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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.4
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 6
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgc-ttaaatatctttgtttcatgta-gtgaaatttattttccta---------aaattccacag
||||||| | |||| || | ||  | ||||||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| |||||| | |||||||| || ||   |||||| |  | |   | | ||       ||  |   | | ||||||  | |  ||||| |||| | ||         ||||| |||||
CAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAACTTGACAGgtattttttt--aaccatctcctttcactctggtccaatgctacgttgttctatttcataaatgcaaaattgatttccatatataatttgaaattacacag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 6
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaa--attccacag-------
||||||| | |||| |  ||||  | ||||||  |||||||||||| |||||||||||||| ||||||||||||||||||||||| |||||| | ||||||||  | ||   |||  | |   | ||||   |    | |||  |   | | ||||||  |   ||||| |||| | || |  |||  | |        
CAGCAGACGATGCTCTTAAGCACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAGGACTTCATGCCAACATTCCCTGCTCTTAATGAACTTGACAGgtaaattttt--aactttctctcccactta-ggctcagtttacgtggttctatttcatacatccaaattgatttccatatataatttgaaaatacacag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G10810.1 (Glycine max), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag----------------------------------------------------------------------------------------
| || || | |||| |  | |||||||||||||||||||||||||| || |||   || || |||||||| ||||| ||||||| | |||     |||||||| ||   |  ||   ||  |  | || |     ||  |  || |  ||| |||  | ||       |  | |   |||||      ||                                                                                        
CTGCCGAAGATGCTCTAAATCATGAGTGGTTCCGTGAAGTTCCTCTCCCCAAAAGTAAAGAATTCATGCCTACATTTCCTGCTCAACATGCTCAGGACAGgtaatttgacctaa---ttggaaatgctggagcaatttttataagaatttttttttgtttatgttctctagtctggataaaagagggaagttgtgtaaaatatttgctgagtctatactatataacatttatcaacttttatttttgacaagttttcataatttcatcatataaatag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G67580.2 (Arabidopsis thaliana), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaatatctttgtttcatgtagtgaaatttattttcctaaaattccacag
| |   |||  ||| |  ||||||| |||||||| ||||| ||||| || ||||| || ||||||||||| || || ||||||| | |||    |||||||||||         | || ||| ||      |    || || | | |  || | ||   || |     || | | ||||           
CTGTTAATGAAGCTCTAAAGCATGATTGGTTCCGCGAAGTCCCTCTGCCAAAATCCAAAGATTTCATGCCTACTTTTCCTGCTCAACATGCCCAAGACAGgtactg----aggtctatctaaactgaaacgatcagtggttgactttaattctgtctcttactttttcttctatgcctag----------

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 5'ss of exon 5
CAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttcgcaaccatttaatctacttgtagtgttgcttaaat----atctttgtttcatgtag-------tgaaatttattttcctaaaat--tccacag
|||| || |||||| |  | ||||| |||||||| ||||||||||| || ||||| || ||||||||||| || || |||||||   |||     ||||||||  |   | | |    | | | ||  ||     |   |   |      | ||| |||  | |||       | ||||  |||||  | |  |  |   |||
CAGCTGAAGCTGCTCTTAACCATGATTGGTTCCGCGAAGTTCCTCTTCCCAAATCTAAAGATTTCATGCCTACTTTTCCTGCTCAGCATGCCCAGGACAGgtatcttgaccctatacatgactttaaatgagagatgagtaggagtgcagtttttattttttatagcaatttctaaaataaattttgttcatttgattatcag

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|29631145|gb|CB636154.1|CB636154
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|218494622|gb|FG958132.1|FG958132
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTTACCAA-CGGTATTTGAAGA
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGT-ACCAAACGGTATTTGAAGA
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTATCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29626550|gb|CB631561.1|CB631561
EST:     TGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: TGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|29631235|gb|CB636244.1|CB636244
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|86910572|gb|CI294713.1|CI294713
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|88979130|gb|CI025633.1|CI025633
EST:     AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTGATCCTCTAGAAGAGCAACGATT
EST: gi|58611941|gb|CK039653.1|CK039653
EST:     AAATCAAAGGATTTCATGCCAACATTCCCGGCTCTAAATGAATTAGACAG                         GCGTACCAAACGGTATTTGAAGAGTCCTG
genomic: AAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAATTAGACAGgtacttcttc ... aattccacagGCGTACCAAACGGTATTTGAAGAGTCCTG