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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatatctaaatgacaatatatatttcccactgtattgcatacaattaaagataaagaaattagctgttaattaaatttttgtgtgacttattttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTTTATATCACTCCTGATGTTGGGTTTGACTGGGTGTCTGGCAAGGGAACTC

Basic information

species Oryza sativa
transcript LOC_Os03g31550.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 7
tcatatctaaatgacaatatatatttcccactgtattgcatacaattaaagataaagaaattagctgttaattaaatttttg-tgtgacttattttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTTTATATCACTCCTGATGTTGGGTTTGACTGGGTGTCTGGCAAGGGAACTC
 | |       |   | |||  | ||   | | | ||    | | ||  |    |  |  |||    |||| |||| | | | | | |    ||||| ||||||| || |||||||||| ||||| |  | ||||||||||||||||| ||||||   || ||| || ||||||||||||||  |  ||||||||||||||
-cctgatactgtagtattattgaattaaaattatctttttaaaattttgactccataattttatggtttaactaaaatgtggatattatgctttttgccagTTGGCTCAAGCATGCTACATGGAACGTGTGGATCTCTCTGCTCATGGGTTTTATGCTACACCTAATATTGGGTTTGACTGGACGATTGGCAAGGGAACTC

upper sequence: LOC_Os03g31550.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 11
-tcatatctaaatgacaatatatatttcccactgtattgcatacaattaaagataaagaaattagctgttaattaaatttttgtgtgactt-att-ttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTTTATATCACTCCTGATGTTGGGTTTGACTGGGTGTCTGGCAAGGGAACTC
  ||  | |   | |  | |  ||      | | |  ||  |||||       |   |     | || || |  |  || |  | ||  || ||| ||  ||| | |||   ||||||||    ||| | ||||| || ||||| |||||||||||||| ||||||||| |||| ||||| |||  | | || || ||||  |
aacaagttttc-tcattacaagtaaccttta-tctgctgt-tacaaggtgtcttgtggttgaaaactattgaacatgttctgttatgcttttattattttcagCTAGTTGGTGCATGCTATGCAGAACGAATAGACCTTTCTGCCCATGGATTTTATATTACTCCTGATATTGGTTTTGATTGGACGACGGGTAAAGGAAAAC
















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|58682426|gb|CK071113.1|CK071113
EST:     CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAG                         TTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
genomic: CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAGgtaaagtcat ... attttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
EST: gi|218479236|gb|FG969139.1|FG969139
EST:     ACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAG                         TTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
genomic: ACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAGgtaaagtcat ... attttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
EST: gi|218495632|gb|FG967039.1|FG967039
EST:     CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAG                         TTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
genomic: CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAGgtaaagtcat ... attttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
EST: gi|29675056|gb|CB671331.1|CB671331
EST:     CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAG                         TTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT
genomic: CTCGGATGGAACCTGTTGCTTCAAGAGGAAACCACAAGTCCTTTGCTGAGgtaaagtcat ... attttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagataaagaaattagctgttaattaaatttttgtgtgacttattttgacagTTGGTTCTAGCATGCTACCTGGAAAGGATAGATCTCTCTGCTCATGGATTTTATATCACTCCTGATGTTGGGTTTGACTGGGTGTCTGGCAAGGGAACTC
                    tgttaat  putative branch site (score: 3)
                                          cttatttt  putative PPT
      ataaagaaattagctg  TA-rich tract