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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgccca...

Basic information

species Oryza sativa
transcript LOC_Os09g29470.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G115304_T01 (Zea mays), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgccca---
|||||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||||| ||||| |||| ||||| ||||| |||  | | | | ||  |||||  |   ||  |   ||||   | |||||||   
GTCCAAACAATCTTTATCCAGATGATCTAATTCCATTTACAAGATATCCACTGTTCCTTGTAATTGATAGTGAAAATAGCCATGCATTCAAGgcaggtttgtcagaacttaatcttggcttg-tagaagaaaaccattaccatcggcactctattgcttttctaaagtaacatgtttacc--aggttgcccatgc

upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G30980.1 (Glycine max), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgccca-
|| |||| ||||| || || |  ||||| || ||||| || ||  | || || |||||  |||| || ||||| || || |||||||||||||||||||||||| |||| |    | |  |   || ||    | |   |  | ||      | | ||    | |   |  | |   | |     || |    
GTTCAAATAATCTCTACCCTGGTGATCTTATCCCCTTCACTAGGAAACCTCTTTTCCTGATTATTGACAGTGATAACAGCCATGCATTCAAGgcaggtttgtcaaaactcagaacttgtgtataagttgcctgtgaactttgttag-gcggagctgttcaggatatttattccttgaatctaattttacttgt

upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G14190.1 (Glycine max), 5'ss of exon 7
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgccca
||  ||| ||||| || || |  ||||| || |||||||| ||  | || || ||| |  |||| || ||||| || || |||||||||||||||||||||||| |||| |    | |  |   || ||    | |   |  | || ||   | | ||                                  
GTTTAAATAATCTCTACCCTGGCGATCTTATCCCCTTTACTAGGAAACCTCTTTTCTTAATTATTGACAGTGATAACAGCCATGCATTCAAGGCAGgtttgtcaaaactcagaacttgtgtataagttgcctgtgaactttgttag-atagagctgttcag-------------------------------

upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G40050.1 (Arabidopsis thaliana), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttag----cttggtagatgaaaatcattatcatgagtattt-tgttatttttcagagccaaacttactaccctggattgccca---
|| ||||||| ||||| || |  || || || || |||||| |  | ||||| ||| |  | || ||||| || | ||| | |||||||||||||||||||||| |||||| | ||      ||  | |||     ||  ||    | ||||  | ||  || |||        |   || ||   |  |    |     
GTTCAAACAACCTTTACCCTGGTGACCTAATCCCTTTTACACGGAAACCACTTTTCTTGATCATTGATAGCGACACTAGCCGTGCATTCAAGgcaggtttgtcataacttagtgtttcatttctctggagagtctgatagtttctctcagtaactatgcgatatttgctgatggattgtaataaaataaacaaactccag

upper sequence: LOC_Os09g29470.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0191g00140.t01 (Vitis vinifera), 5'ss of exon 6
GTCCAAACAAT---CTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgtcagaacttaatcttagcttggtaga-tgaaaatcattatcatg-agtattttgttatttttcagagccaaacttactaccctggattgccca
|| |||| |||   ||||| || |  ||| | ||||| ||||| |||   ||||| ||| |  |||| |||||||| || || |||||||||||||||||||||||| |||||     || |||| || | ||      |||||  |  || | | | | |  ||  | |       ||||| |  |  |  |    
GTTCAAATAATAACCTTTACCCTGGTGATATAATTCCTTTTACCAGAAGACCACTTTTCTTGATTATTGATAGTGACAACAGCCATGCATTCAAGgcaggtttgtcaaaacttgtatataacttgctacactgcttcaaattattctacagcagtgtat-agcttctaaactaggtgttacttctttcaaaagatg-

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|218494056|gb|FG946879.1|FG946879
EST:     GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAG                         GCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgt ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
EST: gi|29637839|gb|CB642848.1|CB642848
EST:     GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAG                         GCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgt ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
EST: gi|58689151|gb|CK077838.1|CK077838
EST:     GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAG                         GCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: GATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGgcaggtttgt ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT