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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaaatttcatttgatctttactcaatgatttagtgttctttgacgtcctgaatgtttcttcagtccctcattgtactaattttgatatctgtcatttc...

Basic information

species Zea mays
transcript GRMZM2G139583_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 11
GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaa--atttcatttg-atctttactcaatgatttagtgttctttgac-gtcctgaatgtttcttcagtccctcattgtactaattttgatatctgtcatttc
|| ||||||||  | ||||| |||||  |||||||||| || |||||||| ||||| || |||||||| ||||| |||||||| ||  |||  ||||||||||||  |    ||||   | || ||||||| ||    ||   | ||||  |  |   | |    | | ||    | | | | |||   ||   ||||  ||| 
GATAATGTTTTCACGATGGTTTCTGCAATTCTATGGCTAGGAGATGTCTCTTTCACGGTCATTGACAACGAAAACCATGTTGAGATTGTTGTAGATGAAGgtaaaggaaaatatttatgttttcactcaataatgctatgagttatgaccatgttttgtatgatctaattctaatactct-ccaatgccga---ctgttctttt
















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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 373

GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaaatttc ... gctattgcagCTTCAAAAATGGTTGCAGAACTTCTTGGCTGCAGTATTGAAGATCTCAATTTAGCTTTGACAAAGCGCCACATGAAAGTAAATAATGAAAACATTGTCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 179

GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaaatttc ... gctattgcagCTTCAAAAATGGTTGCAGAACTTCTTGGCTGCAGTATTGAAGATCTCAATTTAGCTTTGACAAAGCGCCACATGAAAGTAAATAATGAAAACATTGTCCA


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 141

GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaaatttc ... gctattgcagCTTCAAAAATGGTTGCAGAACTTCTTGGCTGCAGTATTGAAGATCTCAATTTAGCTTTGACAAAGCGCCACATGAAAGTAAATAATGAAAACATTGTCCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 303

GAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAATTGACAATGAAAATCATGTTGAAATCATTGCGGATGAAGgtaaaatttc ... gctattgcagCTTCAAAAATGGTTGCAGAACTTCTTGGCTGCAGTATTGAAGATCTCAATTTAGCTTTGACAAAGCGCCACATGAAAGTAAATAATGAAAACATTGTCCA