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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

Basic information

species Oryza sativa
transcript LOC_Os01g63770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggt--gcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
  ||   | || |  |    |          ||  | | |       || ||| || ||  |||  |         | | |   | |||| ||| |  |||| ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||
-tatacactgatgatgaacagctttactgaatgcaggt-agccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------gcatgtgccgaggccgttttgtccgttgatttgt-tgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
                                                          || ||  |    || |  | |    ||||| |  | | | ||        | ||| || || | |    |     |  ||  ||   ||||   |||||||||||||||||| ||||  |||||   ||||||||||||| | | |||| ||||||||||||||||||||||||||||  | || || ||   ||| 
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggcc--ctcaaacttcctaattactattg--ccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
                  |   |  | | ||  ||   |  |  | |||| | |  || |   ||  ||  |              || |||     ||||||||||||||||||||||||||| ||    ||||||||||   |||| ||  | || ||  | ||||| |||||  |||| || ||||| ||  |||| 
-----------------gtaagctttcgcttctttcgctgtt--cttgcatggatcgataggcat--cttctcataaac-------tttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

upper sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
   |  ||    ||   |||  | |||  |   | |||  |||  ||              |  | |    ||     |       || |||     ||||||||||||||||||||||||||| ||    ||||||||||   |||| ||  | || ||  | ||||| |||||  |||| || ||||| ||  |||| 
--gtaagctttcgcttctttcgctgttcttgcatggatcgataggctatg-----------ttgtcatcttttc----tcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

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|58661448|gb|CK050128.1|CK050128
EST:     ACCGGCGCCACCAACATCCTCTACACCTTCGGTGGCCACGCCGTCACAGT                         GGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCT
genomic: ACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCCGTCACAGTgtaagcaaag ... attggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggtgcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC
                    gactgat  putative branch site (score: 3)
     agaaaagaaaataat  TA-rich tract