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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagccttaggtgtccaattggtcttgttgcttttagatcctccaccatttctaatgtcttttactcttatccacccag

Basic information

species Zea mays
transcript GRMZM2G470556_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaag-ccttaggtg----tccaattggtcttgttgcttttagatcctccaccatttctaatgtcttttactcttatccacccag
||||||||||||| ||||||||||| || |||||||||||||| || || ||||||||||||||||| |||||||| ||||| |||||| || | |||||||||| |||| | ||    | |  ||  |||  |  ||||||| || || |   |   | || |||  |   ||| | ||| |||
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgtactt-tacactcag

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA15G00250.1 (Glycine max), 5'ss of exon 11
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagccttaggtgtccaat-tggtcttgttgct----tttagatcctccaccatttctaatgtcttttactcttatc-cacccag--------------------------------------
| ||||||||||| || || || || |||||||||||||| || |||||||| ||||| || ||||| || ||||| |||||||| || ||  | || |||||||  | |    | ||   |   | |  ||      |  || | |   |   |||   ||||     |  || |    || ||                                       
GCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATCCGGAAATTCAGAAAACTCCAAAATCTGATAAGCTTAGGGAATGgtaagtttaaaagcttcaggataaacataatgagaaagtgaagttgcctaattgttttacatgtacaaaatgctcaaggtactcatttctaactatagtttgtttcatgaacaatttccaacag

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagccttaggtgtccaattggtcttgttgcttttagatcctccacc-----atttctaatgtctt-----ttactctta-tccacccag
| |||||||||||||| |||||  |||||||||| ||||| ||| ||||||||||||| || ||||| || || || || ||||| ||||| || || |||| || || |  ||||   |||||  | ||  |  || |   | |        ||   | |  || |     || ||| |  || || |||
GCTACATATGGGCTTGTCCACCACTGAAGGGTGAGGATTATATCCTATATTGCCATCCAGAAATTCAGAAAACACCAAAGTCTGATAAACTACGGGAATGgtcagtct-aattgtct--ttggtgattttcttcatacagttttcgtaggaaaatcctttacatcctccaatttgctcctggtctacacag

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagccttaggtgtccaattggtcttgttgctttt----------agatcctccaccatttc-taatgtcttttactcttatccacccag
| || |||||||| ||||| ||| | |||||||||||||| || ||||||||||||||||| ||||| || || || ||  |||| |||||  | || ||||| |   ||  |       ||   |  ||| ||||          |||   |    ||| |  | |||  |  ||||| |  |    |||
GCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATCCTGAAATTCAGAAAACGCCAAAGACTGATAAACTAAGGGAATGgtatggaatatatactttcctgtaatacttgtttttcacgtgtaagagagaatattgcatataatgatgcataatactccttccttttcag

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT1G79000.1 (Arabidopsis thaliana), 5'ss of exon 12
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagcc---ttaggtgtcca--attggtcttgttgctttt---------agatcctccaccatttctaatgtcttttactcttatccacccag
| |||||||||||||| || ||  ||||||| || ||||| ||||||||||| ||||| || ||||| ||||| || |||||||| ||||| || ||||||| ||     |||  | |     ||     | ||    |||         |  || |  ||    || ||   |      | |||| | |    
GCTACATATGGGCTTGTCCGCCGCTGAAGGGCGAGGATTATATCTTATATTGTCATCCAGAAATTCAGAAGACGCCAAAATCTGATAAACTACGAGAGTGgtcagttcatttacctttttgggatgaacttcgtaaactttcatatgaaaaagtcatttacatcatccaactgcccacgttgttattcgcag--

upper sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 5'ss of exon 10
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagccttaggtgtccaattggtcttgttgcttttagatcctccaccatttctaatgtctttta-----ctcttatccacccag---------------------------------------
| || ||||||||||| || ||||||||||||||||| || || || |||||||||||||| ||||| || || || |||||||| |||||  | || |||| ||  |   ||   |  | |    |     ||| |     |  || | ||  ||| || |  |      | |||| |  ||                                         
GCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATCCTGAAATTCAGAAAACACCAAAATCTGATAAACTCAGAGAATGgtgagagt--agttatcgttagaaaatagaagtttgaatcattttactagtttcaatttcctgaaataagtttttattcctccctaatccttctggttggtgtgcacaaaattttctatttcag

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: 46 (upstream exon), 48 (downstream exon)
Score: 30

GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagcctta ... atccacccagGTACTTATCGATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATCACTATGGGGGGATGCAAGGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 47

GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagcctta ... atccacccagGTACTTATCGATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATCACTATGGGGGGATGCAAGGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagcctta ... atccacccagGTACTTATCGATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATCACTATGGGGGGATGCAAGGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaagcctta ... atccacccagGTACTTATCGATGCTTCGGAAAGCTTCTAAGGAGGAAATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATCACTATGGGGGGATGCAAGGCT