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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgttattttatattgcaag

Basic information

species Zea mays
transcript GRMZM5G830776_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g04450.2 (Oryza sativa), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgttattttatattgcaag
||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||| | |||||||| |||||||||| ||| ||||| |||||| | | ||  |||   ||| || | ||  | ||| | |||   ||| ||| | ||| |||
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTTGAAATGGATGGCCAAAAATACATATATGAGgtaaatgtgatatcgtattat-aataatgaacatgatctgttcacttgccctat-tcttatgtttaatttctgttggaag

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G34340.1 (Glycine max), 5'ss of exon 5
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgta--attgtcatat-catattattagtgatat-acaaattctctttaattttcttatat-attagtgttattttatattgcaag---------------
|| |||||||| ||||||||||||||||||||||| |||||||||||| |  |  | ||||||||  | ||||| ||  ||||||||  | | |    |   |    ||      || |   || ||  |          |||  | || |     || | |    ||                
ATTGCACCTGTCATTCATGAATGGACCTATGATGCTATGTGCCATGATTTGTTGAATATGGATGGAGATAAATATATGCATGAGgtatgacttttgcttgtttgcccttcccttcatcatgtatgctggtcggcccaaggataagactactaaagcttcaaacaaaaaattatttactaacaat

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA03G02740.1 (Glycine max), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgta--attgtca------tatcatattattagtgat--atacaaattctctt----taattttcttata--tattagtgttattttatattgcaag----
|| |||||||| ||||||||||||||||||||||| |||||||||||| |  |    ||||||||  | ||||| ||  ||||||||  | | |        |  | |    ||  | ||  |||||| |   |      |||   |  || |  |  ||     |  |||| |   |||    
ATTGCACCTGTCATTCATGAATGGACCTATGATGCTATGTGCCATGATTTGTTGACTATGGATGGAGATAAATATATGCATGAGgtatgacttttgcttgtttgcccttcccttcatcatgtatacaagtcggccaagaataaggctactaaaacttctaacaaaaagttatttactaagtttt

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G02010.1 (Arabidopsis thaliana), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgtt-attttatattgcaag-------------------------------------------------------------------------------------
|| || ||| | || || ||||||||||||||||| |||||||||||| | || || ||||| || || ||| |  |   |||||||||| | || |    || |||    |   ||| || | |    || |   |        |    | |   ||  |   |                                                                                     
ATCGCTCCTATCATACACGAATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAGgtaattct-atttttctttcttatcctt---caacttttttccgtttctgaaaggccccgatccggactgcctaaagtccggtcgagagaagtcctagccaacgatcctattgaggatcgcgggcgttacagtttctctcttcctaatctctctaccatatgctag

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0048g00970.t01 (Vitis vinifera), 5'ss of exon 9
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgta-attgtcatatcatattattagtgatatacaaattctctttaattttcttatata-ttagtgttattttatattgcaag---------
||||| ||||| || |||||||||||||||||||| |||||||||||| |||| || |||||||| || |||||  |  | |||||| ||  |  | | || ||  |  | ||       |    |  |  |  |||  | |  |  || |     ||| |  ||          
ATAGCTCCTGTCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTGGAGATGGATGGAAATAAATATGTACACGAGgtacatctttttgttatttttgttttcatggttttgtatgttaaatatcacttgaagaacttttgctggaggatactcaaacatatattag

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv15s0045g00060.t01 (Vitis vinifera), 5'ss of exon 2
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgta-attgtcatatcatattattagtgatatacaaattctctttaattttcttatata-ttagtgttattttatattgcaag---------
||||| ||||| || |||||||||||||||||||| |||||||||||| |||| || |||||||| || |||||  |  | |||||| ||  |  | | || ||  |  | ||       |    |  |  |  |||  | |  |  ||||     ||| |  ||          
ATAGCTCCTGTCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTGGATATGGATGGAAATAAATATGTACACGAGgtacatctttttgttatttttgttttcatggttttgtatgttaaatatcacttgaagaacttttgttggaggatactcaaacatatattag

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S468_8V6.1 (Physcomitrella patens), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgttattttatattgcaag----------------------
 |  | || ||||| ||||| ||| | |||||||||||||||||||||||  |  |  | || |||||||| ||   ||| ||||||      | ||  | |  | |||  ||       ||  |||   |   ||||     |  |||   |      | ||                       
GTGACTCCGGTTATACATGAGTGGTCGTATGATGCAATGTGCCATGATCTTTTGAATTTAGAAGGCAACAAGTATTCTTACGAGgtatggaaaacatattttcttcagt--taatgggcctcattttgcatagattatgcggcatcgttgactatggcagtaaattgttctggaaccaggtttagg

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ06496 (Selaginella moellendorffii), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgttattttatattgcaag
 | || ||  |||| ||||| ||||| |||||||| |||||||||||||| || |  || || |||||||||||| |||||||||| |   | |||     |   |  ||   |  |    | ||||  |||||| |                           
GTTGCGCCATTTATACATGAGTGGACGTATGATGCTATGTGCCATGATCTTCTAGGCATCGAAGGCAACAAATACGTTTATGAGgtgaggattatagttcttgccttctgccctgaag---cgcttttcttttctgaag-------------------------

upper sequence: GRMZM5G830776_T01 (Zea mays), 5'ss of exon 10
lower sequence: EFJ05985 (Selaginella moellendorffii), 5'ss of exon 10
ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtcatatcatattattagtgatatacaaattctctttaattttcttatatattagtgttattttatattgcaag
 | || ||  |||| ||||| ||||| |||||||| |||||||||||||| || |  || || |||||||||||| |||||||||| |   | |||        ||  ||     |  |  | ||||  |||||| |                           
GTTGCGCCATTTATACATGAGTGGACGTATGATGCTATGTGCCATGATCTTCTAGGCATCGAAGGCAACAAATACGTTTATGAGgtgaggattata-------gttcttgccgccctgaagcgcttttcttttctgaag-------------------------

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: 43 (upstream exon), 40 (downstream exon)
Score: 25

ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtca ... atattgcaagGTATCAAAGATGGGTTCGGAACCTGAAAAGAAGGAATCTTTATTAGAGGATCATGATCCTCTTTGGCTTGAACTTCGCCATGCTCACATAGCTGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtca ... atattgcaagGTATCAAAGATGGGTTCGGAACCTGAAAAGAAGGAATCTTTATTAGAGGATCATGATCCTCTTTGGCTTGAACTTCGCCATGCTCACATAGCTGAT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 40

ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtca ... atattgcaagGTATCAAAGATGGGTTCGGAACCTGAAAAGAAGGAATCTTTATTAGAGGATCATGATCCTCTTTGGCTTGAACTTCGCCATGCTCACATAGCTGAT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 62

ATAGCACCTGTTATTCATGAATGGACCTATGATGCAATGTGCCATGATCTACTCGAAATGGATGGCAACAAATACATTTATGAGgtaattgtca ... atattgcaagGTATCAAAGATGGGTTCGGAACCTGAAAAGAAGGAATCTTTATTAGAGGATCATGATCCTCTTTGGCTTGAACTTCGCCATGCTCACATAGCTGAT