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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaactttctgattactatttcaaaattgatgtaaactatgtgcttacctctagtctagcttgtagttcccacataagttttttttcttgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g32610.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G059671_T01 (Zea mays), 5'ss of exon 8
TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttga-actttctgattactatttcaaaattgatgtaaactatgtgcttacctctagt-ctagcttgtagttccc--acataagtttttt--ttcttgaatgcag
|||||||||||| |||| |||| ||||| |||||||| ||| ||||||||||||| ||||||||||| || ||||| |||||||| ||||| |||||||||||||| ||||||||| | | ||| ||| || ||||| || |||||||| ||| ||||| || ||| ||||| || | |||||
TTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAAGgtgtgtccttactttctgaatgccttttgaaa-------tatactatctgtgcacctctagagttagtccaaggttccagaacttaacctttttgttttctatgtgcag

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 5'ss of exon 9
TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaactttctga--------ttactatttcaaaattgatgtaaactatgt-gcttacctctagtctagcttgtagttcccacataagttttttttcttgaatgcag
||||||| |||||| | || | |||||||||||||| || ||||||||||||||||||||||| ||| | || || || || |||||||| ||||||||| || ||| | | ||| | | | | | | || | | || | | | |||| | | | | | | || || | | |||||
TTGCAATCATGAAACGCTTGAGGCATCCAAACATTGTTCTCTTTATGGGTGCTGTTACTCAGCCTCCACATCTGTCCATAGTTACAGAATACTTATCAAGgttctttatgattttttagatattgcttattttcttataccctgtttacaagaagtcgtgcaaaatgaatctaatatatcactga-attagaatattggttttgcattgcag

upper sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 9
TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgt-----------tgaactttctgattactatttcaaaattg---atgtaaactatgtgct--tacctctagtctagcttgtagttcccacataagttttttttcttgaa-tgcag
|| | || |||||| | ||||| ||||| || || || |||||||||||||| ||||| ||||| ||||| | || || || ||||||||| ||||||||| | | ||| || || ||||| || || ||| | | | || | | || || | | || | | | | | ||||| |||||
TTTCTATAATGAAACGCCTGCGGCATCCGAATATCGTTCTTTTTATGGGTGCAGTTACGCAGCCCCCAAATTTGTCCATAGTTACAGAATATTTATCAAGgtttttaattttattcccaaacaatccttttttcttttcatttttttttattaaaatgagatattggtattatttattaagtttctgttccctgaactaaatactagttttgaactgcag

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|88585426|gb|CI703056.1|CI703056
EST:     GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
EST: gi|29680716|gb|CB676991.1|CB676991
EST:     AGCCACCAAAACTTTTGATTGGGACAGAATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: AGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
EST: gi|33675051|gb|CF303290.1|CF303290
EST:     GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
EST: gi|29665412|gb|CB661687.1|CB661687
EST:     GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
EST: gi|29664339|gb|CB660614.1|CB660614
EST:     GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: GCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
EST: gi|58595275|gb|CF993583.1|CF993583
EST:     CTGTTACTCAGCCACCAAAACTTTCGATTGTGACGAGGATATCTATCAAG                         AGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA
genomic: CTGTTACTCAGCCACCAAAACTTTCGATTGTGAC-AGAATATCTATCAAGgtgtgttgaa ... ttgaatgcagAGGTAGCCTATACAGGATTTTGCACAAGCATGGTGCAAGGGAAAATCTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAAGgtgtgttgaactttctgattactatttcaaaattgatgtaaactatgtgcttacctctagtctagcttgtagttcccacataagttttttttcttgaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT