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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattttttgcatactgtattcaatttgcaactacaaaggttgag...

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 19
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaa-cttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattttttgcatac-tgtattcaa--tttgcaactacaaaggttgag------------------------------------------------------------------------------
||| ||| ||||||| ||||||||||| ||||||||||||||||||| ||||||| |||| || ||||||||||||||||||||||| |||||||||||||||||||  ||| |  |||      |  ||  |  | || | ||| |  | || |||  ||   ||  |   || | | ||  ||||    || | |  |                                                                                  
TGAAATGTTGTATGGACGTACACCTTTTCGAGGAAAGAACAGGAAAAGGACATTTCATAATATCCTGCACAAAGACCTTACATTTCCAAGTAGCATTCCGgtaagaaatttcatccttatttttgttacc--tacaattgcatgtaaatctggtcaaatttgcctgtgtttgtgcagttaacatttgatggtatagaaataagttttgaaactatctacaatgttttgtaccacatacaacgttgtttattctgttcacctattaacaaatgtttactccag

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA08G33520.1 (Glycine max), 5'ss of exon 3
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagt--ttcctgtcat--gcaggccaatattttttgcatactgtattcaatttgcaactacaaaggttgag
||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  || ||  | ||||| || ||||| ||||| || |||||||||||||  |      | ||||  |  ||  |  | || |  ||   ||  |  ||   |||||   |||| || |  |        || | | | || | |||   
TGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCCAAGCAGCATTCCGgtaaataacaaaatattagt-agttgaactttaaaatatttatagttgtttgccatccaattcattttccaaagagag---gggttcctatttcagaagttttt

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattt-tttgcatactgtattcaatttgcaactacaaaggttgag
||||||||| ||||| ||||| |||||| |||||||||| ||| | ||||||||||  |||||  |||||||||| || || |||||||||||||||||||||| | | ||  |||   |   ||  ||| ||   |    |    |       |  |||   ||   ||||  |     ||    | ||||   |  || 
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga-

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|29613844|gb|CB618857.1|CB618857
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CATTTTATAACATACTGCACNNNGACCTTACATTTCCCAGTAGCATTCCG                         GNNAGTCTTGCAGCAAAG
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAG