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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_Os11g17600.1
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 70 (downstream exon)
Score: 5

TCTAAAGTGCACATTTGTGCGGAGGGCATCCGAGTTTTTAAGGAATTACTTTCCCAGTTTGATTGATTTTATGCTAAATGACAAAGGCAACTTCTCACAGgtaaatttag ... ttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatttaactttaaccggatcatttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG
          ctttaac  putative branch site (score: 5)
                                       ttccttttgctttc  putative PPT
     tttaactttaa  TA-rich tract