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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accagattcaaacaaaatttgtatataaagcacatattgcaattttacctggtttgctaggcaagaacaagctatgatggtttttttctttaaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAGGCACCAACTTGAGTCTAAACTTTTGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G838579_T01 (Zea mays), 3'ss of exon 2
-----accagattcaaacaaaatt-tgtatataaagcacatattgcaattttacctggtttgctaggcaagaacaagctatgatggtttttttctt--taaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAGGCACCAACTTGAGTCTAAACTTTTGCAG
     ||    |||   |  |||| ||| | |||     |||||| ||||  | ||||      ||       |    ||||||| |||| |||||  |   |   |||||||||||||||||||||||||||||||||||||||||||  || ||| |||| || ||||||||||||||  | |||
ttcgcacatttttcttgctcaattctgtgtgtaa-----atattggaatt--atctggaa-aaaagattcattccttttatgatgattttgttcttctttggtcacagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAAGCTCTAAACGGCAACAGCTTGAGTCTAAACTCCTACAG

upper sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 12
accagattcaaacaaaatttgtatataa-----agcacatattgcaattttacctggtttgctaggcaagaacaagctatgatggtttttttctttaaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAGGCACCAACTTGAGTCTAAACTTTTGCAG
     | | |  |    |  |   | ||      ||| | ||    |   || | ||      ||       |    ||||||| |||| ||||||   |   |||||||||||||||||||||||||||||||||||||||||||  |||||||| || ||||||||||||||||| || |||
----aaattatgcgttttacgcgcacaattcttggcataaatattgaaggtatccgggaaaaaagattcattccttttatgatgattttgttctttgg-tcacagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAAGCTCGAAAAGACAACAACTTGAGTCTAAACTGTTACAG
















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|8858038|gb|AU095356.1|AU095356
EST:     CTGGGTTTGGGAAGAAGATCAGCAACCCTTCTTGACAGATGCTTATCAGA                         GTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
genomic: CTGGGTTTGGGAAGAAGATCAGCAACC-TTCTTGACAGATGCTTATCAGAgtgagttcat ... taaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
EST: gi|58665350|gb|CK054036.1|CK054036
EST:     GACAGATGCTTATCAGA                         GTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
genomic: GACAGATGCTTATCAGAgtgagttcat ... taaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
EST: gi|426285|gb|D22147.1|D22147
EST:     CCTGGGTTTGGGAAGAAGATCAGCAACCTTCTTGACAGATGCTTATCAGA                         GTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
genomic: CCTGGGTTTGGGAAGAAGATCAGCAACCTTCTTGACAGATGCTTATCAGAgtgagttcat ... taaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
EST: gi|88665693|gb|CI715849.1|CI715849
EST:     CCTGGGTTTGGGAAGAAGATCAGCAACCTTCTTGACAGATGCTTATCAGA                         GTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG
genomic: CCTGGGTTTGGGAAGAAGATCAGCAACCTTCTTGACAGATGCTTATCAGAgtgagttcat ... taaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctggtttgctaggcaagaacaagctatgatggtttttttctttaaattgtagGTATGACATGGAGGCTATTTATTTTGATGAAGGTGTCAGAACTTCGAAAAGGCACCAACTTGAGTCTAAACTTTTGCAG
                                tggtttttttcttt  CT-rich tract
                                   tttttttctttaaatt  TA-rich tract