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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttcatactgccttttctttattatttgtaagacacttcaaagtgtgatgtgtgtagctcttcgatatctgtgtaagccatcttcattttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAAGCAGCGGATGTTCGACAGAGTGCTCTCGCCCTCCTGGGGGACCTTTCTA

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 20
-----------gtgcttcatactgccttttctttattatttgtaagacacttcaaagtgtgatgtgtgtagctcttcgatatctgtgtaagccatcttcattttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAAGCAGCGGATGTTCGACAGAGTGCTCTCGCCCTCCTGGGGGACCTTTCTA
              ||  | |  || ||| |||| ||  || ||   ||  |   ||||  |  | |||||   || ||||        || ||||||   ||||   |||||| |||| ||||||||||||||| | ||||||||||| || |||||||||||||| ||||||||||| ||||| || ||||| || || ||||||||||
gaagggcgattactctgaagagcgcttttcctttgtttattatacttcaaattttagtgccaaatatgtagaagtttgata--------agtcatcttttctttg---tagGTTGCACAGAGCAGTTTGAGAGATCTGCTTTTGCAATGCTGCATGGATGAAGCAGCTGATGTTCGACAAAGTGCCCTTGCCCTTCTTGGAGACCTTTCTA
















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|58608072|gb|CK036105.1|CK036105
EST:     ATCTG-TGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTGGGGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58671684|gb|CK060370.1|CK060370
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58611878|gb|CK039590.1|CK039590
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58667508|gb|CK056194.1|CK056194
EST:     ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTG                         GTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
genomic: ATCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCTGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAA
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     TCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCCGGG                         GGTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGA
genomic: TCTGTTGTCAGGACTTGCAGAAGGACTTGGCGCTGGTATTGAAAGCC-TGgtaaattcaa ... tttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgatgtgtgtagctcttcgatatctgtgtaagccatcttcattttgttttagGTTTCACAAAGCAGTTTGAGAGATATTCTTTTGCAATGTTGTATGGATGAAGCAGCGGATGTTCGACAGAGTGCTCTCGCCCTCCTGGGGGACCTTTCTA
                                      tcttcattttgtttt  CT-rich tract
                                        ttcattttgtttta  TA-rich tract