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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaactgagctgcgatctgcatctccagattttggaatggttattatttcagaggatgaactgctcatggcattgatgttttcctgaatctttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g17390.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G328908_T01 (Zea mays), 5'ss of exon 5
CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaactgagctgcgatctgcatctccagattttggaatggttattatttcagaggatgaactgctcatggcattgatgttttcctgaatctttgcag
||||||||||||||||||||||| | |||||||||||||||||| ||||| ||||| ||||||||||||||| | ||||||||||||| |    |  ||   |   || | ||||    | ||      | |||  || ||    |  ||  |    ||  | |||||| |    ||   |||   |||
CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaactaaacttgtcatatcatattcatc----ggttcatagctagttggtagtt----gcttgtgcaatgcaatgaattgatttgggtcttg-tctcgccag

upper sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G838196_T02 (Zea mays), 5'ss of exon 5
CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaactgagctgcgatctgcatctccagattttggaatggttattatttcagaggatgaactgctcatggcattgatgttttcctgaatctttgcag
||||||||||||||||||||||| | ||||||||||||||| |||||||| ||||| ||||||||||||||| | ||||||||||||| ||   | | | ||| ||  ||  || |  |     ||   ||| |  |    |      |   || ||  || ||                         
CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACAAACACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATGgtaagtgaacccgtgct-cgtgctatatatatatgccatgccttgggttctgcaacgtttattc--cttcttttgccag------------------------
















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|86260747|gb|CI000195.1|CI000195
EST:     GCGACCGACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86254877|gb|CI016997.1|CI016997
EST:     GCGGCCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|84117395|gb|CD151162.1|CD151162
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGA
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGA
EST: gi|88225708|gb|CI225624.1|CI225624
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|88219694|gb|CI219254.1|CI219254
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|88960463|gb|CI006424.1|CI006424
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|33797795|gb|CF324757.1|CF324757
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCA
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCA
EST: gi|86841820|gb|CI337470.1|CI337470
EST:     GCGACCAACACCGCCCCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86501067|gb|CI143700.1|CI143700
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86859484|gb|CI278882.1|CI278882
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGTCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|88974544|gb|CI022085.1|CI022085
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86889838|gb|CI333489.1|CI333489
EST:     CAACGCCAGGGACAGGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: CAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|89183041|gb|CI003105.1|CI003105
EST:     CGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: CGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|88223495|gb|CI223344.1|CI223344
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|38473524|gb|CF957656.1|CF957656
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|89176875|gb|CI013448.1|CI013448
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86499661|gb|CI142294.1|CI142294
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86255162|gb|CI062067.1|CI062067
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|88225278|gb|CI225194.1|CI225194
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|87021778|gb|CI277945.1|CI277945
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|86504480|gb|CI147113.1|CI147113
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCAT-CCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACT
EST: gi|86485394|gb|CI128027.1|CI128027
EST:     GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
genomic: GCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT
EST: gi|89198167|gb|CI015556.1|CI015556
EST:     CCAGGGACAAGCCATG                         CGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGTCTGTTCCTGCCGTACTT
genomic: CCAGGGACAAGCCATGgttagatcaa ... atctttgcagCGTGGCTCTCTTCTCATCCAAGGAGAAGGCGAGGCTGTTCCTGCCGTACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATGgttagatcaactgagctgcgatctgcatctccagattttggaatggttattatttcagaggatgaactgctcatggcattgatgttttcctgaatctttgcag

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