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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttagtctagtaattgcagattatttaactttaaccggatcatttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG

Basic information

species Oryza sativa
transcript LOC_Os11g17600.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G060949_T01 (Zea mays), 3'ss of exon 1
gtaaatttagtct-agtaattgcagattatttaacttta--accggatca---tttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
|||||| | |  | | |   || |   ||||||| | ||  |    ||||   | ||| | | || | | |      ||| ||| |||| || || ||||||||||| ||  ||||||||||||||||||  ||||| ||||| |||||| ||||   |||||||
gtaaatcttgcttcaatgtctgtaa--tatttaagtataggataaaatcaggatctttgtgatcacactcctgaacacttgcagCGAGGTCATCTGCAGAGGCCTGATCACACTGATATGAGGTACAAATTTAGGACTTATGCACGACTTTTACAACACATCAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 11
---------gtaaatttagtctagtaa---ttgcagattatttaactttaaccggatc-atttttctcaacataattccttttgcttt---cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
         ||||||||  | ||| ||   ||| ||  |  |  | ||| | |  ||  |||  | |||   |   || | ||||| |   ||| | || ||  |  |||||||||| ||||||||  || ||||||| |||||||||||||| || ||||| ||     | |||
gtattttctgtaaatttgttttagaaacttttgaagtcttctgcattttgaacaaatttattggtatcactttg--tcttcttgctctgaacagCGGGGACAGTTAAAGAGGCCTGATCATGCTGACCTGCGGTACAAGTGCAGGACATATGCACGTCTTCTGCAACATTTGAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 11
---------gtaaatttagtctagtaat--------tgcagattatttaactttaaccggatc-atttttctcaacataattccttttgcttt-cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
         ||||||||  | ||| | |        ||  || | || || ||| |  | ||  |||  | |||   |   | |||   ||   ||| | || ||  |  |||||||||| ||||||||  || ||||||| |||||||||||||| || ||||| ||     | |||
gtattttctgtaaatttgttttagaattgtcacttttgaggacttttgaattttgaaggaatttattggtatcactttttcttcttcctctgaacagCGGGGACAGTTAAAGAGGCCTGATCATGCTGACCTGCGGTACAAGTGCAGGACATATGCACGTCTTCTGCAACATTTGAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA14G08520.1 (Glycine max), 3'ss of exon 4
---------gtaaatttagtctagtaat--------tgcagattatttaactttaaccggatc-atttttctcaacataattccttttgcttt-cagAGAGGGCAACTCCA-GAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
         ||||||||  | ||| | |        ||  |  | || || ||| |  | ||  |||  | |||   |   | |||   ||   ||| | |||||  |  | ||||||||| ||||||||  || ||||||| |||||||||||||| || ||||| ||     | |||
gtattttctgtaaatttgttttagaattgtcacttttgaggtcttttgaattttgaaggaatttattggtatcactttttcttcttcctctgaacagcgggggcagttaaaagAGGCCTGATCATGCTGACCTGCGGTACAAGTGCAGGACATATGCACGTCTTCTGCAACATTTGAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
------gtaaatttagtctagtaattgcagattatttaactttaa-----ccggatcattt-ttctcaacataattccttttgcttt-cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
            | | | ||  ||||  | | | || || | | |       | ||||||  || |||   |  || |||   ||   ||| | || ||  |  | ||||| || ||||||||| |||||||||| |||||||||||||| || |||||  ||    | |||
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaatttagtctagtaattgcagattatttaactttaaccggatcattt-ttctcaacataattccttttgcttt-----cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
|||    |  | ||  |||| ||   ||   |  |  |  |   | | |  |||| || ||   ||        ||     ||||||||||| ||  |||||||||||||||||||| || ||||||||||||| |||||||| || ||| | ||     | |||
gtactacttttataa-aattccatcgtaccaatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 11
--gtaaatttagtctagtaattgcagattatttaactttaaccggatcatttttctcaacataattccttttgcttt-----cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
     |||||  |  | |  |     | |||  || | ||    ||| ||  |||| || ||   ||        ||     ||||||||||| ||  |||||||||||||||||||| || ||||||||||||| |||||||| || ||| | ||     | |||
gtactaattttataaaattctattccaatatg-aagtctagt--gattataattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTTTGCAACATTTAAAG

upper sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
------------------gtaaatttagtctag-taattg-cagattatttaactttaaccggatcatttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
                  ||   |||| ||| | |||||  |     ||||     ||        | ||||  |   || | |  | ||     ||| |||| ||  |  ||||||| |||||||||||| |  |||| ||||||||||| ||||| || ||||||||   | | |||
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaa--acagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatttaactttaaccggatcatttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
          ctttaac  putative branch site (score: 3)
                                       ttccttttgctttc  putative PPT
     tttaactttaa  TA-rich tract