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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactgatatgtttatttgcag

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 17
GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactgatatgtttatttgcag
|||||||||||||||||||||||||||||||| ||||||| ||||||||||| || |||||||| ||||| |||||||||||||||||||||||||||||||| || ||||    ||||  |  |       ||| ||| | || |   || |      |||| ||  | ||||  | | ||||||
GATTGAAGTTTGATGCTGCAATTCGTGAGTTCTTGAAAGGGTTTCGCCTTCCTGGGGAGGCACAAAAGATTGATCGCATAATGGAAAAGTTTGCTGAGCGgtatgtgtataaagtcttaatgctact-----tttatttgacatgtcaaccac--tggtctcaaatggt-atattatgacttgcag

upper sequence: GRMZM2G335287_T01 (Zea mays), 5'ss of exon 18
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 5'ss of exon 20
GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgta-ggtttatatgtacttata---gaaaacacaaat-----------ttctttaagattttgcccccgtcaccctcagatactgatatgtttatttgcag
|| ||||||||||| ||||||| ||||| ||||| |  ||||| || || || || || || || |||||||||||||| |||||||||||||| |||||||| ||| |     | ||||||   |      ||  |           |||  | ||  ||| |||| || || |  || | ||| ||  |   |||| | 
GAATGAAGTTTGATACTGCAATCCGTGAATTCCTTAGGGGATTCCGACTCCCTGGGGAAGCTCAAAAGATAGATCGCATCATGGAAAAGTTTGCAGAGCGgtatggtctcaccttgcttatatttggggttccatctgcttactacttttcccttaggcttttccccagttacacctaggtcctg-tagctcactttgtat
















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: 49 (upstream exon), 48 (downstream exon)
Score: 134

GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttat ... ttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 61

GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttat ... ttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 74

GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttat ... ttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 143

GATTGAAGTTTGATGCTGCAATTCGTGAGTTCCTGAAAGGATTTCGCCTTCCCGGTGAGGCACAGAAGATAGATCGCATAATGGAAAAGTTTGCTGAGCGgtaggtttat ... ttatttgcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG