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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagacactgaagttgattttagccaaaaaggagtgtttcttccgataatgctttttaatgatttgctatggttgttcactattgaccatatactctggttatggttttgcagAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC

Basic information

species Oryza sativa
transcript LOC_Os01g41730.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41730.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagagacactgaagttgattttagccaaaaaggagtgtttcttccgataatgctttttaatgatttgctatggttgttcactattgaccatatactctggttatggttttgcagAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC
               ||   ||||     ||   || | |        | |||| || | |||  | || | | ||   | | || |       |   |   || |||| |   |||||||| || || || || ||   ||| ||||||||| |||||||||||||  ||||||||||||| ||  | ||| |||| || ||||| ||||||   
---------------gtaagttttc----aacttgaatatc-------aaaatgtttgtcaatcttatgtttttgtaacttaataat-----cctttcccaattttggtctc-tagAGGGCAAGCTGAGAAGGAATTTCGGGTAGAAGTTGAGGCTATTGGTCATGTACGGCACAAGAATCTTGTTAGGCTTTTAGGATATTGCATAGAGGGAGTT

upper sequence: LOC_Os01g41730.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagagacactgaagttgattttagccaaaaaggagtgtttcttccgataatgctttttaatgatttgctatggttgttcactattgacc------atatactctggttatggttttgc----agAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC
                                   ||| ||||||    |     | |  |||| |    | || ||| |  || || ||        || |  ||    |   |||||     || || ||||| || || || |||  ||||||||||||| |||||||||||||  ||||||||||||| ||  | |||||||| || ||||| |||||    
--------------------------------gtaagtttttctttttttgggtttatcaaatgttggtttgtgcttgcttcctttttacttgtttagtaaatcctaac-acaattttgtctctagGGGACAGGCTGAGAAGGAATTCCGGGTTGAAGTTGAGGCTATTGGTCATGTACGGCACAAGAATCTTGTAAGGCTTCTAGGATATTGCATAGAGGGTGTT

upper sequence: LOC_Os01g41730.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 3
gtaagagacactgaagttgattttagccaaaaaggagtgtttcttccgataatgctttttaatgatttgctatggttgttcactattgaccatatactctggttatggttttgcagAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC
                 | |   |||   ||||| |   | |||       |   ||| | ||| |||| | ||    ||   |  ||||   ||  |   |  |||| ||  ||| || ||||||||||||||||||| ||||||||||||| |||| || |||||| |||| || ||||| ||||||||| | || || ||||| || |||   
----------------gtaagaatagatcaaaagcaccttctctc------actttttatgatgctttggt-tgaaatttggtttatgactgcattat---gaaatgggttcacagGGGACAGGCAGAAAAAGAGTTCAGGGTTGAAGTTGAGGCTATAGGCCATGTTCGGCATAAAAATCTTGTGCGACTTTTGGGCTATTGCATAGAAGGAGTT

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: 75 (upstream exon), 33 (downstream exon)
Score: 3

CTGATGACAATATCATAGGAGAGGGCGGCTATGGGGTTGTTTACCACGGTCGTCTTATAAATGGAACTGATGTTGCAATCAAAAGGCTTTTTAACAACATgtaagagaca ... ggttttgcagAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttgctatggttgttcactattgaccatatactctggttatggttttgcagAGGGCAGGCAGAAAAAGAGTTCAAGGTTGAAGTTGAGTCTATTGGTCATGTTAGGCACAAGAATCTGGTGCGACTTCTAGGTTACTGCATTGAGGGAAGC
                      tattgac  putative branch site (score: 3)
                              atatact  TA-rich tract