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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtcctataggcagcgcttttttaaatttgcattattcacatatctgatcatctttagatctgagacctatttgataaactgcaataggagctgctg...

Basic information

species Oryza sativa
transcript LOC_Os01g54480.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G045366_T01 (Zea mays), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtcctataggcagcgc---ttttttaaatttgcattattcacatatctgatcatctttagatctgagacctatttgataaactgcaataggagctgctg---
||||||||| ||||| ||||| ||||| ||||| ||||||||||| || ||||| ||||||||||  |||||||||||||| ||||||||||||| ||||||||||| ||  ||||       | |||| || | | |  | |  |     || || | | | | |    |||      ||| ||  || ||      || |    
TGATGTGCTGCAACTTATACGTCATCCAAATGTTGTGCAATTTTTGGGCGCTGTGACACAAAGCAATCCAATGATGATTGTCATGGAATTTATGCGCAAGgtttgtcttaagggcaatatcaatgttttcaagtcggacgacttgc-----tggtcgt-tgtggctgaccgactagggcgattaatcgcgattaatcatgattagt

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G09490.2 (Glycine max), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgt---ttgtcctataggca----gcgcttttttaaatttgcattattcacatatctgatcatcttt---agatctgagacctatttgataaactgcaataggagctgctg--------------------
|| | || | ||    || |||||||| |||||||| |||||| | |||||||| || || || || |||||||||||||| |  |||| | | ||||||||   |||||||| ||  |    |  | || ||   |  || ||  |     || |     | | |   |  | | | |   || ||||| |    | |  |  ||                        
TGCTCTGTTCCAGAAGATCCGGCATCCAAATGTCGTCCAATTTCTGGGTGCTGTGACCCAGAGTAGTCCAATGATGATTGTGACAGAATATCTTCCCAAGgtattttgtcctacagttacatggaacattatttcttgggctttgcttgggaattttgatgtttgtttgaagtttaacagtaatgtgatagaaaatattccgttcttaatcttatccccatgttgtgcag

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G29520.1 (Glycine max), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgttt---gtcctata--------ggcagcgcttttttaaatttgcattattcacatatctgatcatctttagatctgagacctatttgataaactgcaataggagctgctg--------------------
|| | || | ||   ||| |||||||| |||||||| |||||| | |||||||| || || || || |||||||||||||| | ||||| | | ||||||||||   |||||| |        | |   | |||||     ||   ||    |      || |  | || |  | | | |   | |||||| |     ||  |  ||                        
TGCTCTGTTCCAGAAAATCCGGCATCCAAATGTCGTCCAATTTCTGGGTGCTGTGACCCAGAGTAGTCCAATGATGATTGTGACGGAATATCTTCCCAAGgttttttgtcctacaatttcatggaccatggtttttggggctttgcttgggaattgggatgtttgt-ttgaagtttaacagtaaattgatagaaaatgatccgttcttaatcttatccccatgttgtgcag

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G45770.1 (Glycine max), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtcctataggcagcgcttttttaaattt-gcattattcacatatctgatcatctttagatctgagacctatt-tgataaactgcaata--ggagctgctg
|    ||||  |   |||| | ||||| ||||| || || ||||| |||||||||||||||||||  || ||||||||||| |  |||| | | ||| ||||| ||   |     ||||||  |  |||| | |||   ||    |     |  |  |    ||     || || | |||||||  |  |||  ||| ||| | 
TACATTGCTTGAGAAAATAAGACATCCAAATGTAGTCCAGTTTTTGGGTGCTGTAACACAAAGCACACCGATGATGATTGTCACAGAATATCTACCCCAGgttagtttca---atagcgctactggaaatctagcacagttggagtgcacaaataattaataattaagaacttaatatgataaaaagttatactggaactgat-

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G03040.1 (Glycine max), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtcctataggcagcgcttttttaaatttgcattattcacatatctgatcatctttagatctgagacctatttgataaactgcaatagg-agctgctg----
|    | ||  |   |||| ||||||| ||||| || || ||||| |||||||||||||||||||  |||||||||||||| |  |||| | | ||| ||||| ||| |   ||     |  |  | |  | | |   ||   ||      | || |||     ||     |||   | | |    | | |  || ||       
TACATTACTTGAGAAAATAAGGCATCCAAATGTAGTCCAGTTTTTGGGTGCTGTAACACAAAGCACACCAATGATGATTGTCACAGAATATCTACCCCAGgttagtctt---ggtcctacactggttatatggaagattttttatgataagttat-tttgcccgtggtgtttatg-aacagatcatattggttagttggccaatg

upper sequence: LOC_Os01g54480.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv10s0003g02060.t01 (Vitis vinifera), 5'ss of exon 5
TGATGTGCTACAACTAATACGGCATCCGAATGTCGTGCAATTTTTAGGTGCTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtcctataggcagcgcttttttaaatttgcattattcacatatctgatcatctttagatctgagacctatttgataaa-ctgcaataggagctgctg---
||   |||| ||    ||||| ||||| ||||| || || ||| | ||||||||||| ||||| || |||||||||||||| |  |||| | | |||||||||| |   ||      |   ||  || | |   || |   |   || | || ||| || || |||  ||  ||| | |    ||   ||    | |  |    
TGCATTGCTTCAGAAGATACGACATCCCAATGTAGTCCAGTTTCTGGGTGCTGTAACTCAAAGTAGTCCAATGATGATTGTGACAGAATATTTACCCAAGgtttttttcatcatt--cagattactagaatgaaataa--aattaatgtaatgatccttggaactgttactgattagctgtttcttggatctttgattttccta

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|117235877|gb|CT847833.1|CT847833
EST:     CTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAG                         GGTGATTTGCGCAAGCACTTGAGTAGG
genomic: CTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtccta ... ttgttctcagGGTGATTTGCGCAAGCACTTGAGTAGG
EST: gi|163928081|gb|EG712985.1|EG712985
EST:     CTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAG                         GGTGATTTGCGCAAGCACTTGAGTAGGAAAGGGGCTCTGGAACCGTCATAT
genomic: CTGTAACACAAAGCAGCCCAATGATGATTGTAATGGAATTTATGCCCAAGgtttgtccta ... ttgttctcagGGTGATTTGCGCAAGCACTTGAGTAGGAAAGGGGCTCTGGAACCGTCATAT