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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g45410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081671_T01 (Zea mays), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                       |    |   |  |     |   || ||  ||||  |||     |   || || |   | ||     | ||   |  |    | |||| |   | | ||| ||  |||      ||| ||||   |    |||||||| || || ||||| |||||||||||||||||||||||||| ||||| || ||||| |||||||| || ||||||
---------------------------------------gtacgtgatacatagagatgcatgctttcagttacgttacgtgttgctacttgccgctgtggaattttatttgatac---gttaattttggttgatttgcatccttccc---taaattcttcgccgtacgtagAGGCAACGCCCAAGACCATCATGAGGGTTATGGGAGTCAAGGGCCTCACCCTCTACCACCTCAAGAGTCACCTTCAG

upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G29620.1 (Glycine max), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgt-ttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                                          ||    |   |   |      | |||||| | |   |  |||| |||||| |   | | ||  |  | |     || | | | ||||  |||||               ||| |||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||||||| || |||||||| ||||||
---------------------------------------------------------aataaaatagaaaagcaaaaggtgttaatttagtgtattcatgtgttcatg-tattattattcttttagtaactctttcctttgtgttctatgat---------------ttgcagAGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAG

upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G17400.1 (Glycine max), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatc----aattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                                                          |||||| |  |  ||  | |  | | ||  |     |      || |  ||  ||   |  |  | || || || |||    |||   |     | ||| |||||| ||||| || || ||||||||||||||||| || ||||| ||||| |||||||| ||||||||||| || |||
--------------------------------------------------------------------------gttcttgtagaccaaaaattattgtattagaca--tatgtctatgttggatgatattatgatcttttgattaatcatctttttctcttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAG

upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G41740.1 (Glycine max), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattacttgtatgtttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                                           | | |  | |    |  |  |  ||  |  |||  ||| ||  | || || |   |||  || |  | |  |||| |  | | ||||         || ||    | ||| |||||| ||||| || || ||||||||||||||||| || ||||| ||||| |||||||| ||||||||||| ||||||
-----------------------------------------------------------tgtagaccaaaaatg--tagtagtacatgttta--tgtttggattat-attatggtctcaatgatcttttgattaatcatctttttct--------cttttttggatttgcagAGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAG

upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S25_131V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggtt-cttcttaattaattacttgtatgt-ttcatgatcaaactcttgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                                                   ||  | | |  ||   |   || | |  ||||||| ||| ||     | | ||     ||   || | ||| || |||  |||  |     ||   ||  |    |||||| || || ||  |  | ||||| || |||||||| ||||| || || ||||||||| | |||||||||||||||
-------------------------------------------------------------------gatgttgctgactaagttggtagtaaaatgtatgtcttcgtgggattagtattaggtcatcaaaactaactcgtctgt--cattgttg--ttcacaatggac---agAGGCTACACCGAAATCTGTAATGAGAGTCATGGGAGTGAAGGGTCTTACTCTTTACCATTTGAAGAGCCATCTTCAG

upper sequence: LOC_Os06g45410.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S201_75V6.1 (Physcomitrella patens), 3'ss of exon 1
gtacgtagctacgctctatacatgactgatcttgatgctgagaatttgatttgattttatttggttcgagttcggttcttcttaattaattact----tgtatgtttcatgatcaaactct--tgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattg-tagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                                                       | || |  |  | |   || |      |||| ||    | | | |    |  |||  || |  || |  || || ||| |  || | |||       |||| ||  |||||| || || ||| |  | ||||||||||||||||| ||||| || || || |||||| | ||||||||||| |||
-----------------------------------------------------------------------tgggcttctgctgagagatgatcggagtgtaggtgatctaaacgattcgtagtgacgaagtccaactctctcgtttgtct-gtggtgaaa-------tcaactgacagAGGCTACACCGAAGTCTGTGATGAGGGTTATGGGAGTGAAGGGTCTTACGCTCTACCATTTGAAGAGCCATCTCCAG

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|29659781|gb|CB656056.1|CB656056
EST:     GCTCCATGACCGCTTCGTCGACGCCGTCACCCAGCTCGGAGGCCCGGACA                         AGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACAC
genomic: GCTCCATGACCGCTTCGTCGACGCCGTCACCCAGCTCGGAGGCCCGGACAgtacgtagct ... tcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACAC
EST: gi|58679249|gb|CK067936.1|CK067936
EST:     GCTCCATGACCGCTTCGTCGACGCCGTCACCCAGCTCGGAGGCCCGGACA                         AGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACAC
genomic: GCTCCATGACCGCTTCGTCGACGCCGTCACCCAGCTCGGAGGCCCGGACAgtacgtagct ... tcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcaattgtaaattacttgtatgtttcatgatcaaactcttgatcaattgtagAGGCGACTCCAAAGACGATCATGAGGGTTATGGGAGTCAAGGGACTCACACTTTACCATCTCAAGAGCCATCTTCAG
                                       tcttgat  putative branch site (score: 4)
     aattgtaaattactt  TA-rich tract