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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcctgctctatcactgtaaatttcattgttctaacttgaagccattatgatcataggagttgttttaactgatatgacattgatgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGCGGCTGCGCCGATAAAAAAGGAGCCAAGAAAGACAATCATGAGAAAGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g19470.1
intron # 26
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|87016323|gb|CI271734.1|CI271734
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|4715027|gb|AU056144.1|AU056144
EST:     CCTCTTATTGTCGGAGTTNCCGTGATTCCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCNTG
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTC-TG
EST: gi|88291400|gb|CI529990.1|CI529990
EST:     GGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: GGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|86478429|gb|CI121062.1|CI121062
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88995505|gb|CI022828.1|CI022828
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|89183106|gb|CI003170.1|CI003170
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88447163|gb|CI531406.1|CI531406
EST:     CGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|86480905|gb|CI123538.1|CI123538
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|27547001|gb|CA765154.2|CA765154
EST:     CCTCTTATTGTCGGAGTTTCTGTGATTGCATTGGTCATCAGCATGCCAAG                         GTTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88508413|gb|CI435919.1|CI435919
EST:     CTCTTATTGTCGGAGGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CTCTTATTGTCGGA-GTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88443093|gb|CI546665.1|CI546665
EST:     AGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTNC
genomic: AGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88490324|gb|CI427596.1|CI427596
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|86250806|gb|CI007669.1|CI007669
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
EST: gi|88725754|gb|CI749013.1|CI749013
EST:     CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAG                         GCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC
genomic: CCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttcctgctc ... atgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagccattatgatcataggagttgttttaactgatatgacattgatgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGCGGCTGCGCCGATAAAAAAGGAGCCAAGAAAGACAATCATGAGAAAGAGG
                                              tgctttt  CT-rich tract
                      ttgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcctgctctatcactgtaaatttcattgttctaacttgaagccattatgatcataggagttgttttaactgatatgacattgatgcttttagGCTAAAAGACTTGTACCAAAGTGCTGTGGGAATGACTACCCTAGGTTCTGCGGCTGCGCCGATAAAAAAGGAGCCAAGAAAGACAATCATGAGAAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG