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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtctattttccctaatttaatactgtgaaattgcaattgaataattatctgatctgtattaaatatagatttcttgcaaacttgttggtctaccctcaaaatataaatgtaacgtaagtaaagttcttcctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCATCCCATCAGGGGAAAAACCAGTTTGTGACAGAGGTTGCAACAATTTCTT

Basic information

species Oryza sativa
transcript LOC_Os08g10320.3
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10320.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv12s0055g00580.t01 (Vitis vinifera), 3'ss of exon 20
gttgtctattttccctaatttaatactgtgaaattgcaattgaataattatctgatctgtattaaatatagatttcttgcaaacttgttggtctaccctcaaaatataaatgtaacgtaagtaaagttcttcctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCATCCCATCAGGGGAAAAACCAGTTTGTGACAGAGGTTGCAACAATTTCTT
|| |   ||| |||     |  |   | |  | ||    ||  || |||||  |     |   ||| || |  || ||   || |  ||  | |    |     | |    ||||    | |    |  |   || |  |||| |  ||  |||||||||||||| | |||||||| ||||| |||  |||||| || || || || || |||||||| |||||| ||||||| || ||  
gtaggtcattatcct---atcgagcttatatattt----ttttatgattatgagtatgattacaaacatgggatttttctcaa-tcattccttttttttt----ttttttggtaat---aattttatattcaattcgttagGGGACACTTTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCACACCAAGGAAAGAATCAGTTTGTAACAGAGATTGCAACCATATCAG

upper sequence: LOC_Os08g10320.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv12s0055g00610.t01 (Vitis vinifera), 3'ss of exon 2
gttgtctattttccctaatttaatactgtgaaattgcaattgaataattatctgatctgtattaaatatagatttcttgcaaacttgttggtctaccctcaaaatataaatgtaacgtaagtaaagttcttcctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCATCCCATCAGGGGAAAAACCAGTTTGTGACAGAGGTTGCAACAATTTCTT
                       ||  || |   | | |||||  |  ||| |  |    ||||    ||   |  || | ||| || |  | | | |   ||   |   | |    |    | | || |   || |  |||| |  ||  |||||||||||||| | |||||||| ||||| |||  ||||||||| || || || || | |||||| |||||| ||||||| || ||  
----------------------gtag-gtcattatcctattgagcagatatttttttatgattatgatta---tgattacgaacatggtatttttctc---aatcttctttttttttttgtcataattttatattcgttagGGGACACTCTCTGATGGAAGAGTTGTTGCTGTAAAGCAACTATCTGTATCATCCCACCAAGGAAAGAATCCGTTTGTAACAGAGATTGCAACCATATCAG
















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|58688732|gb|CK077419.1|CK077419
EST:     ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAG                         GGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCA
genomic: ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAGgttgtctatt ... cctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCA
EST: gi|29620863|gb|CB625874.1|CB625874
EST:     ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAG                         GGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCA
genomic: ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAGgttgtctatt ... cctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCA
EST: gi|29630198|gb|CB635207.1|CB635207
EST:     ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAG                         GGTATGCTACCTGATGGA
genomic: ACAGTTCCCAAAACATTCTTGGGGAAGGTGGATATGGACCAGTCTATAAGgttgtctatt ... cctttggcagGGTATGCTACCTGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggtctaccctcaaaatataaatgtaacgtaagtaaagttcttcctttggcagGGTATGCTACCTGATGGAAGAGTTATAGCTGTAAAACAACTTTCTCAATCATCCCATCAGGGGAAAAACCAGTTTGTGACAGAGGTTGCAACAATTTCTT
                       atgtaac  putative branch site (score: 3)
                                        ttcttccttt  putative PPT
            tcaaaatataaatgta  TA-rich tract