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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagttgatttactatatatttatattattcaaaaagtgttaatgcttttatgtattattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCTTTGGGATCTTTGATGGTTGTTATACTAATCCGAACCATCAAATACAACC

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 9
gtaagcaagttgatttactatatatttatattattca-aaaagtgttaatgcttttatgtattattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCTTTGGGATCTTTGATGGTTGTTATACTAATCCGAACCATCAAATACAACC
|||||| |  |  || | |   || ||   |||||   |||| |||||||  | | | ||   | || ||||||||||    || |||||||||||||||||||| ||||||||||| ||  ||||||||||||||||||| |||||||| || ||||| || |||||||
gtaagccaactagttaatttcttaatttgtttatttgtaaaactgttaataatataacgtgcaactccagGTGCTTCCTGCAGTTCCTTGGTACCATGAGCGCCTGATGCATCAAACGTCACTGGGATCTTTGATGGTTGTAATACTAATTCGGACCATTAAGTACAACC

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G078576_T01 (Zea mays), 3'ss of exon 9
gtaagcaagttgatttactatatatttatattattca-aaaagtgttaatgcttttatgtattattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCTTTGGGATCTTTGATGGTTGTTATACTAATCCGAACCATCAAATACAACC
||||| ||  |  || |||   || ||   |||||   |||| |||||||  | | ||||  |  || ||||||||||  | || |||||||||||||| ||||| ||||||||||||||| ||||||||||||||||||| |||||||| |  |||||||| |||||||
gtaaggaaactagttgacttcttaatttgtttatttgtaaaactgttaataatataatgtgctgctccagGTGCTTCCTGGTGTTCCTTGGTACCATGAACGCCTGATGCATCAAACTTCTATGGGATCTTTGATGGTTGTAATACTAATTCAGACCATCAAGTACAACC
















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|58684083|gb|CK072770.1|CK072770
EST:     TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTG                         GTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
genomic: TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTGgtaagcaagt ... attattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
EST: gi|29628456|gb|CB633467.1|CB633467
EST:     TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTG                         GTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
genomic: TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTGgtaagcaagt ... attattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
EST: gi|58693104|gb|CK081791.1|CK081791
EST:     TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTG                         GTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
genomic: TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTGgtaagcaagt ... attattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTG                         GTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT
genomic: TTCTTATACTCAGTCAAGATTCAACCTTCAATGCTAGTGTACACAAATTGgtaagcaagt ... attattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactatatatttatattattcaaaaagtgttaatgcttttatgtattattctagGTGCTTCCGAGCGTCCCTTGGTACCATGAGCGCCTTATGCATCAAACTTCTTTGGGATCTTTGATGGTTGTTATACTAATCCGAACCATCAAATACAACC
                            tgttaat  putative branch site (score: 3)
                                              ttattct  putative PPT
     atatatttatattatt  TA-rich tract