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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgccattaccaccacctctacttcttcagtgttcagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgtcgattgattgattgattgattgattgattttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g40940.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40940.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G112072_T02 (Zea mays), 5'ss of exon 5
ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgccattaccaccacc---tctacttcttcagtgttcagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgt-cgattgattgattgattg-attgattgattttgcag-----
||||||||||||||||||||  |||||||||||||||| | |||||||| ||||||| ||| ||| ||||||||| |||||||||||||||||||||||||||||  |    |||  || |   ||  ||  || | |      ||    ||||||    | |    |            |    | | |||  |||  |  ||| |  |    || | |      |   || |     
ATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAGCCATgtaaggacagcaaccggcatccaatcgcctagttgatttcctcctgcatttcgccttccttttggaactggggctgcaggactgaagctgcaaccgtgtggctgacttgtctcctgtactcccgcgtcgggctgatcag

upper sequence: LOC_Os04g40940.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G047143_T03 (Zea mays), 5'ss of exon 5
ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgccattaccaccacctctacttcttcagtgttcagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgtcgattgattgattgattgattgattgattttgcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| || ||||||||||||||||||||||||||||||||||||||| |||   |||  || |    |   | | || ||      |             |  | |  |||   || | |   || |||     | |  | |  |  |    |     | || |       
ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagggccgcaaccggcatccagtcgcttcctgtattttcgccttccttttggaaaccggcgctgcaaagtctgcaactgcaaccgtggctgactctggtctcctctcctcccgaactggtcag----

upper sequence: LOC_Os04g40940.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G25980.1 (Arabidopsis thaliana), 5'ss of exon 5
ATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgccattac-caccacctctacttcttcagtgtt-cagtgttcatcgcctctgctctcccccccaattcctcccagctcatccgcattcgtcgattgattgattgattgattgattgattttgcag
   | ||||||||| || |||||||||||||||||||| || || || ||| | ||||| || ||  |  | || ||| | || || || || ||  ||||||||  ||| | |  |  | || |   |  |||   || | |   |  |    | ||   || |             ||  |  |  | ||| |                                    
TCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAAACATgtaagaaccaattcataggaactttgagtgatcatcatttcggaactagtttgatttggattctcgtttttgattgtgcatgttgtttgtattag------------------------------------

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|86257542|gb|CI004359.1|CI004359
EST:     GCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCA
genomic: GCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgcca ... gattttgcagGCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCA
EST: gi|163920022|gb|EG709828.1|EG709828
EST:     GCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCAT                         GCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCA
genomic: GCGCCAGGTCGCCTCCTGCATCACCTACCTCCCCTGCCTCGACGAGCCATgtaagcgcca ... gattttgcagGCATATTCGACGTGCTGGCGTACACCGACATGGACGTCGCGGTGCCCTTCA