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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag

Basic information

species Oryza sativa
transcript LOC_Os01g59340.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G020002_T03 (Zea mays), 5'ss of exon 9
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag
|||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||  | |||||||| |||||||| |||||||     | |||  | | ||| | |  || |  |      | | ||| |    ||  ||  |        | || ||  |   ||||| | |                                       
CTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATGgtagggactctggact-taaatgttagagt-ggtagtaggatctgtaatatgtattgagacatctctcctgagtcctgacta-cttgaacacag--------------------------------------

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA15G06100.1 (Glycine max), 5'ss of exon 9
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaa-taagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag
|| |||||||||||||||||  |||| || ||||| ||||||||| | ||   |||||| ||| | || |||||||||||||| ||||||||||    ||     ||    |  |  ||  ||   ||| |  ||   ||     ||||||||  ||  |  || |   |  | ||  |    | | || |   || |                       
CTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCGGAAAATTCCTAATGGTGTCAATGgtaatcac-atgatggatggccctagatatttccagcctaaatgcattctag-----ttgattttg-aaatatctccttcctaatgtgctttg--caacctgatatatgtag---------------------

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 5'ss of exon 9
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag
||||||||||||||||| ||||| ||||| || ||||| |||||| | ||   |||||||||| | |  || |||||||||||||||||||||   ||       ||  ||    | ||  |   | | |         ||| | | | |   |  | | ||     |  ||||                                              
CTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATGgtaatagctgacttgactggtttcttgctttctctgctcactgcccctgctaacctgtaaatacttttgaacttgtccatatgtttag--------------------------------------------

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 5'ss of exon 9
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataaggaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag----
|||||||| |||||||||||  ||||||| ||||||||||||||||| ||   |||||||||| |||| |||||||||||||| ||||||||| |      ||| | |   ||| |  ||| |  |  |     ||   || | ||  ||   ||   |  ||  ||| ||| | | |   ||   ||||  | | | | | ||  |  | ||    ||     
CTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATGgtaatac----aagttatca---tcaccactgatatttggg-----aagtcaattattatttccctagtta--tcaagtt-ggtctcatttttccgttctaattcttatatttgttgcaatcctgggaacaattag

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S101_168V6.1 (Physcomitrella patens), 5'ss of exon 9
CTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATGgtaatccttgtgggttgtgaatttcaacgttgacaaataagtatataaaagaacttttgattttataag----gaattcgtgtttggtttgaataaacccagctaaggcatctctctcttaaacgcttgaccccag----------------------------------------------------------------------
 | || |  || ||||||  | | ||||| || || ||||| ||  | ||     |||| ||  |   |||||||||||||||||||||||||  ||   ||      |||  ||  |    | ||    ||        |||||  ||| |   ||    ||||||||  |   ||  |||     ||| |   || | |  |  || || | ||  |   ||                                                                      
TTAGTGGCTACAGATCATGCCCCTTTCAATTCAACTCAGAAGGCGCTTGGAAAGCATGACTTTCGGGTGATTCCTAATGGTGTTAATGgtaattattagtggcc----attcaaatttgagtacatgtagatgcgctgacactttctattgttagagtttagaattcgttctc--ttgcaattctttcagttggtgcgtatagcagttgaatgattaccattagcacagttagggtacttgcaagagttgatgagatgtggatctgacaacacaacgtctgcttctgatgtcag

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|87026885|gb|CI259538.1|CI259538
EST:     CTAACGGTGTTAATG                         GTATCGAGGAAAGGATGCATATTATTTGGGACAGTATGGTG
genomic: CTAATGGTGTTAATGgtaatccttg ... ttgaccccagGTATCGAGGAAAGGATGCATATTATTTGGGACAGTATGGTG