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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgcttcttttgataatataatcagaaactgttatgaaatgttttctacattattgcag

Basic information

species Arabidopsis thaliana
transcript AT3G26440.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA08G14050.1 (Glycine max), 5'ss of exon 6
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactc--tgcttcttttgataatataatcagaaactgttatgaaatgttttctacattattgcag-----------------------------
||||||| || |||||||| ||||| || ||  | ||||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | ||||||||||||||| |   |  |   | | ||  | || |  |      |||||    | ||| |  ||||  | ||                             
GGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAAGAgtaagtattagatattatgtgtaattgtgtattttgttttaattatg----gctttgttaattaaggaagttttacttcctctctaatttcaattgcag

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgcttcttttgataatataatcagaaactgttatgaaatgttttctacattattgcag----------------------
||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | || ||||||| |||| |     |     |   || |  | | ||  | ||||  | | ||    | ||| |   |                       
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAAGAgtgagtattggatatgagagggatatttttttaaaagattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcag

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtact---------------ctgcttcttttgataatataatcagaaactgttatgaaatgttttctacat----tattgcag------
||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | |||||||||| |||| |                |  || |||| |  || | ||   ||  | | || |||| |  | | | |    |||| ||       
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAAGAgtgagtattggatatgagagggattttttttttttaaatattttattt-aatttctaatcaaatttcatatgcctctcttatttcaagtgcag

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA08G14040.1 (Glycine max), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactc----tgcttcttttgataatataatcagaaactgttatgaaatgttttctac-attattgcag----------------------------
||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | ||||| |||| |||| |     || | |  |  | | | ||||   ||  |    || || ||||| ||| |||||   |                             
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAGGAgtgagtatttaatatgatacaatacacagtttaatttcaatat-ccgtgtaaagttttatactattatccaattatttattaattgttcattaaaagattt

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactc----tgcttcttttgataatataatca-gaaactgttatgaaatgtt-----ttctacattattgcag----------------------
||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||| || || ||||||||||| || || |||||| | ||  | |||||||||| |||| |     || | |  |  | | | ||||   || |    | | || | ||      ||  | | |||  |                       
GGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAAGAgtgagtatttattgtgatacaatacacagtttaattttgatatccatgtaaagtattacactatcatcctcattaaaagattttaacttttaagttagtt

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 4
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgc-------ttcttttgataatataatcagaaactgttatgaaatgttttctacatt---attgcag
||||||| ||||| |||||||||||||| ||  | || |||||||| |||||||| || |||||||||||||| || |||||  | ||  | |||||||||| |||  |   |       |  |||| ||   ||             ||   ||  | |   |  ||   ||| |||
GGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAAGAgtgagtgttggacataaatatcttttttatggcatttgtgtttcagtctacccaacttatgtcattttccaattccag

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgc-------ttcttttgataatataatcagaaactgttatgaaatgttttctacatt---attgcag
||||||| |||||||||||||||||||| ||  | || |||||||| |||||||| || |||||||||||||| || |||||  | ||  | |||||||||| |||  |   |       |  |||| ||   ||             ||   ||  | |   |  ||   ||| |||
GGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAAGAgtgagtgttggacataaatatcttttttatggcatttgtgtttcagtctacccaacttatgtcattttccaattccag

upper sequence: AT3G26440.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 5'ss of exon 8
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgcttcttttgataatataatcagaaactgttatgaaatgttttc-tacattattgcag-----------------------------------------------------------------------------------------------------
||||||  ||  | ||| ||||||||||| |  | ||||  ||||||||||| |||||||||||||| |||||||   |     | ||| | ||      || |||    | ||||| |  ||||| |  || | || | | |   ||  | |   | ||  ||||                                                                                                        
GGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGGAGgtgagt----tacttctgtc-ataatttgttccggaagtctcagccaacttgtgagtccagaattgtgaaccgcatttacgactttaggatgtgcttttgcaacaataatgtgatacggctttaatataacgaaggctttctaacgaaaataaaataaaaaaaactgcag

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAAGAgtaagtactctgcttcttttgataatataatcagaaactgttatgaaatgttttctacattattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA