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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatacttcggtagtcagtttcaagcaattcctatttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG

Basic information

species Oryza sativa
transcript LOC_Os01g55260.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 6
atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatacttcggtagtcagtttcaagcaattcctatt-tgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
   |  |  |    | ||  ||||   |||   || ||   ||     | ||  |    | | || | |    ||||||| ||     |||| || |  |||||||||||||||| || || ||||||||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||
ggttcagagtcactattatgttgagcatttggtatattctcatgcacttatccctgtacaaagacat-gcctctcagttttaactggatcctgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G34560.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatacttcggtagtcagtttcaagca-attcctatt-tgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
                                                                  ||||   ||     |  | |    |||||  |||   |     |  |   |||  ||   | || ||   |  |   |  ||  |  |||| | || ||||||| ||||| ||||||||||||||||| ||||| || || |||||||||||||| ||||| |||||  |||||||||||||| | |
gtgcgatgattctatctcgaatgtgtttttacttttgaactcttactctcttttgcatttcaattcatatgcacacca-aaccattaactaatttcttgagcctagctcaattagatcttgtaaagtttattttcttgatgcataacagtcttattcgtcttgtgcagACTATGCTTGCAAAGGCTGTTGCTACAGAGTGCAATACAACATTCTTCAACATCTCAGCCTCATCTGTTGTTAGCAAATGGAGAG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 6
atatttgcattgtgagtactttgaaattttctgattttgcaatatctctgtctattactatatact-tcggtagtcagtttcaagca--attcctat-ttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
    |||| ||   |    | |      |  || |  |  |  ||     |||  ||   |  | | |   | || | ||  || |   |||| | | |||||||| ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||| ||||| ||  |||| ||||||||||| |
----ttgcctttccaaatttctctgtcatgatgttgcttgatcatgctcttcttctaggttgaattgttaattgttaattgaaatctccattcttttgttgcagACTATGCTTGCAAAGGCTGTCGCAACCGAGTGCAAAACCACATTTTTCAATATTTCTGCATCCTCTGTTGTCAGCAAATGGCGAG

upper sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S51_233V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------atatttgcattgtgagtactttgaaat--tttctgattttgcaa-----tatctctgtctatta-ctatatacttcggtagtcagtttcaagcaattc-ctatttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG---------------
                                                                           || |  |  ||  |  | | | |   |  |||  || |||  |      |   | |||  | ||  |  |||||    |||  ||||    |    || | | | ||||||||||||||| |||||||| || || || || || || || |||||||||||||| || || || || |||||||||||||| |               
gtatttcgcactcttctccttctttgattgcatcctcaataggttcaagggggttttactctcagctgtattacaatgtgcgggttacgccttcgtcgttttggtttaggactttagaggttggtgggtttgtggagtaattgaatactgaaatag--agttcggcgttgctcacaactggcagACAATGCTGGCGAAGGCTGTGGCGACGGAATGCAAGACCACGTTCTTCAACATTTCTGCCTCTTCCATAGTTAGCAAATGGCGGGGCGATTCGGAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtctattactatatacttcggtagtcagtttcaagcaattcctatttgcagACAATGCTGGCAAAGGCTGTTGCTACTGAGTGTAAAACTACATTCTTCAACATTTCAGCATCATCAATTGTTAGCAAATGGCGTG
                                          ttcctattt  CT-rich tract
       tattactatatactt  TA-rich tract