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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccaggaaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag

Basic information

species Oryza sativa
transcript LOC_Os05g03430.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G155123_T02 (Zea mays), 5'ss of exon 13
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccaggaaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
 ||||||||||||||||||||||| || |||||||||||  |||||||||| |||||||||||||||||||| ||||||||||||||||| || |||||||| |||  ||||| |  | || || |||   ||| ||| || | |||  |    |       | |   ||||||| || |      |||      | |   || ||||                                                       
CGGATCCAGAATGAGGATTGCTGGAAGGTTCAAGCCTTGTGTTCACATGGGCTGTTTTGATCTTGAAACTTTTGTGGAATTGAATCAACGCTCACGCAAGgtcaga--ttgtgcttgcagaagcacat---tcaaatatatatatgtaaactaggcctgttttgaacattttctgtagtt---ggtccaggccaggcctaatttatgc-------------------------------------------------------

upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G29270.2 (Glycine max), 5'ss of exon 10
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccaggaaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
||| || ||||||| |||||| || |||||||| |||||  ||||||| ||||||||||||||||||  ||| |||||| ||||| |||||||  | |||||  |||  |        |||   | ||   ||  |||| |   |||| ||     ||| |         |  || |||    |  |   ||   |                                                                   
TGGTTCAAGAATGAAGATTGCAGGAAGATTCAAACCTTGTGTTCACATTGGTTGTTTTGATCTTGAAGTTTTTGTGGAAATGAATGAACGGTCAAGGAAGgtatgattctaaaaagtttgagcatgatttgtcgtatacct---tgtttattttaaaaaaaaaa------tgttgaagcattaattctttctgcag-------------------------------------------------------------------

upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G07590.1 (Glycine max), 5'ss of exon 14
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccaggaaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
||| || ||||||| ||||||||| ||||| || || || |||||||||||||| ||||||||||||   || |||||| |||| ||||| ||  | ||||| || |  |       |  ||| | ||  | ||   |  |||    ||  |||     | | |  ||   ||||  |     ||       ||                                                                     
TGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTGTTTGTGGAAATGAACCAACGATCAAGGAAGgtaaggttctaa-----caaatgtt-atattgcatg-aagtgtccactc-cccaaagttgtgatttttaagtctgatgaattgaattgtttgttcag------------------------------------------------------------------

upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G15880.1 (Glycine max), 5'ss of exon 14
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgct-catccttcagatacatgtgtgttcatccag-----gaaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
||| || ||||||| ||||||||| ||||| || || || |||||||||||||| ||||||||||||  ||| |||||| ||||||| || ||  | |||||||| |  |        | ||| | |||  || | |  |   |||  | ||         ||   | | | || |||||  ||                                                                                     
TGGTTCAAGAATGAAGATTGCTGGAAGATTTAAACCCTGTATTCACATGGGTTGCTTTGATCTTGAAGTTTTTGTGGAAATGAATCAGCGATCAAGAAAGgttaggttctaacaaatgttatgttgcatgatttaaaccccaatgtagtgattttaagtctgatgaattgaattgtttctacag-------------------------------------------------------------------------------------

upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G40320.1 (Glycine max), 5'ss of exon 10
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccagg-------aaagagttacttttttctggagctcacaacccaccttttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
||| || ||||||| |||||| || |||||||| |||||  ||||||||||||||||||||||||||  ||| |||||| ||||| |||||||  | |||||  |||  |        |||   | ||   ||  |||| | | |  | |   |          |||  ||| || |||||| ||                                                                                     
TGGTTCAAGAATGAAGATTGCAGGAAGATTCAAACCTTGTGTTCACATGGGTTGTTTTGATCTTGAAGTTTTTGTGGAAATGAATGAACGGTCAAGGAAGgtatgattctaaaaaatttgagcatgatttgtcgtataccttttttcttaaaaaaatgttgatgaagcattaattctttctgcag-------------------------------------------------------------------------------------

upper sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 13
TGGATCCAGAATGAGGATTGCTGGGAGATTCAAGCCTTGCATTCACATGGGTTGTTTTGATCTTGAAACTTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatcttgtgttccctgatgctcatccttcagatacatgtgtgttcatccaggaaagagttacttttttctggagctcacaacccacctt-ttgacatgttgatgctttcatattttccttttatatcctctgattgctcttttctcttgtttctatacag
||| || ||||||| | ||||||| |||||||| |||||   ||||||||| |||||||||||||||| ||| |||||| |||| ||||| ||  | ||||  |  |      || || |||     || || |          | ||| || || ||    ||   | |||||| |||   ||    || || || |||                                                                
TGGTTCAAGAATGAAGGTTGCTGGAAGATTCAAACCTTGTGCTCACATGGGCTGTTTTGATCTTGAAATTTTTGTGGAAATGAACCAACGTTCTAGGAAGgc-aagtgacagattgccagatttgtttctttta----------ttttcttctagcaa----ttttgtgtttctg-agcaagcattgtactttgtttacag---------------------------------------------------------------

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|218486779|gb|FG948671.1|FG948671
EST:     TTTCGTGGAATTGAATCAACGGTCCCGCAAG                         TGGCAATGTCCAATATGTTTAAAGAATTACTCTCTTGAGAGCTTGATGATT
genomic: TTTCGTGGAATTGAATCAACGGTCCCGCAAGgttagatctt ... ttctatacagTGGCAATGTCCAATATGTTTAAAGAATTACTCTCTTGAGAGCTTGATGATT