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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgtcatgttgtgtcccctttgagacaaaacggtatttctgacttggtacatattaactgactcttacacgccctcttcag

Basic information

species Oryza sativa
transcript LOC_Os04g40740.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40740.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 16
GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgtcatgttgtgtcccctttgagacaaaacggtatttctgacttggtacatattaactgactcttacacgccctcttcag
|||||||||||||| |||||||||||||||||||||||||  |||||||||||||| ||||| ||||||||||   |||    || | ||   | |||  ||||    |||| | ||  ||   | |||| |  |  || |        | |||||
GAGCTCCGCAAAGACGGTTTTGATCTTGCCGAAACTCGATTCAAGGAACTGAAACCGATACTTGACGAGgtaa--ctgtgtatttttctctggtatgaagcaaag-aatatt-cggagctgtagcgtattta--ggttcgt---tattattttcag

upper sequence: LOC_Os04g40740.4 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G50310.1 (Arabidopsis thaliana), 5'ss of exon 19
GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgtc-----atgttgtgtcccctttga---------gacaaaacggtatttctgac-ttggtacatattaactgactcttacacgccctcttcag
||||| || || ||||||||||||||||| |||||||| |||   ||||| |||||||| || || |||||||  ||||      || | || || ||||            || |      || |  | |   |||  |  |   | | |   ||  | |   ||| |||
GAGCTGCGAAAGGATGGTTTTGATCTTGCAGAAACTCGGTATCTTGAACTCAAACCCATTCTAGATGAGgtaagcttgtaccacaatttagtctctccttctcttctctctcgatactctaatagtgttaaaactggcccggacataataatggttgaatgtaatctgcag
















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|88321248|gb|CI532998.1|CI532998
EST:     TGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88429705|gb|CI548902.1|CI548902
EST:     GCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: GCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|89175699|gb|CI042720.1|CI042720
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88282300|gb|CI403696.1|CI403696
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|29631150|gb|CB636159.1|CB636159
EST:     TTGATCTGGCCGAAACTCGATATAAGGAATTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|86534966|gb|CI175172.1|CI175172
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88266525|gb|CI377427.1|CI377427
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCCACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88264898|gb|CI367549.1|CI367549
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88488975|gb|CI426246.1|CI426246
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88439364|gb|CI536336.1|CI536336
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88464162|gb|CI532097.1|CI532097
EST:     CGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: CGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88446502|gb|CI536533.1|CI536533
EST:     TGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|286456|gb|D15264.1|D15264
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88417822|gb|CI535981.1|CI535981
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
EST: gi|88849715|gb|CI089821.1|CI089821
EST:     TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTTGACGAG                         CTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC
genomic: TTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgt ... ccctcttcagCTGGCTGTGCTCGAGGCTGAACAGAAAGCTGAGGAAGAGGCTAGTGCTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCTCCGCAAAGATGGTTTTGATCTTGCCGAAACTCGATATAAGGAACTGAAACCCATACTCGACGAGgtaaaattgtcatgttgtgtcccctttgagacaaaacggtatttctgacttggtacatattaactgactcttacacgccctcttcag

- - - - - - - - - - - - - - - - - - - - - AAGGAA