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'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaaccagtagttgatgtctcatatggatag

Basic information

species Arabidopsis thaliana
transcript AT3G45780.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: LOC_Os11g01140.1 (Oryza sativa), 5'ss of exon 19
-GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaa--ccagtagttgatgtctcatatggatag-----------------------
 ||  ||||||  | |||| |    |   || ||| | ||  | |||||||| ||||| ||||| || |||||||||||||| || ||||||||||| || ||  ||  ||    | | | || |||  |    |        |    | | ||   | |   ||| || || || | |  ||  ||                          
TGAGAAAAAAGGGAGAAAAAACGGGAGTTACCCCA-TATTTTTTGCTGAACCTATGCGAGCATCCAATTCATTTGTTGGCACGGAGGAGTACATTGCGCCTgtacgtgcatatggtcttctaacttacctgttctatactgtttggcaagcttttattcattcccaatatttcatctttggtactgagtctgtgcatccttgtctgtttgcag

upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 18
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatat-tatatataccaattta----agtacagtgattaaggtatttaccat--tgtcttaaccagtagttgatgtctcatatggatag-----------------------------------------------
||||||||||      |||||       | ||| || ||  | |||||||||||||| |||||||| || |||||||| || || ||||||||||| |||||   ||||| ||||| ||  |  ||        ||  |   || |  |||| || |    | || |    | ||   | | | | |||  |                                                 
GAAGAAAAAGAGGAGGAAGAGCAGGAGTAATCCCATATTTTTTGCTGAACCAATGCGAGCATCAAATTCTTTTGTTGGTACAGAGGAGTACATTGCACCGgtatttatatatatatgtaatatgttgttgctccactttatctatgtgattttccctaacattttcatttcttgtctctatttgacatgtgtgatagtcatcatctgttttatcaatccttgtattgtatgcatgctgtag

upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA13G40550.1 (Glycine max), 5'ss of exon 18
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagt-----------atattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaaccagtagttgatgtctca-----tatggatag
||| || ||| |||| || |||||| |   |||||| || ||||| ||||||||| | |||||||| || ||||||||||| ||||||||||||||||||||| ||           |||||||| ||    ||| |    ||   | || |||    |    | | |||    ||| |  ||||  ||     |||  | | 
GAAAAAGAAGAAACAGAAAAGTCAAGAGGTTCCAATGTTTATGGCAGAACCAATGAGAGCATCAAATTCTTTTGTTGGCACGGAAGAGTACATTGCTCCGgtttgttattcctggacatattatacattattattgagcagcaaaaactacggttcaaatacgtattttatt--gtattgaatgtaccaattattatacaca-

upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA15G04850.1 (Glycine max), 5'ss of exon 19
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagt------------atattatatataccaattta--agtacagtgattaaggtatttac-cattgtcttaaccagtagttgat-gtctcatatggatag
||| || ||| |||| || |||||| |   |||||| || ||||| |||||| || | |||||||| || ||||||||||| ||||||||||||||||||||| ||            ||| |||| ||    ||| |  || | |    |  || |   ||  ||| ||   ||   ||| || || || |   ||| |   
GAAAAAGAAGAAACAGAAAAGTCAAGAGGTTCCAATGTTTATGGCAGAACCAGTGAGAGCATCAAATTCTTTTGTTGGCACGGAAGAGTACATTGCTCCGgtttgttattccctggacatactatacattattattgagcagcaaaaaactacagttcaatatgcatggttcaaatacgtattttattgtgttgaatgta---

upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA12G07890.1 (Glycine max), 5'ss of exon 20
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaaccagtagttgatgtctcatatggatag----------------
 ||||| ||    || ||  | | |||  ||||||| || ||||||||||| ||| | |||||||| || ||||| || |||||||||||||| ||||||||| ||   || |  | |  | ||   |  |||  | | |  | |  |      |  | |   | ||   |||  | |||| | ||                 
AAAGAAGAAAGCTCAGAAAGGCCCACACGCTCCAATATTTATGGCTGAACCTATGAGAGCATCAAATTCTTTTGTGGGGACTGAAGAGTACATAGCTCCGgttcgttgtttctggacattatttcttgagcagaaaatcatttctagattcaaattcttat-ggaagc--atgcatgatatagttaacatgtttcactttata

upper sequence: AT3G45780.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 5'ss of exon 19
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtata-ttatatataccaatttaagtacagtgattaaggtatttaccattgtcttaaccagtagttgatgtctcatatggatag-------------
 ||||||| |||||| ||  ||||||| |  ||||| |||||||||||||| ||||| |||||||| ||||| ||||| |||||||||||||| ||||||||| ||  | || || |       || | |  | |  ||| |  |   |    ||  |  |  ||| || ||||   | | ||  ||              
AAAGAAAAGGCAACATAAAGGTCAACAGAACCCAATATTCATGGCTGAACCTATGCGAGCATCAAATTCATTCGTTGGTACTGAAGAGTACATAGCTCCGgtttgtgcacttttaaacctgcgctttattttattttttatgaaaagaatttctgggtctat-agttgtggatgctgcctctgtttacttgagtacagaca

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|124816045|gb|EH900911.1|EH900911
EST:     CAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCG                         GAAATTATATCCGGAGCAGGACATA
genomic: CAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatat ... atatggatagGAAATTATATCCGGAGCAGGACATA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAAAAGCAACAAAAGAGTCAACAAACTCCAATCTTCATGGCTGAACCAATGCGTGCATCAAACTCATTTGTTGGCACTGAAGAGTACATTGCTCCGgttagtatattatatataccaatttaagtacagtgattaaggtatttaccattgtcttaaccagtagttgatgtctcatatggatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA