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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaacttgtagcaattcaacttgcaggctgtccattttctctacttcaatttataaataccacttctctaattgcctctcccttttttttttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 9
acaaacttgtagcaattcaacttgcag--gctgtccattttctctacttcaatttataaataccacttc---tctaattgcctctcccttttttttttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
       |||||||| |  | ||        | ||  | |      || ||| | |   |||  | ||    ||||| | | | |||       |||    |||||||||||||||||||||||||| ||||||| |  | |||||||||||||
-----gctgtagcaactacattttttactattatctctgtatatggctacaaatcactcatattatttaatgtctaactacatttccaaaaaaatttctgtacagTGGGATTTTGCCGGCTATTGATATCATAGGCAGGAGTGCTATTGTGGGG
















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|25803449|gb|CA759418.1|CA759418
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|11370676|gb|AU164981.1|AU164981
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|87035348|gb|CI189970.1|CI189970
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|89180045|gb|CI044324.1|CI044324
EST:     ATCTGGTCTGCTGTGGCTCCCCCAGTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|55412661|gb|CV725037.1|CV725037
EST:     CATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: CATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|86889655|gb|CI299853.1|CI299853
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|3760903|gb|C98157.1|C98157
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
EST: gi|33683758|gb|CF311997.1|CF311997
EST:     ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGC                         TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
genomic: ATCTGGTCTGCTGTGGCTCCCCCATTTCCTTTCAAAGGAAAGTCTCTGGCgtaagtgttc ... tttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatttataaataccacttctctaattgcctctcccttttttttttgccacagTGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG
                     ctctaat  putative branch site (score: 3)
               ccacttctctaattgc  CT-rich tract
     tttataaata  TA-rich tract