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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttattgccttgttc...

Basic information

species Oryza sativa
transcript LOC_Os09g24650.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 9
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttat-tgccttgttc
|||||||| |||||||||||||| || ||||| || ||||| || |||||||||||| | |||||||||||||||||||||||| |||||||||||   | ||     | |||| |      || |||   |  ||    ||||   |  |  ||||    | |   | ||  |||  ||   ||   | |
CTTTTTCTGTTGCGTGCTGCTGGTTTCCTGCTTCCGTTCTACATCATGGCTTGGGCAATCAGTATCTTGCAGCGCCGCAGACAGAGACAGgtcagttaataatttctaaagtgaatatttgcatcttccttttcttattttttgaaggttccgggaacacctaacg-tatttcttgccatacaccgaatac

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 6
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgttatcatacaggtgatttacattattttctactattttaaatttgttagaacttggaatgtgtgataattttatttgttattgccttgttc-
|||||  |  | ||||||||||| |||||  |||| | |||||| |||||||||||| | ||||| ||||| |||||  ||||  |||| || ||| |    || |     ||| | |  ||  || | ||| |  ||| |  ||      |||   ||| |   ||| ||  || ||    ||   ||  
CTTTTCTTGCTTCGTGCTGCTGGTTTTCTTTTACCTTGCTATATCATGGCTTGGGCAATCAGTATTTTGCAACGCCGGCGACAAAGACAAgtaagt-ttcagtcttggttctgactaatttttgttccgactttgctaattcggtgttggtttgttctgttttgaaatcttgctttttggctccaactttg

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 5'ss of exon 7
CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgtta-----tcatacaggtgatttac---attattttctactattttaaatttgttagaacttggaatgtgtgataatttt--atttgttattgccttgttc-----
||| | ||  | || |||||||||||||| || |||| |||||| |||||||||||  | |||||  | |||||||| |||||| ||||||| ||||   ||     |||| || |   ||| |   |   | || |  | || | | | | |||  | |   | || || |    | |  | ||  | |  ||   ||      
CTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

upper sequence: LOC_Os09g24650.3 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G02960.5 (Arabidopsis thaliana), 5'ss of exon 5
----------CTTTTTCTATTGCGTGCTGCTGGATTTCTGCTACCATTCTATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgtta-----tcatacaggtgatttac---attattttctactattttaaatttgttagaacttggaatgtgtgataatttt--atttgttattgccttgttc-----
          ||| | ||  | || |||||||||||||| || |||| |||||| |||||||||||  | |||||  | |||||||| |||||| ||||||| ||||   ||     |||| || |   ||| |   |   | || |  | || | | | | |||  | |   | || || |    | |  | ||  | |  ||   ||      
CTTATTTTAGCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAGgttagtagtataagaactcatgcaaggatttttccggacagtcttttttttttcttactgttttatgaatcaaactgagtcactggtatcgacttaatgtaacccgattgaacag

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|86431015|gb|CI083438.1|CI083438
EST:     AGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATACATTCTTCAGTCTGGG
genomic: AGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|38471428|gb|CF955559.1|CF955559
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|86831029|gb|CI295513.1|CI295513
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88982076|gb|CI027653.1|CI027653
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|29626393|gb|CB631404.1|CB631404
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTTTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|218496676|gb|FG944369.1|FG944369
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCTGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|88223285|gb|CI223134.1|CI223134
EST:     ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: ATATAATGGCTTGGGCAGTGAGTATCTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
EST: gi|16575403|gb|BI802699.1|BI802699
EST:     CTTGCAGCGCCGCAGACAGCGACAG                         GAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG
genomic: CTTGCAGCGCCGCAGACAGCGACAGgtcagtatgt ... gtttgttcagGAGGCGGCTGCCTTAGCAGCAACTGAGGTGGCATTCATTCTTCAGTCTGGG