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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgcatactttagcctaaagaaacttattttaggacatttgataatgctcactaaacatttgaaaattttgttgtaaccttggtgcctttggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAACTTTTGCCATCAACTACCTCAAAGCTAGAGGTTCCATATGATACTTTAG

Basic information

species Oryza sativa
transcript LOC_Os01g55260.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55260.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 9
ggtgcatactttagcctaaagaaacttattttaggacatttgataatgctcactaaacatttgaaaattttgttgtaaccttggtgcctttggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAACTTTTGCCATCAACTACCTCAAAGCTAGAGGTTCCATATGATACTTTAG
          |  | |||     | ||  ||||    ||   |||| | | || ||    ||||         |||     | ||| || ||  | ||||||||| ||||| |||||||| | |||||||||||| || ||||||||||||||| ||||| |||||||||||||| ||||  | || || || |   |||
---------gtatgtcta---gtagttgatttacattatcatataa-gttgacaaatggattgatctcacctctgt-----ttgtgtctctgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG
















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|86501179|gb|CI143812.1|CI143812
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|88847654|gb|CI018345.1|CI018345
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86432582|gb|CI086193.1|CI086193
EST:     GCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: GCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|87016598|gb|CI275600.1|CI275600
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|3768081|gb|AU032108.1|AU032108
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86493620|gb|CI136253.1|CI136253
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|87036076|gb|CI189523.1|CI189523
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86499978|gb|CI142611.1|CI142611
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAAC-G                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|8858208|gb|AU095526.1|AU095526
EST:     TTNCCCTTGGGAACTGGACGCAGCTATGTC-CCGCCGGCTTGAGAANCGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: TT-ACCTTGGGAACTGGACGCAGCTATG-CTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|88984340|gb|CI020238.1|CI020238
EST:     CAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: CAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctcactaaacatttgaaaattttgttgtaaccttggtgcctttggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAACTTTTGCCATCAACTACCTCAAAGCTAGAGGTTCCATATGATACTTTAG
                           ttgtaac  putative branch site (score: 2)
                                       tgccttt  putative PPT
        taaacatttgaaaatt  TA-rich tract