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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATGGTGTTGATAAGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattgtttatgtattcatgattatgttaacatgaatacatgatatcatgctgcaaatatatgttgttctcatgattatcttaacatgatatcggatgcaaatatag

Basic information

species Oryza sativa
transcript LOC_Os08g09250.3
intron # 3
splice site 5'
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|38483262|gb|CF967064.1|CF967064
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|428745|gb|D24899.1|D24899
EST:     AGTACGACATTNGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGG
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGG
EST: gi|7219920|gb|AU063009.2|AU063009
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58594310|gb|CF992618.1|CF992618
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|88696013|gb|CI739588.1|CI739588
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAG
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAG
EST: gi|58585603|gb|CF983911.1|CF983911
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58688050|gb|CK076737.1|CK076737
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|218493123|gb|FG968720.1|FG968720
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58601044|gb|CK011572.1|CK011572
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58682272|gb|CK070959.1|CK070959
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|2797325|gb|AA750619.1|AA750619
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|11025939|gb|AU162540.1|AU162540
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|218504483|gb|FG959632.1|FG959632
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|163921167|gb|EG710156.1|EG710156
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58676433|gb|CK065120.1|CK065120
EST:     AGTACGACATTGGAGCAGGATTCGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|218502183|gb|FG956191.1|FG956191
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|55828156|gb|AU065471.3|AU065471
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58591117|gb|CF989425.1|CF989425
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58591648|gb|CF989956.1|CF989956
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58684222|gb|CK072909.1|CK072909
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|58586439|gb|CF984747.1|CF984747
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
EST: gi|9886121|gb|AU063011.2|AU063011
EST:     AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGAC                         GTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT
genomic: AGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattg ... gcaaatatagGTGTACAAATTGGCTGAGAAAATTAAATCCAGTTGTTGCTGCAAGATCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTATGGTGTTGATAAGTACGACATTGGAGCAGGATTTGGGCATTTCGCTATTGCAACTGAGGACgtatgtattgtttatgtattcatgattatgttaacatgaatacatgatatcatgctgcaaatatatgttgttctcatgattatcttaacatgatatcggatgcaaatatag

- - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - -  GAGCAG