGGACTGGGCTGTTCACTCCTTCAGAATCA
                                          ttgtccttt  CT-rich tract
                                 tctttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggacctgttctataattttgttctcaagtgaatacgcaaaacatgatcatcttgcttacgtctttttaattgtcctttacagGTCATCCAAATCGATGAGGCTGCTTTGAGAGAAGGTCTGCCCCTCCGCAAGGCGGAGCATGCTTTCTACTTGGACTGGGCTGTTCACTCCTTCAGAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT