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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaagcttagctagctactctcgatctctctcaagtctcaaacagtcgcgcgtacgtatgatcgctagtgagtagtactaggtttgatttttcatgtgatttatgggggtgatcagagatgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA

Basic information

species Oryza sativa
transcript LOC_Os02g36880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g36880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G898290_T02 (Zea mays), 3'ss of exon 2
gtaagccaagcttagctagctactctcgatctctctcaagtctcaaac--agtcgcgcgtacgtatgatcgctagtgagtagtactaggtttgatttttcatgtgatttatgggggtgatcagagatgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA
|||||| | ||  |  ||   | |   ||   ||  |   | ||| |   | |   || || ||  | |  || |    |      | |  |||  |  || ||| |             ||   | ||  | ||  | ||| |  ||||||  ||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||| |||| || |||||||| ||
gtaagc-atgcacatata-tgagtgctgagtgctaactgctatcagatttaattaagc-taggttggtttcctcgctcctccattaatgactgacgtcacacgtgctc----------gccatgtacgtacg-gtgtg-gtgtgtgtgcagCCCGGGCGACGATGGGCGAGAAGGAGTGGTACTTCTTCTGCGTCAAGGACCGCAAGTACCCGACGGGGCTGAGGACGAACCGGGCCACCGAGTCCGGATA

upper sequence: LOC_Os02g36880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S327_64V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagccaagcttagctagctactctcgatctctctcaagtctcaaacagtcgcgcgtacgta-tgatcgctagtgagtagtactaggtttgatttttcatgtgatttatgggggtgatcagagatgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA
|| |  ||| ||   | |     ||  |     |||   ||      | |||   || |  |  |||||    ||||   |   | |     ||  || |  | | ||     ||||   |  ||| |                 ||||| ||  |||| | | |||||||||||||||||||||||| || ||  ||| || ||||| ||||||||  || | || || || || || ||    || ||
gtgacacaaactc--ccaatccttccagtatcatctggtgtagtgtgctgtcctccgaatttggtgatcat--gtgaactgagatggaccgaatcattgaaattagtttcctcggtgggaaatgatct-----------------tgcagAGAAAGCGAAGTTAGGGGAGAAGGAGTGGTACTTCTTCAGCCTGCGGGATCGCAAGTATCCGACGGGAATGCGAACAAATAGAGCCACCGAAAAGGGTTA

upper sequence: LOC_Os02g36880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22540 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------gtaagccaagcttagctagctactctcgatctctctcaagtctcaaacagtcgc---gcgtacgtatgatcgctagtgagtagtactaggtttgatttttcatgtgattt--atgggggtgatcagaga--------tgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA
                                    |      |  |   ||  || ||||||| |  |||   |  | ||   |  ||   || | | |   ||  | ||  | | | | | | |    |   ||  ||    |  | |    |  ||  | |        | |||   |   | |   |  |||| ||  || |  ||||| |||||||| |||||||||||  || ||| |||||||||||||||||||||| || | |||||  |||| || ||| |||| ||
gtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcact-ctctcga-cgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGGAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

upper sequence: LOC_Os02g36880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ11746 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------gtaagccaagcttagctagctactctcgatctctc-------tcaagtctcaaacagtcgc---gcgtacgtatgatcgctagtgagtagtactaggtttgatttttcatgtgattt--atgggggtgatcagaga--------tgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA
                                     |     |  | |||||  ||||||       |   |  | ||   |  ||   || | | |   ||  | ||  | | | | | | |    |   ||  ||    |  | |    |  ||  | |        | |||   |   | |   |  |||| ||  || |  ||||| |||||||| |||||||||||  || ||| |||||| ||||||||||||||| || | |||||  |||| || ||| |||| ||
gtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagAGAAAGCAAACATGGGAGAGAAGGAATGGTACTTCTTTAGCTTGAGGGACCGTAAGTACCCGACGGGGATGCGTACGAATCGGGCAACCGAGGCCGGCTA

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|426774|gb|D22845.1|D22845
EST:     CAACAAGTGCGAGCCATGGGACCTGCCAT                         CGAGGGCGACGATGGGGGAGAAGGAGTNGTACTTCTTCTGCGTNAAGGACC
genomic: CAACAAGTGCGAGCCATGGGACCTGCCATgtaagccaag ... gcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgtgatttatgggggtgatcagagatgtgtgtgtacgtgtgcgcatgcagCGAGGGCGACGATGGGGGAGAAGGAGTGGTACTTCTTCTGCGTGAAGGACCGGAAGTACCCGACGGGGCTGAGGACGAACAGGGCGACGGAGTCCGGGTA
       tgatttat  TA-rich tract