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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCTATACACAAAGAACCATCTTCAATTATTCCTGGAGTTCCAGCAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaagtgttatttccatcatgtgctctaccattagcagattacaaagagttcacttatatgccttgctcctatttcatag

Basic information

species Oryza sativa
transcript LOC_Os12g06810.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06810.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G167999_T02 (Zea mays), 5'ss of exon 11
GTCCCTATACACAAAGAACCATCTTCAATTATTCCTGGAGTTCCAGCAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaagtgttatttccatcatgtgctctaccattagcagattacaaagagt--------tcacttatatgccttgctcctatttcatag
|||||| || ||||||| |||||||   |||| || |||||||||||||||| ||| ||||| ||  |||||||||||||||||||| |||| ||||||            |||||  | || |   ||   ||||  | |  |||| ||||        | | || |   |    ||| | |     ||
GTCCCTGTATACAAAGAGCCATCTTTTGTTATCCCAGGAGTTCCAGCAATAATTCAACATGAAATAATGAATAATAGAAGACATGTACTGACAAAGgtgga----------atttcttttatctatccttttattactaaaccacaaggagtgggcatcatgatttgtgcactcaactcttttaatgcag

upper sequence: LOC_Os12g06810.4 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 5'ss of exon 11
GTCCCTATACACAAAGAACCATCTTCAATTATTCCTGGAGTTCCAGCAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaagtgttatttccatcatgtgctct-accattagcagatt-acaaagagttcacttatatgccttgctc--ctatttcatag-----------------------------------------
|| ||| | ||||| |||||||| |  |  |||||||||   |||| |||    ||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| |   ||  |   ||  |  | |   |  ||||  |  || || |  | ||      |  |  |||      |||||  | |                                         
GTTCCTGTTCACAAGGAACCATCCTTTACCATTCCTGGAACCCCAGGAATTGTGCAGCATGAGATTCTAAATAATAGAAGGCATGTCTTGACTAAGgtaattacgatgcttcctcttattttacgataagataattattacttttacgatcaatttctaattcagatttgaatggttattttgttgaatgtgattttgcaaattgacactatacttctccacaatag
















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|29678630|gb|CB674905.1|CB674905
EST:     CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAG                         GATACTGCTGGTTCTGTCAAAAGGTGGGAGATTACTCGA
genomic: CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaa ... tatttcatagGATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGA
EST: gi|2311999|gb|C28154.1|C28154
EST:     GAAGACATGTATTGACGAAG                         GATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT
genomic: GAAGACATGTATTGACGAAGgtgattacaa ... tatttcatagGATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT
EST: gi|88225951|gb|CI225867.1|CI225867
EST:     CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAG                         GATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT
genomic: CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaa ... tatttcatagGATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT
EST: gi|29670913|gb|CB667188.1|CB667188
EST:     CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAA                         GATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT
genomic: CAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaa ... tatttcatagGATACTGCTGGTTCTGTCAAATTGTGGGAGATTACTCGAGGAGCTGTTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCTATACACAAAGAACCATCTTCAATTATTCCTGGAGTTCCAGCAATAACTCAGCATGAGATCCTGAATAATAGAAGACATGTATTGACGAAGgtgattacaagtgttatttccatcatgtgctctaccattagcagattacaaagagttcacttatatgccttgctcctatttcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC