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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT

Basic information

species Oryza sativa
transcript LOC_Os01g23610.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 4
--catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
    |  | ||||  | |  | ||||| |  || |  |  |||  |   || |||||   | ||   ||||| |||||||||   |  |||   | |  |||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||| || ||||||||||| | |||||||||||||||||
tgtttcctgaattggattacatcatctct--tgatccacaattgggctttgctgtcaatagctggagtttcatctgtatttatgcattttttgatcgatcagGTTACTTTTGTTGAAGCTCTTGATCAATTAATGCCTGGGTTTGATCCCGAGATTGCAAAATTGGCGCAGAGGATTCTTATTAGTCCTCGTAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G16950.1 (Arabidopsis thaliana), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatt-----tcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
     |    | ||| ||       ||    ||||| | |      ||||||   | |     ||  |      || | | | |||        |  |||  ||||| |||||| | |||||||| |||||| | |||||||| ||||||||||||||    ||  | || || ||| || | || |||||  | || |||||||
-----ttttgtgtaaatagtagaaaataagattttaaggtaccaatctgttggtttttcgatttaaattgtagttactgatcgaaaacggaaaccttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTAGCTCAGAGGGTTTTGATAAATCCAAGAAAGATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttc--acctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
      ||||      || | ||  ||  || || | | ||  |      ||  |    | ||  |  |  | ||      | ||   |||   ||  |||||| |||||| |||| ||||| |||||  | |||||||| ||||||||||||||    ||  |||| |||||| |||| || ||| |  | ||||||||||
tcgagcaaatgggcgatagctat--attttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctg-ttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
   ||||   ||   ||     ||| | ||  |    ||  ||       ||   || | ||  || |  |  |  | ||  | | | |    ||  |||||| |||||| ||||||| ||||||||| | |||||||| ||||||||||||||||  || |||||||||||  |||| || ||||| || ||||||||||
-tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 5
-catgttaaattctaattaaccatctatgctgtttta-tgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
      |   || |  ||  |    ||  || | | | |||||||   | |   |  | |   |     |||||     | |||  |   | | |||  |||||||| |||||||||||  | |||||| | |||||||| ||||||||||||||||  |||||||| |   || |||| || |||||||| |||||||| |
ctccacttttttttggttctcttaataatctatataactgattaaatacagaatttttttatagccgagtcacc-aagctgaccacagcatta-ttgtgcagGTTACATTTGTTGAAGCTTTAGATCAGCTTATGCCTGGCTTTGATCCTGAGATTGGGAAATTGGCTCGGCGGGTTCTAATTAATCCTCGAAAAATTGATT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 5
----------catgttaaattctaatta-accatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
          | ||   | |  | |  | |  ||  | |  | | | ||      |  |||  | ||||||  ||| ||       | || |||    |         ||||| || ||||| || || ||||||  |||||||||||||||||||||||||||||  ||  | || || |||||  | |||||||||||||||||||| |
gtaaaatttccttgcgcattattgacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcagGTCACGTTTGTCGAGGCGCTTGATGGGTTGATGCCTGGTTTTGATCCTGAGATTGGCAAGCTTGCACAGAGGATCTTGATCAATCCTCGTAAAATTGATT

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttcacctgtatttacctaaatttcact-tggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
                                                       | |  |  |  |||     | |||   || | | | |  ||  ||||| |||||||||||||| || |||||  ||||||| || ||||||||||| || |  ||  | || || ||| | || ||||| ||||| |||||||| |
------------------------------------------------------gtttagtttttcttctttcctttttctatagaatacgcgatgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATT

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|58684178|gb|CK072865.1|CK072865
EST:     GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAG                         GTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT
genomic: GTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgtacatgaac ... acttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
                                  acctaaa  putative branch site (score: 3)
                                         tttcactt  CT-rich tract
                             tatttacctaaattt  TA-rich tract