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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgccgggatccgatcgctggatctcgccgtatacgtggcccgatcgctcgacctggtctgattgttcgtgggtgtttgtgtgtgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g16980.5
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 2
CGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgccggg-atccgatcgctggatctc-----------------gccgtatacgt-----ggcccgatcgctcgacctgg--tctgattgttcgtgggtgtttgtgtgtgtgtgcag
|| |||||||||||||||| |||||||||||| |  || | |   | ||||||||||||||||||| || ||||| ||||| |||||||||||||||||||| |    ||     |||  | |||||||||||                 ||| | || |      |||| | ||||  |  | ||   ||||||    |||     |||    |   | |||
CGCGATGGCGCAGAAGGAGACCAATGGCAGCAACGGCGAGCACATCTCCACCCGCCCGCCGCCGACCCCGTCGCCCCTCCGCTTCTCCAAGTTCTTCCAGgtcacagcgcgatctatctcaacgctggatctctgtttcacttgccgcgagccatgtatggttcagggcctgctcgcgtgttccggatcctgattaccggtgccaaattgctgcttgatccag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 1
CGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtga-----ttttgccgggatccgatcgctggatc--tcgccgt-atacgtgg-cccgatcgctcgacctgg--tctgattgttcgtgggtgtttgtgtgtgtgtgcag
|| |||||||||||||||| | |||||||||| |  ||   |   | ||||||||||||||||||| |||||||| ||||| |||||||||||||| |||||||     |  |  ||      |||| ||   ||  || |||| | || ||| |  | ||||  |  | |    |||||| || |||     |||    |   | |||
CGCGATGGCGCAGAAGGAGACTAATGGCAGCAACGGCGATCACATCTCCACCCGCCCGCCGCCGACCCCCTCGCCCCTCCGCTTCTCCAAGTTCTTTCAGgtgagagcgtgatctcgactctggatctctatttcactcaccgttagacatgggcttgttcgcgtgttccgaatcctgatttttggtgcccaattgctgtttgatccag
















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|58654932|gb|CK043612.1|CK043612
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|58659240|gb|CK047920.1|CK047920
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     CTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     CCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCGCGCAC
genomic: CCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAG                         GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC
genomic: CCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgc ... gtgtgtgcagGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGATGGCGCAGAAGGAGGCCAATGGCAGCAGCAACGGGGAGCACACCACCCGCCCGCCGCCGACGCCCTCGCCGCTCCGGTTCTCCAAGTTCTTCCAGgtgattttgccgggatccgatcgctggatctcgccgtatacgtggcccgatcgctcgacctggtctgattgttcgtgggtgtttgtgtgtgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGCCG