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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTAAGCTACCTCCTGCAGAAGTTGCTCAACCCTAGCTTCACCTCCTTGCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaatttgtttttcttttcttcttcgatccaaaagcttatatttagatgcacaagtagttaattagatcttgatgttaatatgcttgtttttcatattaatttgatgaag

Basic information

species Oryza sativa
transcript LOC_Os12g03050.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03050.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G018436_T01 (Zea mays), 5'ss of exon 1
ATCTTAAGCTACCTCCTGCAGAAGTTGCTCAACCCTAGCTTCACCTCCTTGCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaatttgttttt--cttttcttcttcgatccaaaagcttatatttagatgcacaagtagttaattag-atcttgatgttaatatgcttgtttttcatattaatttgatgaag
|||   |||||||||||||| ||||| || |||||||||||| |  |     ||||||| ||||| ||||||||||||||||||||||||||||| ||||||||||     ||        ||  | ||||||  |       ||| | ||| ||     | |  | ||  ||  | || || ||  || ||    ||    ||  | | |   | |  
ATCACCAGCTACCTCCTGCACAAGTTCCTGAACCCTAGCTTCGCGCCGCACGCCATCGGGGAGGTGGACCTCAACAAGTGCGAGCCATGGGATCTCCCAAgtaagttgtcattacacacagctgattttcttccttt------cttttcttttgacaagaaggccggtagctactagctagacgtacatgtgtaaatt---aatgcttaatcactaag-

upper sequence: LOC_Os12g03050.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 5'ss of exon 1
ATCTTAAGCTACCTCCTGCAGAAGTTGCTCAACCCTAGCTTCACCTCCTTGCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaatttgtttttcttttcttc------ttcgat-----ccaaaagcttatatt-tagatgcacaagtag--ttaat-tagatcttgatgtta-atatgcttgtttttcatattaatttgatgaag---------------------------------
 |      ||||||  | | |||| |   |||||||    ||        | | ||     | || |||||||||||||||||||| |||||||||||| |||  |     || |     | | ||||      || | |     || ||   || | || |   || |  || |    | ||    |  ||  ||| | ||  || || | | || | |  |||  |   |                                 
GTGAGCTTCTACCTGGTCCGGAAGATTAGCAACCCTCAAGTCGTTGTGAAGACGATTCCAAACGTGGACCTCAACAAGTGCGAGCCTTGGGATCTTCCAGgtatttttttcttttcgcattatccttcagaacatttggtgtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcag

upper sequence: LOC_Os12g03050.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ11746 (Selaginella moellendorffii), 5'ss of exon 1
ATCTTAAGCTACCTCCTGCAGAAGTTGCTCAACCCTAGCTTCACCTCCTTGCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaatttgtttttcttttcttc---ttcgatccaaaagcttatatttagatgcacaa-gtagttaa-ttagatcttgatgt-taatatgcttgtttttcatattaatttgatgaag-------------------------------------------------------------------------
|||     ||||||| |  ||||| |  ||||| | |  |||    |     |||||| ||||||||| |||||||||| ||||||||||||||| ||  |||||    |  | | |    ||   ||   |||| | | |    ||    | |    | | | ||  ||    | ||  ||| ||  |   || | ||   |||  |  || |||     |                                                                         
ATCACCTTCTACCTCGTCAAGAAGGTCGTCAACACAAAATTCGTGGCGCACGCCATCGCCGAGGTCGATCTCAACAAGTTCGAGCCATGGGATCTACCCGgtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcag

upper sequence: LOC_Os12g03050.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ22540 (Selaginella moellendorffii), 5'ss of exon 1
ATCTTAAGCTACCTCCTGCAGAAGTTGCTCAACCCTAGCTTCACCTCCTTGCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaatttgtttttcttttcttc---ttcgatccaaaagcttatatttagatgcacaa-gtagttaa-ttagatcttgatgt-taatatgcttgtttttcatattaatttgatgaag-------------------------------------------------------------------------
|||     ||||||| |  ||||| |  ||||| | |  ||| |  |     |||||| ||||||||| |||||||||| ||||||||||||||| ||  |||||    |  | |      ||   ||   |||| | | |    ||    | |    | | | ||  ||    | ||  ||| ||  |   || | ||   |||  |  || |||     |                                                                         
ATCACCTTCTACCTCGTCAAGAAGGTCGTCAACACAAAATTCGCGGCGCACGCCATCGCCGAGGTCGATCTCAACAAGTTCGAGCCATGGGATCTACCCGgtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcag

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|88327155|gb|CI652194.1|CI652194
EST:     GCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAA                         GCAAGGCGAAGATGGGGAAAAAAGAATGGTACTTCTTCAGCCA
genomic: GCCCATCGGCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTTCCAAgtaagtcaaa ... tttgatgaagGCAAGGCGAAGATGGGGGAAAAAGAATGGTACTTCTTCAGCCA