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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtagacataattttatgattatcctctaatgctgtgatgtactag

Basic information

species Oryza sativa
transcript LOC_Os01g59600.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 5
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtagacataa----ttttatgattatcctctaatgctgtgatgtactag
||||||||||||||||| |||||||||||||||||||||||||| | || || ||||| ||||||||||| ||||| ||| | ||| || ||||| || | |||||| | ||| | | | ||| |||||
GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACGAAGTCAGAAGCTGCCAGTTATGAAAAgtaaacaccttgtctttgagaccatg-ggatgcgagatcttttatatgactgttctgaaaatttaatggactag

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G130398_T02 (Zea mays), 5'ss of exon 5
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtagacataattttatgattatcctctaatgctgtgatgtactag--
||||||||||||||||| |||||||||||||||||||||||||| | ||||| ||||| ||||||||||| ||||| |||| || ||| ||| |||| | | ||| | || | | || | | | | ||
GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACCAAATCAGAAGCTGCCAGTTATGAAAAgtaagcacctagtcttttagaccatctgatgcaagattttttatgactattatgtgttctaaaattttaatg

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 3
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtaga------cataattttatgattatcctctaatgctgtgatgtactag
| |||||||||||| || ||||||||||| |||||||||||||| || ||||| ||||| ||||||||||| ||||| | || || ||| | || || ||| ||||||||| ||||| | ||| |||||
GTTGTTGCTGGTTTGGCAGCAGATGGCAGACAAATTGTTTCAAGGGCCAAATCAGAAGCTGCCAGTTATGAAAAgtaagaacctagtctttcacaccctgcgagatcttttataggaatatgattatattctaaaatattaatgcactag

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G130398_T01 (Zea mays), 5'ss of exon 5
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtag-acataatttt--atgattatc-----ctctaatgctgtgatgtactag
||||||||||||||||| |||||||||||||||||||||||||| | ||||| ||||| ||||||||||| ||||| |||| || ||| ||| |||| | || ||||| |||| ||| ||||| | | ||| || ||
GCTGTTGCTGGTTTAGCAGCAGATGGCAGGCAAATTGTTTCAAGGACCAAATCAGAAGCTGCCAGTTATGAAAAgtaagcacctagtcttttagaccatctgatgcaagattttttatgactattatgtgttctaaaattttaatggaccag

upper sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 5
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtagacataattttatgattatcctcta-atgctgtgatgtactag
|| ||||||||||| || |||||||||||||||||||||||||| | ||||| ||||| ||||||||||| ||||| |||| || | | || || || || |||| |||| |||| | ||| || ||
GCCGTTGCTGGTTTGGCAGCAGATGGCAGGCAAATTGTTTCAAGGACCAAATCAGAAGCTGCCAGTTATGAAAAgtaagcacctagtcatttacaccctgcgagatcttttatatgtttatgttctataaaactcaatgcaccag

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|33692105|gb|CF320344.1|CF320344
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|27576784|gb|CA999478.1|CA999478
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|218496122|gb|FG967266.1|FG967266
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|58601557|gb|CK012085.1|CK012085
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|29668732|gb|CB665007.1|CB665007
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|29668731|gb|CB665006.1|CB665006
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
EST: gi|88694188|gb|CI738226.1|CI738226
EST:     GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAA                         GGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG
genomic: GGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacat ... gatgtactagGGTCTATGGTGAACCCATTTCTGTAAAAGAATTGGCTGATCGTGTGGCTAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGTTGCTGGTTTAGCTGCAGATGGCAGGCAAATTGTTTCAAGAGCAAAATCGGAAGCGGCCAGTTATGAGAAgtacgcacataaacttgtaggccatgtagacataattttatgattatcctctaatgctgtgatgtactag

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