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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag

Basic information

species Oryza sativa
transcript LOC_Os01g68320.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G059020_T01 (Zea mays), 5'ss of exon 7
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag
|||||| ||||| || ||||| |||||||| ||  |||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||||| | |    |   |||||||       ||   | ||  | | |    |  || |||    | |      ||   |||  || || | |   |||
TCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGCGGACCGGATGCTAGATATGGGGTTTGAGCCCCAAATTCGAAAAATAGTAGCACAAgtacatttccgtttagaaatgcagaattcttactaatatct--attgtctttcctagctctaatgcttgtccaacacttctgctatccttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 6
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag
|||||| ||||| || ||||| |||||||| ||  |||||||||| ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||||||| |  | ||  |||||||       ||   | ||  | | |    |  ||  ||    | |      ||   |||  || || | |   |||
TCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGCGGACCGGATGCTAGATATGGGGTTTGAGCCCCAAATTCGGAAAATAGTAGCACAGgtacagtttcgtttagaaatgcagaattcttactaatatct--attgtcttgcctagctctaatgcttgtccaacacttctgctatccttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G09270.1 (Glycine max), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgtt-ttagaatgcttata-tcagttctggtgttttggctaactctccattttttctattgtgctaaacgtttttgttgttaatag----------
 ||||| |||||||| ||||| || ||||| ||| | ||||| ||||| || ||||| |||||||||||||| || ||||| || ||||| || || |||| |  | |||    ||  |||    || | ||| |||     | ||  ||     | |    ||||||    |  |  | | || |  | ||||          
GCACACGAACCTGCGGAGAGTGACTTACCTTGTCTTAGATGAAGCTGATCGAATGCTAGACATGGGTTTTGAACCTCAGATACGGAAAATTGTAGCCCAGgtactgtttgcaactaacatgtaactagttagtactgagtaatggggaaaagaaacctcaaatctatt----tccatttgtgtgctactgatagtttaccaacc

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G02590.1 (Glycine max), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttata-----tcagttctggtgttttggctaactctccattttttctattg----tgctaaacgtt---tttgttgttaatag
 ||||| ||||||   ||||| || ||||| ||| ||||||| ||||| || ||||| |||||||||||||| || ||||| || ||||| || || |||| |    || ||  |     | | ||     | ||| |||     | ||  ||     ||||   ||||||     |  | ||| ||   | || ||||     
GCACACAAACCTGAAGAGAGTGACTTACCTTGTCTTGGATGAAGCTGATCGAATGCTAGACATGGGTTTTGAACCTCAGATACGGAAAATTGTAGCCCAGgtac--ttttttgcaactaacctgtaacaagttagtactgagtagtggggaaaagaaacattgaatctatttccatttttgaaccttaagtgtgctgttgtc--

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g09130.t01 (Vitis vinifera), 5'ss of exon 5
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttgttttagaatgcttatatcagttctggtgttttggctaactctccatt---------ttttctattgtgctaaacgtttttgttgttaatag
 || || |||||||||||||| || ||||| ||  | |||||||||||||| ||| | |||||||| ||||| || |||||  | |||||  |  | || | |||| ||   ||    |||||   |      |   |  |  ||| | | | |||          ||||      |  ||| |  | ||    |  ||||
ACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGCTGACCGAATGTTAGACATGGGATTTGAACCTCAGATCAGGAAAATTATTTCCCAAgtatggttt-ccttgctttgcttcctttctcatttacgagtcagcttaatttgcatcaggaataactttttggaaattataagcactgttcacttctatag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 5
lower sequence: EDP09760 (Chlamydomonas reinhardtii), 5'ss of exon 4
TCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGCTGACCGCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggct-tgttttagaatgcttatatcagttctggtgttttggctaa---ctctccattttttctatt--gtgctaaacgtttttgttgttaatag--
   ||| ||||||||  | || |||||||| || ||||| ||||| ||||||||||| |||||||| |||||||| ||||| || || || ||||  ||||   |||   |     ||     | |||       ||      ||   |   |    ||      | |    | ||    |      |    |  ||   
CATCACCAACCTGCGGCGTGTGACATACCTGGTGCTGGACGAGGCGGACCGCATGCTGGACATGGGCTTTGAGCCGCAGATCCGCAAGATTGTGGACCAGgtggggcggcggggcggaggcggtgtatggagcggggcaaggcggggcagggcagggcagggcagcaagccggggccgggcacgacgggcagtcctacag

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|87023569|gb|CI286320.1|CI286320
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAA
EST: gi|29636635|gb|CB641644.1|CB641644
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29661777|gb|CB658052.1|CB658052
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAA
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCATACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAG                         ATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA
genomic: GCATGCTTGACATGGGTTTTGAGCCCCAGATTCGTAAAATAGTGGCACAGgcatggcttg ... ttgttaatagATCCGGCCAGACAGGCAAACCTTGTATTGGAGTGCCACTTGGCCAAGAGAA