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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccctccgatttttgggccagaattgtagcacctctgacatcaacagaatcagtcgcgctccataatcctcatttattacaaggtctttcaatttcaagCAT

Basic information

species Oryza sativa
transcript LOC_Os01g27020.1
intron # 6
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|86492900|gb|CI135533.1|CI135533
EST:     CCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: CCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|86495956|gb|CI138589.1|CI138589
EST:     CAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: CAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|87028117|gb|CI257277.1|CI257277
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|29665377|gb|CB661652.1|CB661652
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAG--                         -AT
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|29672001|gb|CB668276.1|CB668276
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|88993327|gb|CI257755.1|CI257755
EST:     GAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|87026938|gb|CI259591.1|CI259591
EST:     TTCAAGCAAACCTAGAT                         CAG
genomic: TTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|29688505|gb|CB684780.1|CB684780
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|87036963|gb|CI191585.1|CI191585
EST:     GCTTCAAGCAAACTTAGAT                         CAG
genomic: GCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|87008591|gb|CI315049.1|CI315049
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|88689180|gb|CI732756.1|CI732756
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT
EST: gi|29625908|gb|CB630919.1|CB630919
EST:     GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGAT                         CAG
genomic: GGGCAGGACCAGCTCCAGAGGCTAATGCAGAGCTTCAAGCAAACCTAGATgtaagccagc ... caatttcaagCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatcagtcgcgctccataatcctcatttattacaaggtctttcaatttcaagCAT
                                        tctttc  CT-rich tract
                           atttattacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccctccgatttttgggccagaattgtagcacctctgacatcaacagaatcagtcgcgctccataatcctcatttattacaaggtctttcaatttcaagCAT

- - - - - - - - - - - - -tgtagca
- - - - - - - - - - - - - - - - - - - - - caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctccat