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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgaaagtctgctacctgttactttttttttgtcttgtgtccaatccttgagtgaatgaccgatttgccgattttggcatcttataatagcagCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g07740.2
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|29681553|gb|CB677828.1|CB677828
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|163920524|gb|EG709580.1|EG709580
EST:     AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAG                         CAGCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
genomic: AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAGgttagttgaa ... ataatagcagCA--A-CAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
EST: gi|88903064|gb|CI088602.1|CI088602
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|86437266|gb|CI118988.1|CI118988
EST:     AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAG                         CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCGG
genomic: AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAGgttagttgaa ... ataatagcagCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
EST: gi|88967992|gb|CI098234.1|CI098234
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|86858567|gb|CI273118.1|CI273118
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|86481884|gb|CI124517.1|CI124517
EST:     CAATCAAACCAGTGACAATCCAAGCTTTCATGCCAG                         CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
genomic: CAATCAAACCAGTGACAATCCAAGCTTTCATGCCAGgttagttgaa ... ataatagcagCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
EST: gi|86437349|gb|CI119071.1|CI119071
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAAAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|163929260|gb|EG711021.1|EG711021
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|66913147|gb|CX099995.1|CX099995
EST:     AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAG                         CAGCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
genomic: AACAGCAGCAGCAACAATCAAACCAGTGACAATCCAAGCTTTCATGCCAGgttagttgaa ... ataatagcagCA--A-CAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
EST: gi|87016372|gb|CI271783.1|CI271783
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|86255617|gb|CI065294.1|CI065294
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
EST: gi|86437630|gb|CI119352.1|CI119352
EST:     CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG                         GTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG
genomic: CAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAGgtatgcctga ... caaatggcagGTTCTATAGCTCTTCTCGAGGCAGCGATCAGAGCAGAACAAACAATGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaatccttgagtgaatgaccgatttgccgattttggcatcttataatagcagCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG
                                        atcttataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttgaaagtctgctacctgttactttttttttgtcttgtgtccaatccttgagtgaatgaccgatttgccgattttggcatcttataatagcagCAACAACGATCAACCTGGTGATGGTCTCAGCTTTCATGCCAG

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