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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAACTACTGGTGACCCCAAAGGTGTACTGATCTCCAATGCAAGCATTATTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatgccagcagccctttcattatgcatccatatataatcactgatcaatctttaattgctttaactatgcgggaatctcag

Basic information

species Oryza sativa
transcript LOC_Os01g46750.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G861300_T01 (Zea mays), 5'ss of exon 9
TGGAACTACTGGTGACCCCAAAGGTGTACTGATCTCCAATGCAAGCATTATTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatgccagcagccctttcattatgcatccatatataatcactgatcaatctttaattgctttaactatgcgggaatctcag
|||||||||||||||||| ||||| |||||||| || ||||| ||||||||||| ||  | |||||||| || ||| ||||||||| |||||| ||  |||| |||  | |  | ||| |||  ||||||   |||  | ||  |||||   ||  ||||||  |||  || ||  | |||| ||||
TGGAACTACTGGTGACCCAAAAGGAGTACTGATATCAAATGCTAGCATTATTTGTCTCATTGCAGGTGTGGACCGGTTGCTTAACTATGTAAACGAAGAGgtgagaagttcttgaagctcttcaattatgtggccacct-tatacactgggaaacatttaatatcttatacaatatgagaatttcag

upper sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 9
TGGAACTACTGGTGACCCCAAAGGTGTACTGATCTCCAATGCAAGCATTATTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatgccagcagccc------tttcattatg-catccata---tataatcactgatcaatctttaattgctttaa-ctatgcgggaatctcag--
|||||| || |||||||||||||||||  |||| ||||||| ||||||| ||   ||  | || || ||  | || |||||  |  |||| |||||  |||| |  | |     ||   |      | ||| |||  |||| | |   || |   |  ||   ||  ||      ||||| || ||        | |   
TGGAACAACCGGTGACCCCAAAGGTGTGATGATTTCCAATGAAAGCATTGTTACTCTTATTGCTGGGGTGAAGCGCCTGCTACAGAGTGTCAATGAAGAGgtgatttcttttctcatttcaagttatctcagtatctcatcaacagaatacacggatagaaagatagttgggaattttaagctttgtttcttcattatct
















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|2310480|gb|C26635.1|C26635
EST:     TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAG                         CTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
genomic: TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatg ... ggaatctcagCTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
EST: gi|29673146|gb|CB669421.1|CB669421
EST:     TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAG                         CTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
genomic: TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatg ... ggaatctcagCTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
EST: gi|58672830|gb|CK061516.1|CK061516
EST:     TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAG                         CTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
genomic: TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatg ... ggaatctcagCTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
EST: gi|58655155|gb|CK043835.1|CK043835
EST:     TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAG                         CTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
genomic: TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatg ... ggaatctcagCTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
EST: gi|29618098|gb|CB623110.1|CB623110
EST:     TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAG                         CTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT
genomic: TTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatg ... ggaatctcagCTGGAGCAAACCGATGTTTACATGTCTTATCTTCCACTTGCTCATATCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAACTACTGGTGACCCCAAAGGTGTACTGATCTCCAATGCAAGCATTATTTGCCTAGTCGCAGGTGTAGATCGGCTGCTTAACTGTGTAAATGAGCAGgtaagatatgccagcagccctttcattatgcatccatatataatcactgatcaatctttaattgctttaactatgcgggaatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG