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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM5G873287_T01 (Zea mays), 3'ss of exon 1
gtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG
||||  ||||||| |  ||  | | |   |   || ||| |||||  |||| || |      ||| | |||| ||    |||  ||| ||||  ||  |||||||||||| || | ||| ||||  ||  ||||||||   |||||||| ||||||||||| ||||| |||||||||  ||| ||||||||||| |||||||||||||||||||| || || || ||| ||||||
gtaacaaagctgtattttacatgtcaaatt--tatgtttctctgctgaagcaacaccccagattt-tacttagca----ctttctttaagcacaaa--atatgttttgctgaggagatggcatt--catgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAGGCTGAAACTGAATATACAGTGACTCAAGCCTTAGCTG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 18
gtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG
||||  ||||||| |  ||  | | |   |   || ||  |||||  |||| || |   |||||||  |||| ||    |||  | | ||||  || || |||| ||||| || | ||| ||||  ||  |||||||| | |||||||| ||||||||||| ||||| |||||||||  ||| ||||||||||| || ||||||||||||||||| ||||| || ||||||||||
gtaacaaagctgtattttacatgtcaaatt--tatgttcctctgctgaagcaacacccagttttta--cttagca----ctttctataagcacaaaacacatgtcttgctgaggagatgccatt--catgagcagGTTGCTGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 19
gtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaa----atgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG
                                   ||| | ||||  ||  |   || | ||||  |   | |  ||||  | ||   || ||   | || |      || |         ||| |  |   || ||||||| ||      ||||| || |||||||||||||||||||| ||||| ||||||||||| ||| | || || || || | |||| | ||||||||  |||
-----------------------------------tttaggctgcaaaaatg---ctatattttggtttctctt-gtaatgttttgagagaattttctatcttaggcactgatctgttctgtgtgaaatttccatgcagGTTTCATCCTCTAAAACATTGATTACACCTGTCCAGTGCAAGTCTTTGTGGAGGCAATTCAAGACAGAGACAGAGTACAGTGTCTCTCAGGCCATTTCTG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 19
gtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaacc-atatgttttgctaagtaaatgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG
                         |       |||  |   | || |    |   ||  |    |    || |  ||  |     | | |||| ||  ||||||| ||    || ||    |||| ||   ||||||| ||      ||||| || |||||||||||||||||||| ||||| ||||||||||| ||| | || || || || | |||| | ||||||||  |||
------------------------gaaagaaaaattactaatt-cctatataat--ttaatcccaaaatatagctatacatagcagttatcatgcactgatatgttgtgt---gtgaa----atttccat--gcagGTTTCATCCTCTAAAACATTGATTACACCTGTCCAGTGCAAGTCTTTGTGGAGGCAATTCAAGACAGAGACAGAGTACAGTGTCTCTCAGGCCATTTCTG

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|29641074|gb|CB646081.1|CB646081
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58593976|gb|CF992284.1|CF992284
EST:     CTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: CTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|88340407|gb|CI659613.1|CI659613
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|157650537|gb|EX450171.1|EX450171
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|38474188|gb|CF958320.1|CF958320
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58690187|gb|CK078874.1|CK078874
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
EST: gi|58661468|gb|CK050148.1|CK050148
EST:     ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGG                         GTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG
genomic: ATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagc ... gcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcagGTTCCAGAGGAGAAAACTTTAATTACACCTGTCCAGTGCAAATCTTTATGGAGGCAATTTAAGGCTGAAACTGAATATACTGTCACACAGGCCATAGCTG
                  atatgtttt  TA-rich tract