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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtttgattcaaaatttgtccttttttactactaagtttttccgcagttttcacaaatatgtcagatgacaattgctgaaacttgcaactaaagagtcatttgtatttgttcccataagtccccattgttgctacattactacattacctgatcatggagtgaattactcccaaattattcgtcatgctgcagCATGTCTACATCCCAATAATTTTCTCTAGTGGGGTTGATTACATAGATGCTCCAACACCCTACATGATGGGACTTCATTCAGGTGTTGACACATCCACAG

Basic information

species Oryza sativa
transcript LOC_Os01g39380.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G074572_T01 (Zea mays), 3'ss of exon 6
gtaggtttgattcaaaatttgtccttttttactactaagtttttccgcagttttcacaaatatgtcagatgacaattgctgaaacttgcaactaaagagtcatttgtatttgttcccataagtccccattgttgctacattactacattacctgatcatggagtgaattactcccaaattattcgtcatgctgcagCATGTCTACATCCCAATAATTTTCTCTAGTGGGGTTGATTACATAGATGCTCCAACACCCTACATGATGGGACTTCATTCAGGTGTTGACACATCCACAG
|||||||| | |||||   | | |  ||| |    |||  |||  |   |  || | ||  || |   |  ||||||||||  | |       |   | |||||  | | |||  |||||| ||     || || ||   | ||      ||| ||||||| |||| || |    |  ||||||    |||||||||||||||| || |||||||| ||||||||||||||||||||||| ||||| || ||||||||||||||||| |||||||| ||||||||||||||  |||
gtaggtttcaatcaaa---tatgcgatttca----taaactttcac-tggacttgaaaagcatcttgtaaaacaattgctgtgattg------aggaattcattcatgtctgtatccataattc----gtgctgataatatgct------cctaatcatggtgtgactt-catatagcttattctgtttgctgcagCATGTCTATATTCCAATAATATTCTCTAGTGGGGTTGATTACATTGATGCCCCGACACCCTACATGATGGGGCTTCATTCTGGTGTTGACACATCTGCAG

upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtttgattcaaaatttgtccttttttactactaagtttttccgcagttttcacaaatatgtcagatgacaattgctgaaacttgcaactaaagagtcatttgtatttgttcccataagtccccattgttgctacattactacattacctgatcatggagtgaattactcccaaattattcgtcatgctgcagCATGTCTACATCCCAATAATTTTCTCTAGTGGGGTTGATTACATAGATGCTCCAACACCCTACATGATGGGACTTCATTCAGGTGTTGACACATCCACAG
             |   |||| |   |||   ||| ||||  |     |  ||   | |  ||   |     |  |      || |     ||  | ||   ||  ||||  |||     ||   |  |||||     ||| ||  |        | |     | |  || ||      | || ||  | ||| ||||||| ||||| ||| || | || |  ||||| || || || || |||||||| ||||| || |||||||| || ||||||||||||||||| || |   
-----------gtagggtttggctcctttgtgtac-aagtgctctttta--ttgggctaggattaaaagcttccttcatatgaatt-----ctgtataggttttcatattacttc-----agcttcacttgttatattattgctgaaaattaaagttaaactctcatctaatctttttatgtttgttgttctgaagCATGTATACATTCCATTACTATTTTTCAGTGGAGTGGACTATATTGATGCTCCTACACCATATATGATGGGTCTCCATTCAGGTGTTGACACTTCTAATC


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacattacctgatcatggagtgaattactcccaaattattcgtcatgctgcagCATGTCTACATCCCAATAATTTTCTCTAGTGGGGTTGATTACATAGATGCTCCAACACCCTACATGATGGGACTTCATTCAGGTGTTGACACATCCACAG
        acctgat  putative branch site (score: 4)
                                  aaattatt  TA-rich tract