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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaactctctattgcatttag

Basic information

species Arabidopsis thaliana
transcript AT4G28370.1
intron # 8
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os07g31850.1 (Oryza sativa), 5'ss of exon 8
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattt-tacgtgttccttaactctctattgcatttag
||| ||||| ||||| || ||  | ||| | || ||||| ||  | ||||||||||| || || |||||||| || || ||||||||||||||||||||||||||||||             || || | |  | ||    |   |   | |  || | | | |  |  |||||||| |   |||  ||     
TGATGGAGAGTGTTTCTCACCGATCTTATTAAATGCAACATCATTGAATGTTGAAGTTTATTACAACAAAGCAGTCAATTATACACTGATGGTCACTTTTgtatcctttgtgactcttcaactttctttgttctgattttttattggtatgtactgtactctatgtgaattccttaattgagtataccag----

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G356198_T01 (Zea mays), 5'ss of exon 7
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatccttta-ctgaaaagtcgtttactctttcat-aatagaatgccgagtt-cttgtgcaattttacgtgttccttaactctctattgcatttag----
||| || || || || || ||| | ||| |||| ||||||||| | ||||||||||| || || |||||||| || ||||| ||||||||||||||||||||||||| |  |||        |||| | ||   |  |||  ||    | |    ||| || || | |    |    |  |||  | |  | |  |    
TGATGGGGAATGCTTCTCTCCTATCTTATTGAATGCAACTTCTTTGAATGTTGAAGTTTATTACAACAAAGCAGTCAACTACACACTGATGGTCACTTTTgtatcctctggctgtttttatttttatttttatgtcgatattatctttattgatctgtccacttgtccagtctgtgaatttcttaactaaagtatggtag

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA13G37150.1 (Glycine max), 5'ss of exon 8
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactga-aaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaactctctattgcatttag
||| || || || || || || ||  |  | || ||||| ||||| ||  |||| ||||||||||||||||| |||||||||||  |||||||||||||||||||||| | | |  ||     ||||    | ||       |   ||    || ||      |  | | ||| | | | |  ||   |     
TGATGGGGACTGCTTCTCACCATTACTGTTAAATGCAACGTCTGTCAAAATTGAGGTCTACTATAACAAAGCAGTGAACTATACCTTGATGGTCACTTTTgtatccttcaatcatgaacattcttaccgccttatgtctctgtcttgatccattatgg-----tgtgagctcccttaatgtacat-ataccag-

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G33270.1 (Glycine max), 5'ss of exon 7
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaac-tctctattgcatttag
||| || || || || || || ||  |  | || ||||| ||||| ||  |||| ||||||||||||||||| |||||||||||  |||||||||||||||||||||| | | |  |     ||| |    | |  ||     | |  ||  |     ||  |  | | |||||||  |   |||  ||     
TGATGGGGACTGCTTCTCACCATTACTGTTAAATGCAACGTCTGTCAAAATTGAGGTCTACTATAACAAAGCAGTGAACTATACCTTGATGGTCACTTTTgtatccttcaatcatgaacg--ttattacagctt--taagtctctgtcttgatccattatggtgtgagctccttaatgtacatataccag----

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA06G44530.1 (Glycine max), 5'ss of exon 8
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactga--aaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaactctctattgcatttag-------------------------------
 || || || || || || |||||     | || ||||| ||| | ||  |||||||||||||||| ||||| |||||||||||  ||||||| |||||||||||||| | | |  ||  |  |||   |||  | | |   ||   |  ||  ||||   |||      ||| | | |    |||||    |                                 
CGATGGGGACTGCTTCTCGCCTTTACAGTTAAATGCAACATCTATTAACATTGAAGTCTACTATAATAAAGCAGTGAACTATACCTTGATGGTTACTTTTgtatccttcagtcatcaacattctttcagcttcaaaactgttattgtgcattactgtgtgttttcct---ttcttcaccctgttattgtgcattactgtgtgatttccttaatttacttataccag

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G13220.1 (Glycine max), 5'ss of exon 8
---------TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactga--aaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttcc-----ttaactctctattgcatttag------------------------
          || || || || || || |||||     | |||||||| ||  | ||  |||||||||||||||| |||||  ||||||||||  ||||||| |||||||||||||| |   |  ||  |  |||   |||| | | |   ||      ||  ||||   |||    | ||||      | | | ||  || |  |  |                        
CGTGGATGACGATGGGGACTGCTTCTCGCCTTTACAGTTAAACGCAACATCCATCAACATTGAAGTCTACTATAATAAAGCATTGAACTATACCTTGATGgttacttttgtatccttcagccatcaacattctttcagctttaaaactgttattgtccattactgtgtgttttcctttcttccaccctgttattgtccgttactctgtgatttccttaatgtacttataccag

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S19_103V6.2 (Physcomitrella patens), 5'ss of exon 9
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttcctta--actctctattgcatttag------
  | || || ||||| || ||| |  |  | || || || || || || || |   | || ||||||||||| || || |||||  |||||||||||||||||||||||        ||  | ||  |    || |         |   |   |  |  | ||| |  ||| |||  || ||  |  |   || |      
GCAAGGCGAATGTTTCTCACCTCTTGTCGTAAATGCTACGTCAGTGAACGTGGCTTTGTATTATAACAAAGCCGTCAATTATACGTTGATGGTCACTTTTgtatcctttttatctgggtaatatagacaag-atgaagtctccttgcagttgaggtctttattaagctttcattattacgctacacagagatttgaatcgc

upper sequence: AT4G28370.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ27372 (Selaginella moellendorffii), 5'ss of exon 6
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaactctctattgcatttag
 || || || || ||| |  |  |     | ||||||||||||||||||||||| |  ||||||| ||| || || || || ||  |||||||||||||||||||||| | |     |  ||||||       | ||  |    | |    |   |  ||       |                         
CGAGGGCGAATGCTTTCCGTCGATAGCGATCAACGCAACTTCTGTAAATGTTGAGGCGTACTATACCAAGGCCGTCAATTACACGTTGATGGTCACTTTTgtatccttcattcctttgctgtttacc------tgatgcagctgctatccttgacgagatgcctttag-------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGGAGATTGTTTTTCCCCTTTGTTACTGAACGCAACTTCTGTAAATGTTGAAGTCTACTATAACAAAGCTGTGAACTATACACTGATGGTCACTTTTgtatcctttactgaaaagtcgtttactctttcataatagaatgccgagttcttgtgcaattttacgtgttccttaactctctattgcatttag

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG