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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTCCGACGTGTTCTACATCATGTCGGGCATGTGGAAGACCCCCACCGAGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatcgatctgcactgcacacatgtactccagagcttcaaaaccactagtgccagttgattttttttacatgacatgatggcaactctctctctctctctcgttgttgcttctgctatcag

Basic information

species Oryza sativa
transcript LOC_Os04g54474.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g54474.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G445575_T01 (Zea mays), 5'ss of exon 9
CAACTCCGACGTGTTCTACATCATGTCGGGCATGTGGAAGACCCCCACCGAGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatcgatctgcactgcacacatgtactccagagctt-caaaaccactagtgccagt--tgattttttttacatgacatgatggcaactctctctctctctctcgttgttgcttctgctatcag
|||| | |||||||||||| ||||||||||| |||||||||||||| ||||| ||||||| || |||||||| ||||||||||| ||||| || |||||||||  |   ||  |   || |   | |||| | ||    |   | || | ||      ||||  |||||  | ||        || |||||                                      
CAACGCGGACGTGTTCTACGTCATGTCGGGCTTGTGGAAGACCCCCGCCGAGAGGTTCTTTCTCTGGATCGGCGGGTTCCGGCCGTCGGAAGTCCTCAAGgtacgtg--cgtgcgtgaccggctagatgttcccctctccccgcgaacctacacacagcagtgatgattcatcttgttgttgctggtggcatgcag---------------------------------

upper sequence: LOC_Os04g54474.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G131961_T02 (Zea mays), 5'ss of exon 8
CAACTCCGACGTGTTCTACATCATGTCGGGCATGTGGAAGACCCCCACCGAGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatcgatctgcactgcacacatgtactccagagcttcaaaaccactagtgccagt-------tgattttttttacatgacatgatggcaactctctctctctctctcgttgttgcttctgctatcag
|||| | ||||||||| || ||||||||||| |||||||||||||| ||||| |||||||||| |||||||| |||||| |||| |||||||| || ||||| ||    | | ||| |      ||     | |||  ||  ||  |||||  | | |||         || |  |||    |  |||| ||     |         | |   | || ||  |       |||
CAACGCGGACGTGTTCCACGTCATGTCGGGCGTGTGGAAGACCCCCGCCGAGAGGTTCTTCCTCTGGATCGGCGGGTTCAGGCCGTCGGAGGTCCTAAAGgtggccgg-ctacctgtatacattacccacccaccacggcaccaccaccaccggcggcagaacgcacgcgagtgatttcgtcttgcatggtgattggtgatgacggatgtt--gctggtggatggaacg-cag

upper sequence: LOC_Os04g54474.2 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ29724 (Selaginella moellendorffii), 5'ss of exon 6
CAACTCCGACGTGTTCTACATCATGTCGGGCATGTGGAAGACCCCCACCGAGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatcgatctgcactgcacacatgtactccagagcttcaaaaccactagtgccagttgattttttttacatgacatgatggcaactctctctctctctctcgttgttgcttctgctatcag
 || || || || ||| |  |  | || || ||||||||||||||  ||||| ||| |||| ||||||| ||||| |||||||| || ||  |||| ||||| |||  |   |||    |   | | | |  | |  |              |||||    | |   |||||   |||||  |  |                                        
GAAGTCGGATGTCTTCCATCTAGTCTCCGGTATGTGGAAGACCCCTGCCGAGAGGTGCTTCATGTGGATGGGTGGATTCCGGCCTTCAGAACTTCTAAAGgt-gctgctgtgtctttcttttcctcgtttttttcgaa--------------agtgc----ttaacgtttttgtgtgacaccacag----------------------------------------

upper sequence: LOC_Os04g54474.2 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ28227 (Selaginella moellendorffii), 5'ss of exon 6
CAACTCCGACGTGTTCTACATCATGTCGGGCATGTGGAAGACCCCCACCGAGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatcgatctgcactgcacacatgtactccagagcttcaaaaccactagtgccagttgattttttttacatgacatgatggcaactctctctctctctctcgttgttgcttctgctatcag
 || || || || ||| |  |  | || || ||||||||||||||  ||||| ||| |||| ||||||| ||||| |||||||| || ||  |||| ||||| |||  |   |||    |   | | | |  |||  |              |||||    | |   |||||   |||||  |  |                                        
GAAGTCGGATGTCTTCCATCTAGTCTCCGGTATGTGGAAGACCCCTGCCGAGAGGTGCTTCATGTGGATGGGTGGATTCCGGCCTTCAGAACTTCTAAAGgt-gctgctgtgtctttcttttcctcgttttttccgaa--------------agtgc----ttaacgtttttgtgtgacaccacag----------------------------------------

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|58667915|gb|CK056601.1|CK056601
EST:     AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAG                         AATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
genomic: AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatc ... ctgctatcagAATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
EST: gi|29642525|gb|CB647532.1|CB647532
EST:     AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAG                         AATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
genomic: AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatc ... ctgctatcagAATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
EST: gi|29640853|gb|CB645860.1|CB645860
EST:     AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAG                         AATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
genomic: AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatc ... ctgctatcagAATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
EST: gi|29659308|gb|CB655583.1|CB655583
EST:     AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAG                         AATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG
genomic: AGCGGTTCTTCCTGTGGATCGGTGGGTTCCGGCCATCGGAGGTTCTCAAGgtagctaatc ... ctgctatcagAATTTGAGACCGCAGCTGGAGCCTCTGACGGACAAGCAGGTCGTGGAAGTG