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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaactatttgatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g41990.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G153332_T01 (Zea mays), 5'ss of exon 4
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaac-tatttgatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgtgcag
  || |||||||||||| ||||| || ||||| |||||||| |  ||||| || || ||||| || |||||||||||||| ||||| ||||||||||||||||||||  | | ||| | |   |||||| | |||  | |    |  | |   |  |   |  ||||||  |||| |  |       
GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGCAGAGGACCCATCACAGTCATATGCTTTGATATGTGGCAACTGCCATATGCATAATGgtgtgtattatagacaaagcacttttgatatttttcacataccataattacctaacccagt--attact-aatatttgcag------

upper sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G074436_T01 (Zea mays), 5'ss of exon 4
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaactattt-gatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgt--gcag
  || |||||||||||| ||||| || ||||| |||||||| |||||||| || || |||||||| |||||||||||||| | ||| ||||||||||| ||||||||  | | |   | || ||| ||| | |||  | |    |    ||| |  | |||||||||| | ||||| |||  |  ||||
GATGGTGGTGGATGGATTGCAAAGATTGCTGCCTTACTTGTGGGGGAGGACCCATCACAGTCGTATGCTTTGATATGTGGCAGCTGCCATATGCATAACGgtgtgtattatagatcaagctcttttgatatttttcacataccatacctaaatat-cggatgcattacctaatataccaatttttgcag

upper sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G07860.1 (Glycine max), 5'ss of exon 5
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaac--tatttgatctcttttgcctgttgtgttaaaaaagactgatgcat-tacttga--tatatcaacgtgcag----------------------------------------------------------------------
   || || |||||||| |||  ||| || ||||||||||| || ||||||||  | |||||||| ||| | |||||||| |||||  ||||||||||||||  |   |  | |    |   | | || ||   |     ||   | ||  | || |  ||||  | |||| |   ||| |     |  |                                                                       
CAAGACGGAGGATGGATTGCACGAATTGCAGCTTTACTTGTGGGTGAGGATCCAACACAGTCGTATGCTCTCATATGTGGTAACTGCTATATGCATAATGgtaagggggctagatttgatcttgtatgctcatgtccttttgcattattgcagaataaagatgattgtactagggctattttgttttttacaatagaccatgttaatagatgaatacaacagtcaaaaaaattgtattcttatctgcttattttctttcag

upper sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0432g00020.t01 (Vitis vinifera), 5'ss of exon 2
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgt--------------------acgacaaacagaactatttgatctcttttgcctgttgtgttaaaaaagactgatgcattacttgatatatcaacgtgcag--------------------------------------------------------
  |||||| |||||||| ||   ||| |||||  ||||||| |||||||||||  |  |||| || ||  | ||||||||||||||||||||||||||||||  ||                    |                                                                                                                                       
CATGATGGGGGATGGATTGCTCGAATTGCTGCACTACTTGTGGGGGAGGATCCAACAGAGTCTTATGCACTTATATGTGGAAACTGTCATATGCATAATGgtaagtggagtgaggacctcatccttannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgaagtagttttgtcctgtttttgtttttgtgcag

upper sequence: LOC_Os02g41990.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv00s0215g00090.t01 (Vitis vinifera), 5'ss of exon 5
AGTGATGGTGGATGGATAGCAAAAATCGCTGCTTTACTTGTTGGGGAGGATCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacgacaaacagaactatttgatctcttttgcctgttgtgttaaaaaagactgatg-----cattacttgatatatcaacgtgcag-----------
  |||||| |||||||| ||   ||| |||||  ||||||| |||||||||||  |  |||| || ||  | ||||||||||||||||||||||||||||||  ||      |   || ||  |   |      ||  | |    || |  |  |||  ||     ||||||||  |   || | || |             
CATGATGGGGGATGGATTGCTCGAATTGCTGCACTACTTGTGGGGGAGGATCCAACAGAGTCTTATGCACTTATATGTGGAAACTGTCATATGCATAATGgtaagtggagtgag--gacctcatccttacaaaatgtatttctgcttcaggattacttttgttcatcattacttttttcctccatgtcccctactgttaatt

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|87029215|gb|CI276483.1|CI276483
EST:     TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATG                         GCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
genomic: TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacga ... caacgtgcagGCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
EST: gi|87026863|gb|CI259516.1|CI259516
EST:     TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATG                         GCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
genomic: TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacga ... caacgtgcagGCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
EST: gi|29680846|gb|CB677121.1|CB677121
EST:     TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATG                         GCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
genomic: TCCGTCGCAGTCGTACGCTTTGATATGTGGAAACTGTCATATGCATAATGgtgtgtacga ... caacgtgcagGCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
EST: gi|88515692|gb|CI443346.1|CI443346
EST:     ATGTGGAAACTGTCATATGCATAATG                         GCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT
genomic: ATGTGGAAACTGTCATATGCATAATGgtgtgtacga ... caacgtgcagGCTTGGCCAGGAAAGAAGATTACCCGCACATTACCTACTACTGCCCCCATT