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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAACATGGGCTTGAGTATCATGAAAGTTGTAGTGGGGATATTCATTCAGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccatttagacaaaaatcacttgtaaatgctcttggaggtctcaattccaacgtcctcaacctttccgtgtgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g03700.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g03700.2 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ14411 (Selaginella moellendorffii), 5'ss of exon 15
TGAAAACATGGGCTTGAGTATCATGAAAGTTGTAGTGGGGATATTCATTCAGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccatttagacaaaaatcacttgtaaat-gctcttggaggtctcaattccaacgtcctcaacctttccgtgtgtttgcag
                                          |  | | |||||||| ||||||||||||||  |||| |||||||  |||||||| ||||| ||       |     |  ||||| |  | | | || | |    | ||                                   
---------------------------------------AGCAGCCGTGCAGTTCCTGTGCAGCTACAGCACTCTCCCACTCTACGTTCTCGTCACTCAGgtaaagat-ccaacgtttatctcactcgagagtagttcctcg----cacag----------------------------------

upper sequence: LOC_Os03g03700.2 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ26004 (Selaginella moellendorffii), 5'ss of exon 15
TGAAAACATGGGCTTGAGTATCATGAAAGTTGTAGTGGGGATATTCATTCAGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaa---ccatttagacaaaaatcacttgtaaatgctcttggaggtctcaattccaacgtcctcaacctttccgtgtgtttgcag
                                          |  | | |||||||| ||||||||||||||  |||| |||||||  |||||||| ||||| ||    | |  |  |  | | ||    |||  | |||    ||                                         
---------------------------------------AGCAGCCGTGCAGTTCCTGTGCAGCTACAGCACTCTCCCACTCTACGTTCTCGTCACTCAGgtaaagatccaacgtttatcacactcgagagtagttcctcgcacag-----------------------------------------
















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|29642232|gb|CB647239.1|CB647239
EST:     AGTTCCTATGCAGTTACAGCACCTTCCCTCTGTACGCACTCGTCACACAG                         ATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
genomic: AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccat ... gtgtttgcagATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
EST: gi|58586874|gb|CF985182.1|CF985182
EST:     AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAG                         ATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
genomic: AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccat ... gtgtttgcagATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
EST: gi|29658708|gb|CB654983.1|CB654983
EST:     AGTTCCTATGCAGCTACAGCACCTTCCCTCTTTACGCACTCGTCACACAG                         ATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
genomic: AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccat ... gtgtttgcagATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
EST: gi|29642233|gb|CB647240.1|CB647240
EST:     AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAG                         ATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC
genomic: AGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccat ... gtgtttgcagATGGGATCAAACATGAAGAAGACCATCTTCGAGGAGCAGACGATGAAGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAACATGGGCTTGAGTATCATGAAAGTTGTAGTGGGGATATTCATTCAGTTCCTATGCAGCTACAGCACCTTCCCTCTCTACGCACTCGTCACACAGgtgaaaccatttagacaaaaatcacttgtaaatgctcttggaggtctcaattccaacgtcctcaacctttccgtgtgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT