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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctagttatgtttccctgaggattctgctactacctgtcattttttcttgacatctctctctcacgcacatttcattctgcagcatctttcatctttcatgacttgttttcacttctcagttcatttgtgatgctctgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTA

Basic information

species Oryza sativa
transcript LOC_Os04g51400.3
intron # 2
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|29676639|gb|CB672914.1|CB672914
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|33675698|gb|CF303937.1|CF303937
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|58691609|gb|CK080296.1|CK080296
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|89196993|gb|CI021833.1|CI021833
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|12622915|gb|AU173128.1|AU173128
EST:     CGGCATNTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCCCCGTAAGCACTGGCCTTTCA
genomic: CGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|29666124|gb|CB662399.1|CB662399
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|11173166|gb|AU164645.1|AU164645
EST:     ATGATCGNTACAGAGGGATGAGAATGGNCATTGACGGCATGTCTTATGCG                         GAATTGCTAGCATNGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|29671277|gb|CB667552.1|CB667552
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|29666123|gb|CB662398.1|CB662398
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|29676637|gb|CB672912.1|CB672912
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|29626982|gb|CB631993.1|CB631993
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGNGAGATAGAATTGGC
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGC
EST: gi|86841641|gb|CI337348.1|CI337348
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
EST: gi|9865894|gb|AU101644.1|AU101644
EST:     ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAG                         GAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA
genomic: ATGATCGGTACAGAGGGATGAGAATGGACATTGACGGCATGTCTTATGAGgtatgctagt ... tgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttcatgacttgttttcacttctcagttcatttgtgatgctctgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTA
            ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctagttatgtttccctgaggattctgctactacctgtcattttttcttgacatctctctctcacgcacatttcattctgcagcatctttcatctttcatgacttgttttcacttctcagttcatttgtgatgctctgcactgtagGAATTGCTAGCATTGGGAGATAGAATTGGCACCGTAAGCACTGGCCTTTCAGAAGACGCGCTGTCCAAGTGTCTAGACAGAAGCATGTACATGGCCACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC