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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaccgaagaaatgacgcaacttcgttgcattgtcgctttgagttttgtgaggtgatgtggggtaactaacatctgcacttgggttggttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA

Basic information

species Oryza sativa
transcript LOC_Os08g43400.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G37340.1 (Glycine max), 3'ss of exon 2
gtaagcaccgaagaaatgacg-------caacttcgtt-gcattgtcg----ctttgagttttgtgaggtgatgtggggtaactaacatctgcacttgggttggttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA
|| ||   |       || |        |  |||| |  ||||  ||     |   |   |||    | | |  |    |   | |  ||| | | |||  |     |   |||||||||| || || ||||| |||||||||||||| ||||| ||||| ||||  || ||||| || || |  ||    ||||| | | ||||||| |||||
gtgagtttcttctctttgtctgcttttcctccttcatcagcatcatcaaaatccacgtaatttccttgttaacatcttctt-ttgatctctccccatggtgtctaattgatcagCAAGCATTTTTGCATATGGACAAACAAGCAGTGGGAAGACATACACCATGAGTGGCATAACTGAATACACAGTGTCAGACATTTTTAACTACATAGAAAA

upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G51150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcaccgaagaaatgacgcaacttcgttgcattgtcgctttgagttttgtgaggtgatgtggggtaactaacatctgcacttgggttggttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA
                    | ||      |    |   |||||    ||| | |     |||||   |  |   ||    | ||    || ||     |||| ||  | || || |||||||||||||||||||| ||||| ||||| ||||  || || || || |||    |    || || ||||| ||||| || ||
--------------------gtaaggcatgtctcctactgctttttagttttttatcctctgtggctcatgtttgatacaaatttcaactgtttt----cagCTAGTGTCTTTGCATATGGGCAAACAAGCAGTGGAAAGACATACACTATGATTGGTATTACGGATTATGCCTTGGCTGATATATATGATTACATTGAGAA

upper sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G66310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcaccgaagaaatgacgcaacttcgttgcattgtcgctttgagtt-ttgtgaggtgatgtggggtaactaacatctgcacttgggttg-gttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA
                         || ||     | || || || |||  |      |         |  ||  ||| |  | ||    ||  || ||  |||| ||  ||||||| |||||||||||||||||||| ||||| ||||| |||| ||| || || || |      |  | || || |||| |||||| || ||
------------------------gtttgtcatcct-tccctctgcgttactactctttctctccccttgtcttgcatatataattcaaatgcattgttttcagCTAGTGTATTCGCATATGGGCAAACAAGCAGTGGAAAGACGTACACTATGAGCGGAATTACTGACTGCGCCTTGGTTGATATATATGGCTACATTGACAA

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|88367346|gb|CI566312.1|CI566312
EST:     CGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACT                         CAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGA
genomic: CGAGGAAGGAGCGAAAGAAGTTGCTCTATCAGTTGTCAGTGGAATCAACTgtaagcaccg ... ttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgaggtgatgtggggtaactaacatctgcacttgggttggttcttggcagCAAGCATATTCGCGTATGGGCAAACAAGCAGTGGCAAGACTTACACGATGACCGGGATAACCGAGTATAGTGTTCTCGACATCTATGACTACATCGAAAA
                     aactaac  putative branch site (score: 1)
                                             ttctt  putative PPT
                    taactaa  TA-rich tract