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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 5
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
                                                             | |  |||  |   ||     | ||||| |  |  ||  ||||| |||||||| ||||||||||| || ||||| ||||||||||||||||| ||||| ||||||| |
-------------------------------------------------------------gtatttaccttgggat-----tttctttcttcatatgtgtagGTCATGATGAGGTTGTTCAGTCCTCGCAAAACAACATTGTTGTTTGTTATACGTGACAAATCAAGG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 7
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
            ||   |         | ||||   |   |    |  || | || |     ||| |  |||  || | ||||  |  ||||          |||| |||||||||||||| |||||||| ||||| ||| |||||||||| || ||||||||  |||||
------------gtatcatt-caactacctattgattacaagcaatagtt-tccaatctaaaaagttggtatttatctaattgcatgcttgtatttgctttcagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
    || |||   || |    | | | ||        |||| || ||| |||| |    ||  |  |   ||  || | | ||     |             |||| |||||||||||||| |||||||| ||||| |||||| ||||||| || ||||||||| ||| |
----gtatgt-gttgttggcctattgactacaagaacttgaatcttgaatcttgaaacttgtcaattgtcatttatttaactgcacactaaattttactttcagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGCTGTTTGTCATACGTGATAAAACAAGG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 6
gtcagt-ttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
||  || |||| ||  |||     |      | ||   |||| || |||  |||      ||  |  || |  |||         |   | | |   |    |||| |||||||||||||| |||||||| ||||| |||||||||||||| || || |||||| ||| |
gtatgtgttgtcagc-ctattgactacaagcaattatcttgaatcttgaaacttgtcgattgacatttatttaaatgc----acattcattttacttt---cagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGTTGTTTGTCATACGCGATAAAACAAGG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
            ||   |     |   | ||||  ||   |       || | || |     ||| |  |||  || | ||||  |  ||||          |||| |||||||||||||| |||||||| ||||| ||| |||||||||| || ||||||||  |||||
------------gtatcattcaataa-cctattgactacaagcaacagtt-tccaatctaaaaagttgttatttatctaattgcatgcttgtatttgctttcagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttg---tcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
||   ||| ||  ||||       |   |||         | || |  |   |||       |   |  ||   ||   |||  ||||||   |     |    |||| |||||| ||||||| |||||||||||||| ||| || ||||||| || || |||||| |   |
gtattttttttgatgct----caggaagttaaa------aactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttc--agtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
                             ||| |  ||    |    ||| |||  | |      || | |  |  | | | | | |  |  |  | |   | ||||||||||| ||||||| |||||||| ||||| || ||| |||||||||||||||||||| ||| |
----------------------------gtatctctttatgctgacaattattctgaatctcaagagcttcagttgtctaactttatgatgttatatccttacagGTTATGATGCGATTGTTTAGTCCACGAAAAACAACTTTGATGTTTGTTATTCGTGATAAAACAAGG

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|29675672|gb|CB671947.1|CB671947
EST:     TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG                         GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST: gi|29671821|gb|CB668096.1|CB668096
EST:     TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG                         GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST: gi|29664221|gb|CB660496.1|CB660496
EST:     TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG                         GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST: gi|29632288|gb|CB637297.1|CB637297
EST:     TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG                         GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
                 atactataatatcatt  TA-rich tract