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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag

Basic information

species Oryza sativa
transcript LOC_Os08g44400.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G825090_T05 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag--------------------
|| ||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | ||||||||  ||||  |    ||  || | ||  |   ||  | |   |  |  | ||  |    ||     |     |||| ||                      
GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgtattcaacacatctccttttcacttt--tgctcttaaaggttgatcctccctatttgtgggggaaaaggcttgtctcggtttaaccctgagacccca

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G085000_T05 (Zea mays), 5'ss of exon 3
------------------------------GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctcc-ctgtccctggggcctcctactaacctcctgcatttgc-ccttgcttttcag
                              |||||||||||||| ||||| |||||||||||||| |||| ||||||||||||||| || |||| ||||||||  ||||  |  | || ||| |   | ||  || |    ||    ||||  ||  | |||   ||||  | ||| |||||||
ACAGTTATATAAGATACATGTCTATTGCAGGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcag

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G022866_T02 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag--------------------
|||||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | ||||||||  ||||  |    ||  || | ||  |   ||  | |   |  |  | ||  |    ||     |     |||| ||                      
GTGGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgtattcaacacatctccttttcacttt--tgctcttaaaggttgatcctccctatttgtgggggaaaaggcttgtctcggtttaaccctgagacccca

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G825090_T03 (Zea mays), 5'ss of exon 6
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag--------------------
|| ||||||||||||||||| |||||||||||||| |||| |||||||||||| || || || | ||||||||  ||||  |    ||  || | ||  |   ||  | |   |  |  | ||  |    ||     |     |||| ||                      
GTAGATCCAAACACAGGGGTCGCCATGTATGAATCCGATGACATCATAAAATATCTAGCTGATACATATGgtgtgtattcaacacatctccttttcacttt--tgctcttaaaggttgttcctccctatttgtgggggaaaaggcttgtcttggtttatccccgagacccca

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G085000_T03 (Zea mays), 5'ss of exon 5
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctcc-ctgtccctggggcctcctactaacctcctgcatttgc-ccttgcttttcag
|||||||||||||| ||||| |||||||||||||| |||| ||||||||||||||| || |||| ||||||||  ||||  |  | || ||| |   | ||  || |    ||    ||||  ||  | |||   ||||  | ||| |||||||
GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcag

upper sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 5'ss of exon 6
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtg---cctatttcatctctcatctgtacatctccctgtccctggggcctcctactaacctcctgcatttgcccttgcttttcag---------------
||||||||||||||||| ||||| ||||||||||| |||| ||| || || ||  |||  |  |||||||||    |  ||| || |  ||   | |   |     |||  | ||    |  |  |   ||| |   ||   | |   |     |               
GTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATGgtatacctcattacaccaatctagtttcggtggatttgtttcaggcagttgattgttttctcatcagttaatcatcaataaattgcacatctatgacaga

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|55408882|gb|CV721258.1|CV721258
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
EST: gi|58590549|gb|CF988857.1|CF988857
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
EST: gi|29687876|gb|CB684151.1|CB684151
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
EST: gi|58593409|gb|CF991717.1|CF991717
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
EST: gi|27548923|gb|CA767585.2|CA767585
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
EST: gi|29685102|gb|CB681377.1|CB681377
EST:     TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG                         GTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA
genomic: TGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctattt ... tgcttttcagGTGATGGAACAGTTCCAATTATGCTATCACTTGGTATATTAACA