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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGTGTCAAGGACATTTGCCAAGATGGTGGTATATTCAAGAAGATACTGAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttgctcattgaaacatattgctatcttatatattgccctgtagctgaccctttgcattgctgtag

Basic information

species Oryza sativa
transcript LOC_Os08g41390.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 3
ACAAGTGTCAAGGACATTTGCCAAGATGGTGGTATATTCAAGAAGATACTGAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatattt--gctcattgaaacatattgct---atcttatatattg---ccctgtagctgaccctttgcat--tgctgtag
|| |||||||| ||||||||| ||||||| || |||||||||||||| || || |||||||| ||||||||||||||||| |||| |||||||||| |||||||| |||  ||| ||||  |||  || |    | || || ||||     ||| || || |  || | | |  |  |||||
ACCAGTGTCAAAGACATTTGCAAAGATGGCGGCATATTCAAGAAGATCCTTAAAGAGGGAGAGAAATGGGAGAACCCAAAGGATCCTGATGAAGTACTTGgtaatttttttgcttattgcgacacttttcatagagctgatttatttggttcctataacttatactctccttgctcttgtag
















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|58656111|gb|CK044791.1|CK044791
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAGGGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|58690253|gb|CK078940.1|CK078940
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAG
EST: gi|58675080|gb|CK063767.1|CK063767
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|218486102|gb|FG952697.1|FG952697
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|4880950|gb|AU065249.1|AU065249
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|29624443|gb|CB629454.1|CB629454
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|58599096|gb|CK009624.1|CK009624
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|58682636|gb|CK071323.1|CK071323
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCT
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCT
EST: gi|29675035|gb|CB671310.1|CB671310
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|29666721|gb|CB662996.1|CB662996
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|29626371|gb|CB631382.1|CB631382
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     AAGGAGGGAGAAAAATGGGAGAACCCAAAGAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: AAGGAGGGAGAAAAATGGGAGAACCCAAA-AGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTG                         TGAAATATGAGGCTCGGCTTGAGGATGGTACTGTTATATCAAAGTCTGAGG
genomic: GAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttg ... attgctgtagTGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGTGTCAAGGACATTTGCCAAGATGGTGGTATATTCAAGAAGATACTGAAGGAGGGAGAAAAATGGGAGAACCCAAAAGATCTTGATGAAGTATTTGgtaatatttgctcattgaaacatattgctatcttatatattgccctgtagctgaccctttgcattgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA