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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcgcaaaccttgtccttaaatttgcatgtaatttattctaccattattgggtttgtttttttgccttatcccttggaaagagctatctgatattggaagaaacatcacatatacatcaacaaatgctgtaaaatgaacttagttggtaacttgaatttgacatcattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAGGATTCAAAAAAGGCAAATGGGCCAGAGAAAGGCCCAAGTCTCGTCTTTA

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 4
gtgtgtgcgcaaaccttgtccttaaatttgcatgtaatttattctaccattattgggtttgtttttttgccttatcccttggaaagagctatctgatattggaagaaacatcacatatacatcaacaaatgctgtaaaatgaacttagttggtaacttgaatttgacatcattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAGGATTCAAAAAAGGCAAATGGGCCAGAGAAAGGCCCAAGTCTCGTCTTTA
                                                                           |||| | | | || |||    ||   |   ||| ||  | |  |  |||| ||   |||| | ||| |||   || | ||||||  | ||   ||||| |||||||||| |||||||| || |||||||||||||||||  ||||||| |  || || |||||||||||||||||  |||| |||  ||||||||| || ||||
-------------------------------------------------------------------------gaccctagtagaaagatatact-tacctggcaaaatatggcttg-atgtcaagaa---ctgtgagatggactgctttagcaacttgcttatgtattcatt-tgcagGAGTGCAACCTTGAGGAGGTAGAGGAGGAAGAACCATCTAAAAGCTCAAAAGACTCAAAAAAGGCAAATGGATCAGAAAAACCCCCAAGTCTTGTATTTA

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 16
gtgtgtgcgcaaaccttgtccttaaatttgcatgtaatttattctaccattattgggtttgtttttttgccttatcccttggaaagagctatctgatattggaagaaacatc-acatatacatc-aacaaatgctgtaaaatgaacttagttggtaacttgaatttgacatcattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAGGATTCAAAAAAGGCAAATGGGCCAGAGAAAGGCCCAAGTCTCGTCTTTA
                                                                             | | ||||||  || |||||     || |    |  |  || | | |  | |    |||    |  ||||| | |  |    | |  |  |  ||||| |||||||||| |||||||| || |||||||||||||| ||| |||||||||  ||||| |||||||||||||||||  |||| |||  | ||||||| || ||||
-----------------------------------------------------------------------------cgtagaaagatata-ctgatggcaaaacatgtcttgatgtaaagaactgatatggactgctttagcaactt-gcttatgttgttagctgtat-tcatt-tgcagGAGTGCAACCTTGAGGAGGTAGAGGAGGAAGAGCCTTCTAAAAGTTCAAAGGACTCAAAAAAGGCAAATGGATCAGAAAAAATCTCAAGTCTTGTATTTA
















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|29657562|gb|CB653837.1|CB653837
EST:     ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG                         GAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG
genomic: ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAGgtgtgtgcgc ... cattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG
EST: gi|58652777|gb|CK041457.1|CK041457
EST:     ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG                         GAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG
genomic: ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAGgtgtgtgcgc ... cattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG
EST: gi|33795777|gb|CF323758.1|CF323758
EST:     ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG                         GAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG
genomic: ACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAGgtgtgtgcgc ... cattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaatgctgtaaaatgaacttagttggtaacttgaatttgacatcattgtgcagGAGTGTAACCTTGAAGAAGTAGAGGAGGAAGAACCTCCTAAAAGTTTGAAGGATTCAAAAAAGGCAAATGGGCCAGAGAAAGGCCCAAGTCTCGTCTTTA
          taaaatgaa  TA-rich tract