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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag

Basic information

species Oryza sativa
transcript LOC_Os12g27520.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G179308_T03 (Zea mays), 5'ss of exon 5
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag----
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||||| ||||||||||||||| ||| ||| ||||||||   ||  ||||||||||||||||||||| ||  |||||| ||||    
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacattgttagattgtggcaattatgaactgacccaaaaagataaccatgtggtgcttaaacattggtgaatttggatcaatggtgagcaggtct

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G179308_T01 (Zea mays), 5'ss of exon 5
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||||||| ||||||||||||||| ||| ||| ||||||||   ||  ||||||||||||||||||||| ||  |||||| ||||
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacattgttagattgtggcaattatgaactgacccaaaaagataaccatgtggtgcttaaacattggtgaatttggatcaatggtgagcag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G063792_T04 (Zea mays), 5'ss of exon 5
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |||||||||| |||||||| ||| ||| ||| | ||||||  |||  |||||||| |||||||||||| ||  |||||| ||||
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacattgttagattatgacaattatgcactgacccaaaaatataaccatatggtgcttaaacgttggtgaatttggattaatggtgagcag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G13440.2 (Glycine max), 5'ss of exon 4
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag
|||||| ||||| ||||||||||||||||||||||| |||||||||||||||||||  | ||| | | |||| |    |   | ||   | | |  |||      |  | | | |||   |||||||| ||||| |  |   |||
TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtatttaatttg-tgatggaatcatttccccaatttacaaa--taatttg--ggggttaagacaacagtgaatttaaatggtt--ttaacag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA06G18530.1 (Glycine max), 5'ss of exon 4
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag
|||||| ||||| ||||||||||||||||||||||| |||||||||||||||||||  | |||   || ||     | |||  |  |||| | | ||||     ||  | ||||     ||||||||  ||||| ||     |||
TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtatttgattgatttgtgatggat-tgatttccccaatatacataa-----tgggggttaag----ggtgaattcaaatggttgc--aacag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G02740.3 (Glycine max), 5'ss of exon 4
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacattggtgaatttgaatggatggtgggcag
|||||| ||||| ||||||||||||||||||||||| |||||||||||||||||||  | ||| | | |||| |    |   | ||   | | |  |||      |  | | | |||  ||||||||| ||||| |  |   |||
TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATTgtaagtatttaatttg-tgatggaatcatttccccaatttacaaa--taatttg--ggggttaagacaacggtgaatttaaatggtt--ttaacag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 5'ss of exon 4
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagatt-atggcaattatgaactaaccaaaagagataaccccatgaagcttaaac--attggtgaatttgaatggatggtgggcag
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||  |  | |  ||  ||     |||||  |  ||      |  ||     ||  | | ||     | | |||| || ||  | | |    |||
TTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgcta-cag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 5
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaacatt----ggtgaatttgaatggatggtgggcag
|||||| ||||| ||||||||||||||||||||||||||||||||||||||||||| |  |||  ||||||     | |||  |  ||||       ||     ||  | ||||   ||    | ||||||  ||||| |  |   |||
TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtataaaattgaattatgatggct-tgatttccccaatttcacgaatattttgggggttaagactttgtggatgaattcaaatggtt--tcaacag

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 5
TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacatcattagattatggcaattatgaactaaccaaaagagataaccccatgaagcttaaa---cattggtgaatttgaatggatggtgggcag
||| | |||||| ||||||||||||||||||||||||||||| ||||||||||||| || | |   ||| |   || ||||  |  ||||       ||     ||  |||||||     || |||||||| |||||    |   |||
TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATTgtaagtatatgactgatttacgatgat-atgatttccccaacttcatgaatattttggggcttaaaacttgttagtgaatttaaatggtc--ttaacag

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|29665166|gb|CB661441.1|CB661441
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
EST: gi|29668017|gb|CB664292.1|CB664292
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTGTGAGAAGCTTGGACCA-GCTTATATGATTTTCTGCGGAAAAACAGT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
EST: gi|29689119|gb|CB685394.1|CB685394
EST:     TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT                         GTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT
genomic: TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATTgtaagtacat ... tggtgggcagGTCTGTGAGAAGCTTGGACCAAGCTTATATGATTTTCTGCGGAAAAACAGT