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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATATCTCCTGGGACGACTACTTCATGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaaagtgcatcttcgttgcttgctaaactgcccgtgtaaggattccaacgaacgattgtcgacgtttaacgtgtttgagctcatgcagtcatactgttt...

Basic information

species Oryza sativa
transcript LOC_Os01g55974.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55974.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124091_T05 (Zea mays), 5'ss of exon 2
GTATATCTCCTGGGACGACTACTTCATGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaaagtgcatcttcgttgcttg-ctaaac---tgcccgtgtaaggattccaacgaacgattgtcgacgtttaac--gtgtttgagctcatgcagtcatactgttt
 ||||| ||||||||||||||||||||||||||||| |||||||||||  ||||||| ||||||||||| |||||||||||   |||||    ||  || ||  |     |  ||   ||  ||      | |   |  | |  || |  |    | | || |     ||| | ||      
ATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatatgcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta------

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124091_T04 (Zea mays), 5'ss of exon 2
-----------------------GTATATCTCCTGGGACGACTACTTCATGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaaagtgcatcttcgttgcttg-ctaaac---tgcccgtgtaaggattccaacgaacgattgtcgacgtttaac--gtgtttgagctcatgcagtcatactgttt
                        ||||| ||||||||||||||||||||||||||||| |||||||||||  ||||||| ||||||||||| |||||||||||   |||||    ||  || ||  |     |  ||   ||  ||      | |   |  | |  || |  |    | | || |     ||| | ||      
ATTCGTGGCGCTTGTTTGTGCAGATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatatgcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta------

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G124091_T03 (Zea mays), 5'ss of exon 1
------------------------GTATATCTCCTGGGACGACTACTTCATGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaaagtgcatcttcgttgcttg-ctaaac---tgcccgtgtaaggattccaacgaacgattgtcgacgtttaac--gtgtttgagctcatgcagtcatactgttt
                         ||||| ||||||||||||||||||||||||||||| |||||||||||  ||||||| ||||||||||| |||||||||||   |||||    ||  || ||  |     |  ||   ||  ||      | |   |  | |  || |  |    | | || |     ||| | ||      
GATTCGTGGCGCTTGTTTGTGCAGATATATTTCCTGGGACGACTACTTCATGGCGATCGCCTTCCTTTCGGCTGAGCGGTCTAAGGATCCTAACCGGCAGgtaaacaacatctgtactggatgtctggatatgcgttcgcacaaatatgtttgtggaaattccttggtgtctcgctgacgctggaacatgcacaggccta------

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S426_43V6.1 (Physcomitrella patens), 5'ss of exon 3
GTATATCTCCTGGGACGACTACTTCATGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaa-agtgcat-----cttcgttgcttgctaaa----ctgcccgtgtaaggat--tccaacgaa-cgattgt----cgacgtttaacgt-gtttgagctcatgcagtcat---actgttt------------------------
 ||  | || ||||| |||||||||||||| || || || || ||||| ||||| || |||||||| ||||| ||||||  |||  ||     |||  ||  || | | |     | ||  ||||  |||     |  ||| |  |  |    |||    |  | | ||| ||   |    || ||    |||| ||                        
ATACTTGTCATGGGATGACTACTTCATGGCTATTGCATTTCTGTCGGCGAAGCGTTCAAAGGATCCCAATCGCCAGgtaggagtagataccaacttaatttattccgagaaaacttaccactgtatagatgacttactgaagccgtccttacacgagacctttcatcgttggaaacctaaaagccacttgactgattgtgcttctcgctgctcttatctag

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|88395592|gb|CI613114.1|CI613114
EST:     TGGCGATAGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATAGGCAG                         GTTGGAGCATGCTTGGTTAGACAAGAGGGGATAATCCTAG
genomic: TGGCGATCGCGTTCCTTTCGGCCAAGCGGTCCAAGGATCCTAATCGGCAGgtaaagtgca ... ttgtatgcagGTTGGAGCATGCTTGGTTAGCCAAGAGGGGATAATCCTAG