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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctag

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179308_T02 (Zea mays), 5'ss of exon 3
--------TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctag
        ||||||| |||||| | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||| ||  ||  | ||||    |   |||     | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||
TGTTGCAGTTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063792_T03 (Zea mays), 5'ss of exon 4
--------TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctac--ctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctag
        |||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||||||  |||||||| ||    || || ||||    |   |||     ||  | |  ||   |  ||    ||  |  |   |     |   |   |||  | || |||||  |      | ||| ||
TGTTGCAGTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatatcttgttcttttatatttaattcacctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G063792_T04 (Zea mays), 5'ss of exon 7
TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctac--ctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctag
|||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||||||  |||||||| ||    || || ||||    |   |||     ||  | |  ||   |  ||    ||  |  |   |     |   |   |||  | || |||||  |      | ||| ||
TTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatatcttgttcttttatatttaattcacctacccaagatttaccttgtgctatgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179308_T03 (Zea mays), 5'ss of exon 6
TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctacctatttgacct-tttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatc-tctgctag
||||||| |||||| | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||| ||  ||  | ||||    |   |||     | | | |  ||      ||  | || | ||   | |   | | |    |||  | || |||||  |    || | ||||||
TTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAAgtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttg-taataggttagtgaatattgaatatggtactgatcctctttttttcatttgctag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 7
TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaatt-ttatgttatctttctaatccttctacaatctctgctag
|||||||||| || |||||||| || || ||||| ||||||||||| || ||||| || |||||||| ||  ||||||| || || ||||| |||  ||       |  || |  |     | |||       ||  || ||  |||       |||       ||  || |     || || |   || | | |  | | | | ||           
TTATGCATGATTTACGCCTCATACATACGGATTTGAAGCCTGAGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAGgta--ctccagatgttaacttgat--gtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcag----------

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 7
TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactt-----tgttcttctacctatttgaccttttagcctttttaacgtcttcttttt----acccggtt-tagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgc-tag-------------------
| |||||||| |||| |||||| |||||||| || |||||||||||||| ||| ||||||||||||| ||  | |||||  | || ||||| |||||  |     ||||||  || || ||  |  | || ||  || |   ||  | |   |    |||   || | | |  | | | ||   |  ||   ||||  ||||| |   |   ||  ||||   | ||                    
TCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATACTTTTTGTTTCTCCAGAATATGTAAAAGTATCAGACTACAAGgtatatctacttctgttctggtagcttttcaatttgtttgcacttctgttgttctttcaatcaagaccttattgttgatattcaggcttttccttttccctgttccctttccatatcagttattatctggtcataatgtttctttctaattgcag

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|86900381|gb|CI296424.1|CI296424
EST:     AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA                         GTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG
genomic: AGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAAgtatactttg ... tctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAG