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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtccattgcctacaaaagcacactgatcataacatacataattacacaaacacgtataagctaatgcaatgtgctcgcgtacacaagcagcatacacgcattctcctgcatgtgtgatcgattcgatgctaaacgtatgcgtgatctgcttttcagTCGCTGTGCAACGCGTGTGGCATCCGGTACAAGAAAGAGGAGAGGCGCGCCGCCGCGGCGGCCGTGGCGCCGACGGCGCTGGCGTCGGACGGCGGGGTGG

Basic information

species Oryza sativa
transcript LOC_Os01g47360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G123909_T01 (Zea mays), 3'ss of exon 1
gtactgtccattgcctacaaaagcacactgatcataacatacataattacacaaacacgtataagctaatgcaatgtgctcgcgta--cacaagca-gcatacacgcattctcctgcatgtgtgatcgattcgat--gctaaacgtatgcgt-------gatctgctttt-----cagTCGCTGTGCAACGCGTGTGGCATCCGGTACAAGAAAGAGGAGAGGCGCGCCGCCGCGGCGGCCGTGGCGCCGACGGCGCTGGCGTCGGACGGCGGGGTGG
                          ||  | | | || | | |     | | ||    |   |   |||||||||    |   |    || ||||  || |||| |  || |   |     | |||||    |    |||| ||||    |       |||||| |  |     |||||||||||||||||||| || |||||||||||||| |||||| ||||||| || || ||||| ||||||||| |||||   |    ||  | |   |  |
------------------------gtacgtaacgtgacgtgcgtgggc-cgcgaagcgatgccatgcaatgcaatgcatgcatttcgttactagcacacacacacacgctcgctgtcgatcctaatcgaagtaagcgactaagcgtacatatccatttcgatctgttgctgcgtgcagTCGCTGTGCAACGCGTGCGGGATCCGGTACAAGAAGGAGGAGCGGCGCGCGGCGGCCGCGGCGGTGGCGCCGGCGGCGGACGGCGGGGTGGACTACGCCG

upper sequence: LOC_Os01g47360.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G18380.1 (Arabidopsis thaliana), 3'ss of exon 1
gtactgtccattgcctacaaaagcacactgatcataacatacataattacacaaacacgtataagctaatg-caatgtgctcgcgtacacaagcagcatacacgcattctcctgcatgtgtgatcgattcgatgctaaacgtatgcgtgatctgctt--ttcagTCGCTGTGCAACGCGTGTGGCATCCGGTACAAGAAAGAGGAGAGGCGCGCCGCCGCGGCGGCCGTGGCGCCGACGGCGCTGGCGTCGGACGGCGGGGTGG-
                                                   | || |  ||| |   |||  | || |  || | |    |      |||    |||| ||    || | |       | ||||   ||| ||| |    |   |||  | |||||| | || ||||||||||| ||||| | |||||||||||||||||| ||  | ||      | |  ||    | | |  |  ||    | ||||      
---------------------------------------------------ctaatatttattatacaatctccatataatcacatgtctata----ataactacattttcaaagatattt-------tggatgt--aacatatacaatgttaacttggtgcagTCGTTATGTAACGCGTGTGGAATCCGATTCAAGAAAGAGGAGAGGCGTGCGACGGCCAGAAACTTAACGATCTCCG-GTGGAGGTTCATCAGCGGCAGAAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctgcatgtgtgatcgattcgatgctaaacgtatgcgtgatctgcttttcagTCGCTGTGCAACGCGTGTGGCATCCGGTACAAGAAAGAGGAGAGGCGCGCCGCCGCGGCGGCCGTGGCGCCGACGGCGCTGGCGTCGGACGGCGGGGTGG
                         tgctaaa  putative branch site (score: 2)
                                           tctgcttttc  putative PPT