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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTTGGACGTTTCTCAACGGAGACGGTTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaatatccccaacttgcacatttcagtgctttctttttgtgtattataatcttgtcactctctaaggaacaagtactgcattaaagcaattta...

Basic information

species Oryza sativa
transcript LOC_Os01g36840.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36840.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G030596_T02 (Zea mays), 5'ss of exon 17
CACTTGGACGTTTCTCAACGGAGACGGTTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaatatccccaacttgcacatttcagtgctttctttttgtgtatta-taatcttgtcactctctaaggaacaag-tactgcattaaagcaattta--
      || ||||||||||| ||||||||||| |||||||  |||||||| || |||||||| ||||||||    ||||||||   |   || |||||||  |||| |  | | | ||||   | || |  |  |   ||   | ||| ||| ||||  || ||   | || ||||| |  
------GATGTTTCTCAACGAAGACGGTTTAATGAATACAAAACTTTGACCCTGGAGAATGACAAGTTGCGAAATGAgtaagtgcta---ccacaacttg-gcattgccttacatactttaattctagtggttgtaaagttgttttctgagggacaaactattgaggtcaaacaattaaga
















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|86850875|gb|CI338851.1|CI338851
EST:     GATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: GATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|88850945|gb|CI096335.1|CI096335
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|116875003|gb|EC365511.1|EC365511
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGACAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|86437853|gb|CI119773.1|CI119773
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|116874995|gb|EC365503.1|EC365503
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGACAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|86257213|gb|CI004031.1|CI004031
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|33793365|gb|CF322564.1|CF322564
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|116875534|gb|EC366042.1|EC366042
EST:     TTTAACGAATACAGGACTTTGACACTAGAGAATGACAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: TTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|86901270|gb|CI326113.1|CI326113
EST:     ATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: ATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
EST: gi|88831097|gb|CI080521.1|CI080521
EST:     GAGAATGATAAGTTGCGTGGCGA                         ATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG
genomic: GAGAATGATAAGTTGCGTGGCGAgtaagtaaaa ... tttttctcagATGCTTGCAATACGAGGAGTCAGCAAAACAACTTGCTCTGAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTTGGACGTTTCTCAACGGAGACGGTTTAACGAATACAGGACTTTGACACTAGAGAATGATAAGTTGCGTGGCGAgtaagtaaaatatccccaacttgcacatttcagtgctttctttttgtgtattataatcttgtcactctctaaggaacaagtactgcattaaagcaattta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccaac