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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA

Basic information

species Oryza sativa
transcript LOC_Os01g56670.1
intron # 11
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 11
lower sequence: GRMZM2G173868_T04 (Zea mays), 3'ss of exon 11
gtttggattactcgtatatcagagataaaaaaaaa---tgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
|||||| |||| | ||| || || |    |        ||  ||||| ||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| || |||||||| ||||| || ||||| ||||| |||||||||||||
gtttgg-ttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaagGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGCGTCTGGAAAAAGTATGGTTTTACCCCTGAAGGTTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 10
-----------------gtttggattactcgtatatcaga---gataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                  |||    || | |||| |         |    | |||| ||     |||  | |      |  ||   ||  |   || ||||| |||||||||||| |  |||| || ||||| || |||||||||||||| ||||| |||| || |||||| || || || || || |||||||||||||
gttttcattttcctagtttttaatataatagtatttttagctgactctggataaataataatatcatggtggggataattgtaacatgtattttttcaagGTTTTAGCTGGAGATATCAATCCCGCAATTCGCACCCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACTCCTGAGGGCTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 6
gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattc--tagatgatttcttattctgcttagatttaagGTGT---------------TAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA-------
||||  |||  || | | |  || ||||    |  |   |   ||  |   || || || || |  |  |  ||  | ||| ||||               ||||||||||| |  ||||||| ||||| ||||||||||||||||| ||||| |||| || |||||| || ||||| ||  | |||||||||||||       
gttttcatttttcttgtttttgatataatggtatttttagttgactctggataaataatatcatggtggggctaattgtaatgtgtatttttgcaatgttttagCTGGAGATATCAATCCTGCAATTCGCACTCATGCTGCCTTCTTGAGTGTCTGGAGAAGATATGGTTTTACCCCTGAGAGCTTTAATCTTGCTAGTCTCAG

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G43710.1 (Arabidopsis thaliana), 3'ss of exon 11
----gtttggattactcgtatatcagagataaaaaaaaat-----gatgcacacattctagatgatttcttattc-tgcttagattt---aagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
     |   ||||   ||| |  |  |  |   || | ||     | || | |  ||    |||||||  |||   || ||   | |   ||||| ||||||||||| |||||||| || ||  |||||||  |||||||||| || || ||||||  |||||| |||||||| || || |||||||||||||
gtaaatagtgattctacgtttgaccaaattgttaatatatttcaggctggaaaatttaactatgattttgtatctatgtttctctctcaaaagGTTTTAGCTGGAGACGTTGATCCAGCAATAAGAACTCACACTGCCTTCTTTAGCGTCTGGAAACGATATGGTTTCACCCCTGAGGGTTTTAATCTTGCTA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 12
gtttggattactcgtatatcagagataaaaaa-aaatgatgcacacattctagatgatttcttattct-gcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
       |   |  | ||| |   ||| |  | ||||  ||||       |  || |   |  ||| |  ||| |    |||||  ||||||||||  |||| ||||| |||||||| ||| ||||||| || ||||| ||||||| |||||||||||||||||| || ||||||||||| |
------gtattttatctattatttatatattataaattttgcattgtcgattaatcaaaaccgattatcactttgg---aagGTTCTAGCTGGAGACATTGACCCTGCTATTCGAACGCATACTGCCTTTTTTAGTGTTTGGAAAAGATATGGCTTCACCCCAGAGGGTTTTAATCTTGCCA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ28925 (Selaginella moellendorffii), 3'ss of exon 11
gtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagattta--agGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                         |||| |  |    | |  |  || ||      || | |||| | |     | |  |||| || || |||||||| || || || | || ||||||  | || || |||  ||| ||||| || | |||||||||||||||||| ||||||||||| |
------------------------gtaaagatgatgtgttccaatgttttaac---attttgattccgatcgccataatcagGTCTTGGCAGGAGATGTAGAACCCGCTACTCAAACTCACACAGCATTTTTCTCTGTGTGGAAGAAGTTTGGCTTCACCCCAGAAGGATTTAATCTTGCAA

upper sequence: LOC_Os01g56670.3 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ13630 (Selaginella moellendorffii), 3'ss of exon 11
gtttggattactcgtatatcagagataaaaaaaaatgatgcac-acattctagatgatttcttattctgcttagattta--agGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                              ||| ||||||    ||| | |       || | |||| | |     | |  |||| || || |||||||| || || || | || ||||||  | || || |||  ||| ||||| || | |||||||||||||||||| ||||||||||| |
----------------------------gtaaagatgatgtgttacaatgttttaacattttgattccggtcgccataatcagGTCTTGGCAGGAGATGTAGAACCCGCTACTCAAACTCACACAGCATTTTTCTCTGTGTGGAAGAAGTTTGGCTTCACCCCAGAAGGATTTAATCTTGCAA

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|33796226|gb|CF323979.1|CF323979
EST:     CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
EST: gi|58601755|gb|CK012283.1|CK012283
EST:     CAGTCTCCAGGCATTCTGGCCAGGACTTCAG                         GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
                               tttcttattctgctt  CT-rich tract
                              atttcttatt  TA-rich tract