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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttgtgtgttttaaatgtattttaacagttttgtgtgtcaacactcaacaggcgtatttattatttggagatgaagaatatttgtatatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g56670.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 9
------------------------------------------tttttttgtgtgttttaaatgtattttaacagtt----ttgtgtgtcaacactcaacaggcgtatttattatttggagatgaagaatatttgtatatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
                                           |||| | | |  | | || | ||||||||||||    | || |||||||  ||||||||| |||||||| |||||||||||||||||  |||| || ||||||||||||||||| ||||||||||| ||||||||||||||||| ||
ttgaacaaaactaggttcatcacctagctttgttcattcttcgttttctttttactatcaa-gcattttaacagttaatttcgtatgtcaacgttcaacagGCATATTTATTGTTTGGAGATGAAGAATACCTGTACATTTTTCAGGAGGCTTACAAAGCTGCCATGCACTATCTCCATCATGATCCTTG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 8
-----------------------------------------tttttttgtgtgttttaaatgtattttaacagttttgtgtgtca---ac-actcaacaggcgtatttattatttggagatgaagaatatttgtatatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
                                          ||| ||   || | || ||  | ||      |||||| |  ||   || ||    ||||| |||||||||||||||||||| || || ||||||||||| || || |||||    |||||||||||||||||  | ||||| || ||
tttcttttctttttttgttattttttcttttgggggcattactttgttagttgatatacatcaagttctctgattttgttttccatgtacgacctttcagGCTTATTTATTATTTGGAGATGAGGAGTACTTGTATATATTCCAAGAAGCTTATGCTGCTGCCATGCATTATCTTTACCATGACCCTTG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 3
-----------------------------------------tttttttgtgtgttttaaatgtattttaacagttttgtgtgtca---aca-ctcaacaggcgtatttattatttggagatgaagaatatttgtatatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
                                          ||| ||   || | |  ||  | ||      |||||| |  ||   ||| |    ||||||||||||||||||||||||||  | ||||| |||||||| || || |||||    |||||||||||||||||  | ||||| || ||
ttttcttttcttttttttcgtttttccttttgggggcataactttgttagttgatatgcatcaagttctctgattttgttttccatgcacaacctttcagGCGTATTTATTATTTGGAGATGAGCAGTATTTATATATATTCCAAGAAGCTTATGCTGCTGCCATGCATTATCTTTACCATGACCCTTG

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|88361880|gb|CI682051.1|CI682051
EST:     ATGCAGGAATTGGCACAAGCATTGACTCATTCTATGAGTATCTTCTAAAG                         GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
genomic: ATGCAGGAATTGGCACAAGCATTGACTCATTCTATGAGTATCTTCTAAAGgtaaggaatc ... tatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
EST: gi|88394177|gb|CI684850.1|CI684850
EST:     ATGCAGGAATTGGCACAAGCATTGACTCATTCTATGAGTATCTTCTAAAG                         GAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
genomic: ATGCAGGAATTGGCACAAGCATTGACTCATTCTATGAGTATCTTCTAAAGgtaaggaatc ... tatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcaacaggcgtatttattatttggagatgaagaatatttgtatatatttcagGAGGCTTACAAGGCTGCCATGCATTATCTCCATCATGATCCCTG
                             atgaagaatatttgta  TA-rich tract