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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgctcttcatattgctcagttatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtag

Basic information

species Oryza sativa
transcript LOC_Os04g53240.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G076826_T02 (Zea mays), 5'ss of exon 4
AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgctcttcatattgctcagt-tatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtag
||| ||||||| |||||||||| || |||||||| ||||||  |||||||||||| |||||||||  |      ||  || || |    |||||| ||| |  |  ||  |||  || ||||| | ||   |    | ||||| ||
AGAAGAGGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgtaccc----ttcttctgtatgcactgtttctttcttcat--ttgcttttatccaatttatgactagtt--gtataatgcag

upper sequence: LOC_Os04g53240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G419694_T05 (Zea mays), 5'ss of exon 3
AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgctcttcatattgctcagttatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtag
||| ||||||  |||||||||||||||||||||| ||||||  |||||||||||| |||||||||  |         |     |    ||||   ||| |  || ||  |||  || ||||| | ||| || | |  ||||| ||
AGAAGAGGCAATCTGAGGCTAACCGTATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgtaccct------cctgcatgcactgttcgtttcttcatgattgctttcatccaatttatgaca-atgtga-ataatgcag

upper sequence: LOC_Os04g53240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G076826_T04 (Zea mays), 5'ss of exon 1
--------------------------------------------AGAGGAGGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgctcttcatattgctcagt-tatgttgtttccttcattgtggtttttttgctctaatttgttacatatctaatgtaatgtag
                                            ||| ||||||| |||||||||| || |||||||| ||||||  |||||||||||| |||||||||  |      ||  || || |    |||||| ||| |  |  ||  |||  || ||||| | ||   |    | ||||| ||
TTACATAACTGAACCCTTAATCTGTGTGATGCCTTTTCTTACAGAGAAGAGGCAGTCTGAGGCTAATCGGATCAGAGAGAAGTACCCTGACAGAATTCCAgtaagcttgtaccc----ttcttctgtatgcactgtttctttcttcat--ttgcttttatccaatttatgactagtt--gtataatgcag

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|33655349|gb|CF277963.1|CF277963
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33670400|gb|CF298639.1|CF298639
EST:     CGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: CGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86822106|gb|CI357784.1|CI357784
EST:     AAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: AAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33655295|gb|CF277909.1|CF277909
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|38481968|gb|CF966032.1|CF966032
EST:     GTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|33688345|gb|CF316584.1|CF316584
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86836082|gb|CI346147.1|CI346147
EST:     AGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: AGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
EST: gi|86418393|gb|CI032602.1|CI032602
EST:     GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCT                         GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA
genomic: GGCAGGCTGAGGCTAACCGTATCAGAGAAAAGTACAGTGACAGAATTCCTgtaagcttgc ... tgtaatgtagGTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAA