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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgctaaaatttactatttcaaagtataatacattcatccttctgataatctataatgaacttcaatgcacatgagaattaaattgctccatcccatatgtcaacttttaactaatgccttactttattatgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC

Basic information

species Oryza sativa
transcript LOC_Os06g46310.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G069198_T01 (Zea mays), 3'ss of exon 12
gtaattgctaaaatttactatttcaaagtataatacattcatccttctgataat-ctataatg---aacttcaatgcacatgagaattaaattgctccatcccatatgtcaacttttaactaatgccttactttattatgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
|||||   | || |||||| ||  |   |   ||||  |||      | ||| | ||||||||   ||  ||| | | ||||  ||||||  |  |     || ||| |      |||||||||||||| ||    ||    |||||||||||||||||||| || ||||||||| ||||||||||||| |||||||| |||||||  ||||| ||||||||||| |||||||||| |  |
gtaatcagtgaactttactgttgtactcttctatac-ctcaaaaacttaatagttctataatgtttaatctcattactcatgtcaattaaggtttttagctccgtatat-----gttaactaatgccttgctcggctacatgcagATGATACTGTCATTTGAACTCCCTTTTGCTTTAGTTCCACTCCTTAAATTCACCAGCAGCAAAACAAAGATGGGGCAGCATACAAATTCAATATTC

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G23320.1 (Glycine max), 3'ss of exon 12
gtaattgctaaaatttactatttcaaagtataatacattcatccttctgataatctataatgaacttcaatgcacatgagaattaaattgctccatcccatatgtcaacttttaactaatgccttactttatta--tgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
                                          |  |  ||   | |||    || |    || |    | |||| |  |  |         || |    || |  || | | | | || |||    ||  |||||||| || ||||||||||||||||||||| |  |||||||||| || ||||| |||||||  |  || |||||  | ||    || ||||   | 
------------------------------------------ctgttagactgtgtattgataaatcttgtgtatgatacaattgaccttgtgagattatcat-ttgggttattgctgaagtccttctgtatctgctgatcagATGATCCTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACG

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G02680.1 (Glycine max), 3'ss of exon 10
gtaattgctaaaatttactatttcaaagtataatacattcatccttctgataatctataatgaacttcaatgcacatgagaattaaa-ttgctccatc-ccatatgtcaacttttaactaatgccttactttatta--tgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
                                             || |||  | |||    || | |  || |    | |||| |  |||    ||   ||| ||     | |   || | | | | || |||    ||  ||||||||  | ||||||||||||||||||||| |  |||||||||| || ||||| |||||||  |  || |||||  | ||    || ||||   | 
---------------------------------------------tcagattgtgtattgataaatcccgtgtatgatacaattgaccttgtgagattatcatttgggctatatgtgctgaagtccttctgtatctgctgatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCG

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 11
gtaattgctaaaatttactatttcaaagtataatacattcatccttctg-ataatctataatgaacttcaatgcacatgagaattaaattgctccatcccatatgtca-acttttaactaatgccttactttat-tatgca-cagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
                                            || || ||  | |  | | |  ||   |  |||  ||| ||   |  ||   |||  | || || ||  |   || | ||| | |||| | ||| || ||||||||  | ||||||||||||||||||||| | ||||||||||| || || ||||||||||  || || ||||||   ||    || || |     
-------------------------------------------tttgtgtatggtatgca-taattttttgtttacaacagagttgg-tctctggctcctctctgccataccatgtgctgaagcccttctttgtctattcatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAGATGGGGACACATGTCAACTCTACCATG

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G44710.1 (Glycine max), 3'ss of exon 10
gtaattgctaaaatttactatttcaaagtataatacattcatccttctg-ataatctataatgaacttcaatgcacatgagaattaaattgctccatcccatatgtca-acttttaactaatgccttactttat-tatgca-cagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
                                            || || ||  | |  | | |  ||   | ||||  ||| ||   |  ||   |||  | || || || ||   || | ||| | |||| | ||| || ||||||||  | ||||||||||||||||||||| | ||||||||||| || || ||||||||||  || |||||||||   ||    || || | |   
-------------------------------------------tttgtgtatggtatgca-taattttttgttcacaacagagttgg-tctctggctcctctctgccataccttgtgctgaagcccttctttgtctattcatcagATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAAATGGGGACACATGTCAACTCTACAATG

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|218490953|gb|FG953072.1|FG953072
EST:     CGATAATTGGAGGTTCCTCAGCAGCTGGACAGTTGATTATCATTGCATCG                         ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTC
genomic: CGATAATTGGAGGTTCCTCAGCAGCTGGACAGTTGATTATCATTGCATCGgtaattgcta ... ttatgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTC
EST: gi|25802710|gb|CA758671.1|CA758671
EST:     CGATAATTGGAGGTTCCTCAGCAGCTGGACAGTTGATTATCATTGCATCG                         ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCC
genomic: CGATAATTGGAGGTTCCTCAGCAGCTGGACAGTTGATTATCATTGCATCGgtaattgcta ... ttatgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctccatcccatatgtcaacttttaactaatgccttactttattatgcacagATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC
                                        ctttatt  CT-rich tract
                    aacttttaactaat  TA-rich tract