Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagagaaaattaaaaaatgaggcatgcatagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT

Basic information

species Zea mays
transcript GRMZM2G313536_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 15
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagagaaaattaaaaaatgaggcatgcatagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT
                                      ||  ||| ||| |   |  |  |    || ||| ||      | | || | |||||  ||  |||| |    | || |   | |  ||    |||    | |       ||||    ||||||||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||
------------------------------------gtatgtgcgcatgcctttagctcctgaaagtcacatta------tgcctgaaattcttgtttgatttcgattt-gtgacatacataggatataacattt-caatg------cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAAT

upper sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 15
gtatgtgtcactgttgtatataactcctttgttttttaataagcgtatgacccgatattatttgtgttacactagaaacatacatgcatttctttattcttttctagagagagaaaattaaaaaatgaggcatgcatagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT-----------------------------
                                      ||  ||| ||| |   |  |  |    || ||| ||      | | || | |||||  ||  |||| |    | || |   | |  ||    |||    | |       ||||    ||||||||||||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| |||||||||                             
------------------------------------gtatgtgcgcatgcctttagctcctgaaagtcacatta------tgcctgaaattcttgtttgatttcgattt-gtgacatacataggatataacattt-caatg------cttatatatatggacagGTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAATGTGAGTTGAATTAATAATATGTTGCCTTG
















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), 49 (downstream exon)
Score: 89

CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTGgtatgtgtca ... ttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTGgtatgtgtca ... ttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTGgtatgtgtca ... ttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

CTGCCATCATGAATTGGAGACTGCACGGATTAATGGGCTGCTTGGAAATATCGATGCAAACACTGGTGATCCTCAAGTTGgtatgtgtca ... ttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaaaattaaaaaatgaggcatgcatagtaacttaccttaccgttatggacagGTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAAT
     aaattaaaaaatga  TA-rich tract