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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG

Basic information

species Oryza sativa
transcript LOC_Os02g58090.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaatttt---ggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
           || | || | ||  |||  |  || |  | ||       |  |||  | |   | ||||||| || ||||     ||||||||||||||||| || ||||||||||| |||||||| || ||  | |||||||| ||||| ||||| ||||| || || ||||  || || |  ||||
---------gtaatatcagtgtctttgtggcatgtatgtt-gtattcttctggtcttggccctttcataacatcaatttttttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG

upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 9
gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
||| | || |      |  ||    || ||      |  || ||  |    |  |  | | | |  || | || |  ||||  ||||||||||||||||| || || |||||||| |||||||| ||||| || |||||||| || || ||||| |||||||| || || |  ||||| | |||||
gtaatattata---gcctcttctgttgcatttttcatatta-ttctgttcctggcctttttaccccattaaat-atgttttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAGATCCCTGGACTGAATGCTCCAATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG

upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
||| | || |    | |   |||  |   | |  | |||   ||  |    |  |  | | | |  || | ||   |||||  ||||||||||||||||| || || |||||||| ||||| || ||||| || |||||||| || || ||||| |||||||| || || |  ||||| | |||||
gtaatattat----agcgtcttctgt---tgcatttttcatattctgttactggccttttgaccccattaaatatgattttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG

upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 1
---------gtatttttctgaagaacaatttccatgtatccggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
         |    |||||    |   ||||  |  | | | |     |         ||| | |   | | ||||     || | ||||  |||||||||||||| || || || ||||| || ||||| || |||||||| |||||||| |||||||||||||||||||| || || |  ||||| |  ||||
gtcagatgagctaatttctcgcaattgattttgacctttacagaaccttcaactt--tgttttttcctttagctgac--tgtttattttt--cagAGATATGGTCCGCCACCATCATATCCACATCTGAAAATCCCTGGGCTGAATGCTCCTATTCCTCCTGGTGCTAGCTTTGGTTATCATCCTGGTGGTTGGG

upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S98_7V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------gtatttttctgaagaacaatt--tccatgtatccggtgttctag---ttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
                                                                                       || | || ||||  |  | |  ||     ||   || ||  |    |     ||| |  |  |   |||            |||  |||||||||||| ||||| || ||||||||||| || |||||||||||  | ||||| || || ||    || ||    || || || |   |||| |  ||||
gtgcgtgcagttgctctccactcttgtgaagttagggagtaaatctttttctttttactcaacattacacgtgtaacctgaactttttactgttatgaatgaagactattctgcaaattttgtttttcatgcctctgttagtgcctttggctgactttgtctgcggtttttctgcagAGATATGGGCCTCCTCCTTCTTATCCTCATCTTAAGATTCCTGGATTGAATGCACCAATACCAGAGGGGGCCTCTTTTGGCTATCATGCTGGAGGCTGGG

upper sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 9
lower sequence: EFJ25450 (Selaginella moellendorffii), 3'ss of exon 6
gtatttttctgaagaacaatttccatgtatccggtgttc-tagttgagaagtt-ctctatgtcaactgataacattaaattt-tggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
                                   || | ||||    |   | |  | | |  ||| |  | |    | |  | ||||||||| || || ||||| |||||||||||||||| |||||||||  | || || || |||||    |||||   |||||| || |  ||||| |  ||||
-----------------------------------gtacgtagtcactacactacattctatagactaaggaaagcggactgattgcagAGATACGGGCCACCGCCTTCTTATCCTCAGCTGAGGATTCCTGGATTGAACGCACCTATTCCCGTCGGTGCGTCCTTCGGTTATCATCCTGGAGGCTGGG

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: 73 (upstream exon), 74 (downstream exon)
Score: 50

CAAGCTTAGGGAAATGAAGCCAGGCATGCTGTCGCGAGAACTTAAAGAGGCTCTTGGTATGCCTGATGGTGCGCCACCTCCATGGCTTATAAACATGCAGgtatttttct ... attttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgttctagttgagaagttctctatgtcaactgataacattaaattttggcagAGATATGGTCCTCCGCCCTCTTATCCTCAGCTGAAGATTCCTGGGCTAAATGCTCCGATTCCTCCTGGTGCTAGCTTCGGATACCGACCTGGGGAATGGG
                                 tgataac  putative branch site (score: 50)
                                 tgataacattaaattt  TA-rich tract