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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaagcttttaccttttctcgaccatgccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG

Basic information

species Oryza sativa
transcript LOC_Os01g48760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G092152_T02 (Zea mays), 3'ss of exon 1
----------------gtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaa--------gcttttaccttttct-------cgaccatgccgcacg----cagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG
                     |||  |  || |  |       || |  | ||||   ||||||        |||||| | ||  ||       || |  ||  |   |    ||||| ||||||||||||||||||| |||||||||| ||||||| ||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||
gcgtgtggccctctctacctgcgatgtt-tctctcgcgagaaaatcttcccttcggctgccaaattcttagagctttttctttggcttacggatcggcggtggtgggtggctgcagCCAGTGATCTCGTACACGCAGAAGACGTGGAAGACGGCGTCTGGCGAGCCGATGCACGCCGAGAGCGGGTACTGGCGGCCCCGCCCTGACGGCTCCGTCG

upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S177_18V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------gtaaacgacctcctcgcctgtatctgtatatctctttcgctcgccaaagcttttaccttttctcgaccatgccgca-cgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG
                    | |||| | |    |  |     | |    |||| | |||         || |   | | ||    | ||       ||||||||||||  | ||| ||||||  |||||||| || || ||||| ||||| |||||||| |||||||| |||||||| |||   || || |||||| | |
agcggtaacgttctaagcattcaacggcgttggtgaattgggtttttggactctct-gcttattctgatttctcgttatgctgagacgtgttttggtgcagCCGGTGATTGCATACTCGCAGAAAACGTGGAAAGCAGCATCAGGAGAGCCTATGCACGCAGAGAGTGGATACTGGCGTCCCAAGCCTGATGGCTCCATAG

upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ33662 (Selaginella moellendorffii), 3'ss of exon 1
------gtaaacgacctcctcgcctgta-tctgtatatctct---ttcgctcgccaaagctt--ttaccttttctcgaccatgccgcacg-------cagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG
       |       || || |  |||  | || || | | |   ||   | ||||    ||  || |   | |   || | |  | ||        ||||| |||||  | |||||||| | ||| ||||||||  |||| || ||||| ||||||||||||||||| |||||| ||||| | ||||| |||||  |||
cagtgcttgcgttttcttcttgtttgttctttgcatttttttaattttttttgccatgatttgtttgctcatccggtactacgatggacttgttttccagCCAGTGATGGCCTACACGCAAAAGACATGGAAGGCATCGTCCGGGGAGCCTATGCACGCCGAGAGTGGCTACTGGAGGCCCAGGCCCGATGGCTCGCTCG

upper sequence: LOC_Os01g48760.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ37014 (Selaginella moellendorffii), 3'ss of exon 1
-------gtaaacgacctcctcgcctgta-tctgtatatctct--ttcgctcgccaaagctt--ttaccttttctcgaccatgccgcacg-------cagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG
        |       || || |  |||  | || || | | |  ||   | ||||    ||  || |   | |   || | |  | ||        ||||| |||||  | |||||||| | ||| ||||||||  |||| || ||||| ||||||||||||||||| |||||| ||||| | ||||| |||||  |||
tcagtgcttgcgttttcttcttgtttgttctttgcatttttttattttttttgccatgatttgtttgctcatccggtactacgatggacttgttttccagCCAGTGATGGCCTACACGCAAAAGACATGGAAGGCATCGTCCGGGGAGCCTATGCACGCCGAGAGTGGCTACTGGAGGCCCAGGCCCGATGGCTCGCTCG

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|86898820|gb|CI296101.1|CI296101
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88334302|gb|CI642547.1|CI642547
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88762854|gb|CI772410.1|CI772410
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88349798|gb|CI634333.1|CI634333
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88317589|gb|CI672171.1|CI672171
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTNGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88761445|gb|CI771001.1|CI771001
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCC
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGC-AGAGGACGTGGAAGGCGGCGTCAGGCGAGCC
EST: gi|88587859|gb|CI705639.1|CI705639
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88577442|gb|CI674029.1|CI674029
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88665244|gb|CI710078.1|CI710078
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88308803|gb|CI654086.1|CI654086
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88734582|gb|CI758090.1|CI758090
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|25799413|gb|CA755374.1|CA755374
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88210949|gb|CI212589.1|CI212589
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88580222|gb|CI692224.1|CI692224
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|86850381|gb|CI307610.1|CI307610
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCA-CCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88593295|gb|CI709458.1|CI709458
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88408609|gb|CI686112.1|CI686112
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|56157672|gb|C25211.2|C25211
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88290434|gb|CI665223.1|CI665223
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|87012916|gb|CI297143.1|CI297143
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88761851|gb|CI771407.1|CI771407
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
EST: gi|88825494|gb|CI776059.1|CI776059
EST:     CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAG                         CCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG
genomic: CCCCCTTCCGCTACGGCGAGGAGCTCCTCTTCTCCCACCACCCCTCCAAGgtaaacgacc ... ccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatctctttcgctcgccaaagcttttaccttttctcgaccatgccgcacgcagCCGGTGATCTCGTACACGCAGAGGACGTGGAAGGCGGCGTCAGGCGAGCCGATGCACGCCGAGAGTGGGTACTGGCGGCCCCGCCCCGACGGCTCCGTCG
                        tttta  TA-rich tract