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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATCATGGCCCTGAAAACTGGACTAGTGGGGTTGATCTTGGCCGTCTACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattcttttccctctattcatttgcattcatcttcagatattccagaaatacgttggactatccaatttacttgatgttttcatactactttgtattgaatctgtacacttttgctccattacaaagctgacagaatttgcctactataaag

Basic information

species Oryza sativa
transcript LOC_Os04g52479.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G102346_T01 (Zea mays), 5'ss of exon 5
AGTGATCATGGCCCTGAAAACTGGACTAGTGGGGTTGATCTTGGCCGTCTACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattcttttccctctattcatttgcat-tcatcttcagatattccagaaat---acgttggactatccaatttacttgatgttttcatactactttgtattgaatctgtacacttttgctccattacaaagctgacagaatttgcctactataaag
 |||| |||||||||||||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||  ||||||| ||||||||||||||| ||||||     ||| || | | |||| ||   | |  |   ||  | || ||  | |   || | |||  ||||| |    |  |   ||     ||  || |                                                           
TGTGACCATGGCCCTGAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGACCTTATCATAACCAATGAATCACTCAAAGgttcggcatttcccttgttttcagttatgtgttttacacaatttttgcatcacttagacatcggagaatccactagcgtccagaattagggtctgtttgg-----------------------------------------------------------

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G020210_T01 (Zea mays), 5'ss of exon 1
AGTGATCATGGCCCTGAAAACTGGACTAGTGGGGTTGATCTTGGCCGTCTACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattcttttccctctattcatttgcattcatcttcagatattccagaaatacgttggactatccaatttacttgatgttttcatactactttgtattgaatctgtacacttttgctccattacaaa--gctgacagaatttgcctactataaag
 |||| ||||||||| |||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||| ||||||| ||||  ||||||||| ||||||     |||||| |   |||| ||  ||   | ||    |  |      || | ||      | ||  | ||| ||   |     |||    | ||  |  |||||    ||||| ||||  ||| |   |||||| |||||  |  | ||||||
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattttccttgctttcagttatatatgtgttttactcgtttttgcatccctt------ttcagat-actggaaaatcc---actgtgatatac-gcttctgttgctttttgttccacgacagataactgacataatttaacctcgataaag

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G454412_T01 (Zea mays), 5'ss of exon 1
AGTGATCATGGCCCTGAAAACTGGACTAGTGGGGTTGATCTTGGCCGTCTACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattcttttccctctattcatttgcattcatcttcagatattccagaaatacgttggactatccaatttacttgatgttttcatactactttgtattgaatctgtacacttttgctccattacaaagctgacagaatttgcctactataaag
 |||| ||||||||| |||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||| ||||||| ||||  ||||||||| ||||||     |||||| |   |||| ||  ||   | ||    || ||      |   |    |  |   |  |||| ||   |     |||    ||||  |  ||| |    ||||| |||||         |||| |||||  |  | ||||||
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattttccttgctttcaattatatatgtgttt---tactc----gttttttcatcccttttcagatactggaaaatcc---actgtgatgtac-gcttctattgctttttgttccat---------gacataatttatcctcgataaag

upper sequence: LOC_Os04g52479.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G033724_T02 (Zea mays), 5'ss of exon 5
AGTGATCATGGCCCTGAAAACTGGACTAGTGGGGTTGATCTTGGCCGTCTACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattcttttccctctattcatttgcattcatcttcagatattccagaaatacgttggactatccaatttacttgatgttttcatactactttgtattgaatctgtacacttttgctccattacaaa--gctgacagaatttgcctactataaag
 |||| ||||||||| |||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||| ||||||| ||||  ||||||||| ||||||     || ||| |   |||| ||  ||   | || |    ||   | |   | ||      ||  |  |||| ||   |     |||    ||||  |  |||||    ||||| ||||  ||| |   |||||| |||||  |  | ||||||
TGTGACCATGGCCCTCAAAATTGGACCAGTGGAGTTGATCTTGGCCGCCTTCTGGATCGTCTTGAACTTGATCTTATCATAACCAGCGAATCACTCAAAGgttcggcattctccttgctttcagttatatgtgt-tttactcgtttttgcatcccttt------tcaga--tactggaaaatcc---actgtgatgtac-gcttctgttgctttttgttccacgacagataactgacataatttatcctcgataaag

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|218497576|gb|FG948930.1|FG948930
EST:     ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAG                         ATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
genomic: ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattctt ... tactataaagATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
EST: gi|58686413|gb|CK075100.1|CK075100
EST:     ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAG                         ATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
genomic: ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattctt ... tactataaagATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
EST: gi|218484706|gb|FG949605.1|FG949605
EST:     ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAG                         ATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
genomic: ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattctt ... tactataaagATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG
EST: gi|86437602|gb|CI119324.1|CI119324
EST:     ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAG                         ATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGNCCGCCGTTACCTCAGCTG
genomic: ACTCGACCGTCTGGAACTTGATATTATCATTACCAATGAATCACTCCAAGgttgattctt ... tactataaagATGCCGTGCAGCAGCAAAGATTTGCTTTGGTGGCCGCCGTTACCTCAGCTG