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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC

Basic information

species Oryza sativa
transcript LOC_Os02g40880.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G168330_T02 (Zea mays), 3'ss of exon 1
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcct------ttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                                     |  |  || || |  || ||||| | ||     |  || ||  | ||| | |||||||| |||  ||| ||||| |      |  ||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||| 
----------------------------------gtatgtcaattgcgct--tgctggtgttagttcgagtaggggttatgagcg-gggtttgacctgggggtttgtgtgcttgcgctatgtgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGCGTGGCCCTTGTGAACTACGGCAAAGACTACGGCCGCCTCGTCGTCATCGTCGATGTGGTCGACCAGAACA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 1
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttt-----tttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                  |  |||||      |||  ||   ||  | |||||| | ||   ||||| | ||  || |  | ||| ||  |     ||||||||     |||||||  | |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||  ||||||| ||||| ||||| |||||||| ||||| |||||||||||| 
------------------gtacgtcg----atcgcgcttagtgt--cagtggtgttagttccggtgggggttatgagt-tgtgcgggttctgacttggggttttgtgtgtttgtgctatgcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGCGTGGCCCTGGTGAACTACGGGGAGGACTATGGCCGTCTCGTTGTCATCGTCGATGTGGTCGACCAGAACA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G32580.1 (Glycine max), 3'ss of exon 1
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                             ||   ||  | ||  ||               | ||  |  ||   |||   | ||| |  || |   |   |||| | ||  | | || ||||| |||||||||| ||| ||||||||| |||| || |   | |||||||||||||| || ||| | |||||||||||||| || ||| | ||||||||| 
----------------------------gtgattcctcttcctctcttcactctacaccacttgttctctttcaaatt---ctcgtattcttaatgtg---ttttctctgtttcttgttcagCCTTTCAAGAGGTACGTTGAGATCGGGAGGGTTGCTCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATCGTCGACGTCATTGACCAGAACA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G35000.1 (Glycine max), 3'ss of exon 1
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                             ||   ||  | ||  |||  |         | |  |  | || |  | |   | ||| | | | || | |  |||| | ||  | | || ||||| |||||||||| ||| ||||||||| |||| ||||   | |||||||||||||| || ||| | ||||||||||| || || ||| | ||||||||| 
----------------------------gtgattcctctccctctccttttcactctacgctacttcttctctttaatattctcgtat-tctaactgcg--ttttctctgtttcttgttcagCCTTTCAAGAGGTACGTTGAGATCGGGAGGGTTGCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGACGTCATTGACCAGAACA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G06380.1 (Glycine max), 3'ss of exon 1
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                         |  |   | || |  |  || |  |      | |  |  |  |  ||   ||||      ||| ||| | | | ||||| |  ||  | | || ||||| ||||||||||  || ||||| ||| ||||  |||   | |||||||||||||| || ||| | ||||||||||| || |||||| | ||||||||| 
-----------------------gtgattcctctccctctctttttcact--ctacgctacttcttctctttcatattgt-----tgtattttaactgcgttttctc-tgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 2
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
||  |||  ||  |     |||    | | |      |     ||    || |  || |  | ||  || ||||  |||    | |  || |||    |  |  ||| |   ||| ||| |||| |||||| ||| ||||||||||||||| || || || || ||||||||||| || |||||| | ||||||||||| || |||||| | || ||||| |
gtgagtgtctcagca-actctcaaattttcgttctgataaatatt----tgattttgtt--ttgttttgttttgttttgttttcttcagtctgaaattgaatcatttcta--ttttgtgtagCCTTTCAAGCGGTACGTGGAGATCGGGCGAGTCGCTCTCGTCAACTACGGCAAAGAATACGGCAGGCTCGTCGTCATAGTCGATGTCATTGATCAGAATC

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 2
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
    |||  || | |    ||| || | ||  |   |||  | ||| | |     |  |  |     || |||| ||||      |   | |||  | |  |  |||   |  ||  || |||| |||||| ||| ||||||| ||||||| || || || || |||||||| || ||||||||| | ||||||||||| || || ||| | || ||||| |
----gtgagtctctgcaa-ctc-tcatttt-tctttgttttctttctgatcaatattctatt-----tgttttgcattgttttatttaatctgaatgtgaatcgttt---ctatttctgtagCCTTTCAAGCGGTACGTGGAGGTCGGGCGAGTCGCTCTCGTCAACTACGGAAAAGACTACGGCAGGCTCGTCGTCATAGTCGACGTCATTGATCAGAATC

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|86599617|gb|CI253602.1|CI253602
EST:     GACCGCCGCCGCGAGAATG                         CCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGG-CCTGGTNGAACTACGG
genomic: GACCGCCGCCGCGAGAATGgtaggtggat ... tttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGT-GAACTACGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
                     gtttgac  putative branch site (score: 4)
                                 tttttttgtgcctttc  putative PPT
                                 tttttttgt  TA-rich tract