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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaatttgttctttacagaaatagagagatttgtttgaacttaacttgtggttcccggttgataaaatatgcgatgcttatgtactgttttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAAGACTCCATTTGTTCGAAGCAAATCTGCTGGAAGAGGGCTCTTTCGATGC

Basic information

species Oryza sativa
transcript LOC_Os01g34480.2
intron # 1
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|29640618|gb|CB645627.1|CB645627
EST:     GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
EST: gi|29616459|gb|CB621471.1|CB621471
EST:     GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCGTCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
EST: gi|117221000|gb|CT845506.1|CT845506
EST:     GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCGTCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
EST: gi|11026105|gb|AU162706.1|AU162706
EST:     GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
EST: gi|58610521|gb|CK038233.1|CK038233
EST:     GCTGCTCCTCGCCCGCGGCTACGCGGTCCGCGCCACCGTCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
EST: gi|84117052|gb|CD150819.1|CD150819
EST:     GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCGTCCGGGACACCT                         CTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA
genomic: GCTGCTCCTCGCCCGCGGCTACACGGTCCGCGCCACCATCCGGGACACCTgtgagccacc ... tttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgtggttcccggttgataaaatatgcgatgcttatgtactgttttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAAGACTCCATTTGTTCGAAGCAAATCTGCTGGAAGAGGGCTCTTTCGATGC
                                            ttttatttc  CT-rich tract
               ttgataaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaatttgttctttacagaaatagagagatttgtttgaacttaacttgtggttcccggttgataaaatatgcgatgcttatgtactgttttatttcagCTGACCCAAAGAAAACACTACACCTGCGTGCCCTGGATGGAGCCAACGAAAGACTCCATTTGTTCGAAGCAAATCTGCTGGAAGAGGGCTCTTTCGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG