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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaaccctgttcttttgcttcttaggcaattttctttagttgctgttgacaaagacctttgtgtactgttgatgctctgtcaa...

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaaccctgttcttttgcttcttaggcaattttctttagttgctgttgacaaagacctttgtgtactgttgatgctctgtcaa---------------------------------------
||||||||||||| |  ||||| |||||||||||||| |||||||||||||||||||||||||||||||| || || ||||| |||| ||| ||||| ||||||||  ||||    |||     ||  ||||   |     |   ||| |   ||     |   |         | | | | ||| | || | |   |||                                       
AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgctaacgc-tgtg-ttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaaccc----tgttcttttg--cttcttaggcaattttctttagt----tgctgttgacaaagacctttgtg---tactgttgatgctctgtcaa---------------------------------------------------------
|||| ||||| || |  || || || || ||||||||||| ||||| |||||||||||||| |||||||| || |||||||| ||||||||| |||||||||| | |     |   | | |       |||  | | |  ||| ||||| |  |||  ||| |    || ||||  ||     |||| |    |||     | |   | || |                                                         
AAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGAACTTCAGgtttgtcttagctgaattttatttctggtgtaatctaggtcttattaggaagcttttgttaatgaaatgatgttttcatgttgctttttaatttacatacaaggacatttccatttatgaatatgtacagtgatcctgtttgtgcaatgctttaatatggattcatgcag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaaccct---gttcttttgcttcttaggcaattttctttagttgctgttgacaaaga-----ccttt-------gtgta-ctgttgatgctctgtcaa----------------------------
|||||||||| || ||  | || ||  | ||||| || |||||||| |||||||| ||||| ||||||||||| |||||||| ||||||||| | ||||||||          |    | ||| |    |   ||    | ||    |||||  ||    | |   ||| | | |     |||||        || | |||||  || |   | ||                            
AAGCTGAAGAAACAGTGCAGAAGCTAAACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCAAACACAAATGCATGCCTCCTTGCTGAGCATTTCAGgttctatgaagggaaaaattacctttccatctgttcatctgttgtataatttgtttggcatacacatgagagaaaaattacctttcataaatatgcagctgttcctgtttctttaactatttctgtttaatttggattatacag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaacc-ctgttct--tttgcttcttaggcaattttc----tttagttgctgttgacaaa---gacctttgtgtactgttgatgctctgtcaa---------------------------------------------------------
|||| ||||| || |  || || || || ||||||||||| ||||| |||||||||||||| |||||||| || || ||||||||||||||| | |||||||| | |     |   | | |   ||| | |  | |   ||||||| |  |||     || |  |  ||||  ||     |   ||  | |||  |  | |   | || |                                                         
AAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGAATTTCAGgtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggccc-----------ctaatatgtgtaaccctgttcttttgcttcttaggcaattttcttt--agttgctgttgacaaagacctttgtgtactgttgatgctctgtcaa-------------------------
|||||||||| || | ||| || ||||||||||||||| | || || || ||||| |||||||| ||||| || || ||||||||||||||  |||||||||   ||            ||  |||||  || | | ||  | |    |  | | | || |  ||  || | |   |||| |  | ||||      || |||| |    |                            
AAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv12s0059g01220.t01 (Vitis vinifera), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccctaatatgtgtaaccctgttcttttgcttcttaggcaattttctttagttgctgttgacaaagaccttt---gtgtactgttgatgctctgtcaa---------
||||||| || || | |   |||||||| ||||||||||||||||| |||||||| ||||| ||||| ||||| || ||||| ||||||||  | || ||||    |    ||  || | |    ||  ||||     | | |    | |  ||  |   | | | || ||| | |     || |   ||| |  |   | ||         
AAGCTGATGAAACAGCATCAAAACTTGAGTTGGATGGGCTTGTTGTTATTGGTGGAGATGACTCAAATACAAATGCTTGCCTACTTGCTGAAAATTTTAGgtacagc----atgagtcttatatggtctttttaagcttgaagagtctcttatttatatatttagtcagagatcctcttgatgaaggtttgttatttctttaaaattttcag

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgt-tggccc---ctaatatgtgtaaccctgttcttttgcttcttaggcaattttctttagttgctgttgacaaagacctttgtgtactgttgatgctctgtcaa
|||||||||| || |     || |||||||||||||| ||  ||||||||||||| ||||| ||||||||||| || ||||||||||||||  |||| |||| |||  |     ||| |   | |     |  |   | |||| |||       |||||||||  | | |      ||||  | || | ||  |  | |     
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaa--ctttagttggcgatcagctttgccttcttttattttttctttttttct--

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|58598594|gb|CK009122.1|CK009122
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAA-GACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|218497540|gb|FG953486.1|FG953486
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|58675628|gb|CK064315.1|CK064315
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|5003496|gb|AU068645.1|AU068645
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAN                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG