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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc...

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044629_T02 (Zea mays), 5'ss of exon 11
--------------------------------ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgct------tctataactgttttaagtctgaa--gcagtaggaattca--ttgtgtttactttctttgcaaattacagtagtt--atctattttctcgttatgccc------------------
                                || ||| |||| ||||||||| |||| || ||||| ||||| ||||||||||||||||||||||||  ||||||| |      | |    |||  ||   ||  ||  || || |  | |||     ||     |    | |  ||   ||   |||  | ||   |    ||| ||                     
AAACTGTTCTCTCCTTTTTTTTTTTTTTGTAGATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G019986_T02 (Zea mays), 5'ss of exon 3
--------------------------------ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc-----------------------
                                || ||| |||| ||||||||| |||| || ||||| ||||| || |||||||| ||||||||||||  ||||||    |  |     |  |  | ||   |    ||  |||           |    |   | |  || |||||  | | |  ||      |||                          
CCTCTCTCTCTCTCGTTTTCCCCCTCCCCTAGATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatccccgtgttcttggttcgcct--tgtttcagagatttgcaagccaggcagcttcaacga--tagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 11
ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgct------tctataactgttttaagtctgaa--gcagtaggaattca--ttgtgtttactttctttgcaaattacagtagtt--atctattttctcgttatgccc------------------
|| ||| |||| ||||||||| |||| || ||||| ||||| ||||||||||||||||||||||||  ||||||| |      | |    |||  ||   ||  ||  || || |  | |||     ||     |    | |  ||   ||   |||  | ||   |    ||| ||                     
ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcag

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 12
ATTTGCTTGCATATGTTCACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgcttctataactgttttaagtctgaagcagtaggaattcattgtgtttactttctttgcaaattacagtagttatctattttctcgttatgccc-----------------------
|| ||| |||| ||||||||| |||| || ||||| ||||| || |||||||| ||||||||||||  ||||||    |  |     |  |  | ||   |    ||  |||           |    |   | |  || |||||  | | |  ||      |||                          
ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCGAACAGCCTCGAGAAGGACAGTGTgtgagtatccccgtgttcttggttcgcct--tgtttcagagatttgcaagccaggcagcttcaacga--tagagtaggcaaccacgtttgttacatgagggtttgtgtatcttgtgtgaccag

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|3768106|gb|AU032133.1|AU032133
EST:     ACTTTGGATTTTTTGAATCAAGTAGCANACAGCCTTGAGANGGACAGTAC                         TTATCATNTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|88389670|gb|CI603169.1|CI603169
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAAGACAGTAC                         TTATCATCTTGCTGA
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGA
EST: gi|88961150|gb|CI096554.1|CI096554
EST:     AGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: AGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|86831371|gb|CI297640.1|CI297640
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG