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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtttggagctgattttgctgtgtaatatatttttgcagtcctggtatctatctgtactgattttttctggtgcaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g29380.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 13
ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtttggagctgattttgctgtgtaatatatttttgcagt--cctggtatctatctgtactgatttttt-ctggtgcaaatgcag
 ||||||||||| ||||||||||| |||||||| ||| |||||||||| ||||||||||||||||| ||||| ||||| || |||||||||||||| | |   ||| | |||||||| | |  |   | | | || |||  ||||||| |||   |  |  ||||||||
GTATGATTCATCAAAGACATTCACTCAGAATGTCGAATTGACGGATCCCATTATTTCACGTTTTGACGTCCTCTGTGTGGTTAAGgtttggagctgttatacatgtctgatatatttgttccatgatcagttttcaatcactactgatctttaatttttaaaaatgcag

upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA17G03920.1 (Glycine max), 5'ss of exon 12
ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtttggagctgatt--ttgctgtgtaatatatttttgcagtcctg-gtatctatctgtactgattttttctggtgcaaatgcag
||||||||| || || |||||| | || ||||||||| |||| |||||||||||||| ||||||||| |||| |||||||||||||||        |||  |||||   |  | ||  | | || |      ||| ||| ||      || ||| |  | ||       
ATATGATTCCTCAAAAACATTCTCTCAAAATGTTGAATTGACAGATCCAATTATTTCTCGTTTTGATATCCTCTGTGTTGTGAAGgttatatttatattcattgcttctttgtttacctcttcatttgaatatatttat-tgagggagttctttattttacag------

upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 12
ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtttggagctgatt--ttgctgtgtaatatatttttgcagtcctggtatctatctgtactgattttttctggtgcaaatgcag
||||||||| || || |||||| | || ||||||||| |||| |||||||||||||| ||||||||  |||| ||||| |||||||||        |||  |||||   |  | ||  | | || |     ||| ||| ||      || ||| |  | ||       
ATATGATTCCTCAAAAACATTCTCTCAAAATGTTGAATTGACAGATCCAATTATTTCTCGTTTTGACATCCTCTGTGTAGTGAAGgttatatttaaattcattgcttctttgtttacctcttca-tttgaatatttat-tgagggagttctttattttacag------

upper sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 12
ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtt----tggagctgattttgctgtgtaatatatttttgca-gtcctggtatctatctgtactgattttttctggtgcaaatgcag
||||||||| |||||||||||  | || ||||||||| |||| ||||||||  |||| || ||||||||||| |||||||| ||||||    |    ||  | ||    | |  | ||  |||  | ||  |  | |      |     |  || | |  ||||       
ATATGATTCCTCGAAGACATTTTCACAAAATGTTGAATTGACAGATCCAATCGTTTCTCGGTTTGATGTCCTCTGTGTTGTCAAGgttatttttctactactcttatcttttcctttacatttctatgtgttactttaagcacgggggaaacttgtttaatgcag------

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: 72 (upstream exon), 41 (downstream exon)
Score: 14

ATATGATTCATCGAAGACATTCACCCAGAATGTTGAACTGACGGATCCAATTATTTCACGTTTTGATGTCCTTTGTGTTGTGAAGgtttggagct ... gcaaatgcagGACATTGTTGACCCATTTACAGATGAAATGCTTGCAAGGTTTGTTGTAGATAGTCATGCAAGATCTCAACCCAAGGGTGCTAACCTTGAAGATAGGGTTC




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