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

gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT

Basic information

species Arabidopsis thaliana
transcript AT3G16785.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 12
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
  ||  ||| | |  || | | ||||        |  | |||| | || |       |   ||||    || | | |   |  |||||||| ||||| ||| |||| ||||||||||||||||| || ||||| ||||| ||  | ||||| |  ||||| | ||| |||||| | |  |||||||
-gtatgttctgttgtaacaat-tatt-------gatggttttgatgcttcgtgttggccggttaatt--acatgtttaatta-cagGGAGGCATTGATGACGGTGGAGCAGCATCTGTTAGAGCAATTATGCACTGGCAATACAGGACCATTTGTAGAGGGCCTAATTCAATACTTAAGAATCTTT

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 14
------gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaat-gca-actttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
       ||| |||    |     | | | |||||||| || |   |   |  |||  | |||    | ||| ||  |  | |  ||     |||| ||| |||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| | | |||| || || || ||  ||  ||||||||
gttctgattaatttta-ttcttttatttttttctgtttcaacactgtaaatattgcttttgcatgaatgttagactgatttcttagttatctagGGCGGTCTTGATGATAGTGGTGCAGCATCTGTGAGAGCCATAATGCATTGGCAGTATCGAACCATTTGCCGAGGGCAGAATTCTATCATGCATAATCTTT

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 14
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaat-gca-actttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
|||    |    |  |    | |||||||||| || |   |   |  |||  | |||    | ||| ||  |  | |  ||     |||| ||| |||| || || ||||||||||| || || ||||||||||||||||||||||||||||| | | | || || || || || |||  ||||||||
gttccgattaattttattcttttattctgtttcaacactgtaaatattgcttttgcatgaatgttagactgatttctcagttatctagGGTGGTCTTGATGATAGCGGTGCAGCATCCGTGAGGGCCATAATGCATTGGCAGTATCGAACCATTTGCCGGGGGCAGAATTCTATCTTGCATAATCTTT

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 15
--gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
    || | | |  ||   |  |   |    ||| |||  |        ||         ||||||        |     |    ||||| ||| | || ||  |||| || |||||||| ||||||||||||||||||||||||||||| |||| | ||||| |||| ||||||||    |||||||
gtactattcttgatta---agttccttgacatttgaaataaaagagatttg--------ttttttatttttgtcttgaatttcaacagGGTGGTTTGGATGATGGTGGGGCGGCATCTGTAAGAGCCATAATGCATTGGCAGTATCGAACTATATGCCGAGGAAATAATTCAATATTACAAAATCTTT

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ12042 (Selaginella moellendorffii), 3'ss of exon 14
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
                               |||         ||| |  ||||      |||||||  | || |   | | | |||| ||| | || || |  || |||||||| ||||||||||| || |||||||| ||| ||||||||| | | ||| ||   ||  | ||||    |||  
------------------------------gtaaggttccaaactcgttaaatggcgacatttaaac--atgttttccttttgtagGGTGGTGTCGATGATACAGGAGCAGCATCCGTTAGAGCCATCATTCATTGGCAATATAGAACCATATGCCGTGGAAATTCGTCGTTGTTGAAGCGTCTAA

upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: EFJ21271 (Selaginella moellendorffii), 3'ss of exon 14
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
                               ||| |       ||| |  ||||      ||||| |  | || |     | | |||| ||| | || || |  || |||||||||||||||||||| || |||||||| ||| ||||||||| | | ||| ||   ||  | ||||    |||  
------------------------------gtaagattccaaactcgttaaatggcgacatttaagc--atgttttccatttgtagGGTGGTGTCGATGATACAGGAGCAGCATCTGTTAGAGCCATCATTCATTGGCAATATAGAACCATATGCCGTGGAAATTCGTCGTTGTTGAAGCGTCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT
                        aactttttaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttcggctagaaaagtgtattctgtttaaaaagatttgctcctgcaatgcaactttttaaaccaacgtatgtgtctggcagGGAGGTATTGACGACAGTGGTGCAGCATCTGTTAGAGCCATAATGCATTGGCAGTATCGAACCATATACAGAGGACATAACTCAATATTGACTAATCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA