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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtataatgaaatcgacttgaattaggagtgaatatgtcaattagaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC

Basic information

species Arabidopsis thaliana
transcript AT5G37340.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G37340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA20G02690.1 (Glycine max), 3'ss of exon 15
-------ctgtataatgaaatcgacttgaattaggagtg--aatatgtcaattagaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC
         || ||||| |||  |  |   |||| | ||     |||| |  || |  | |   | | |  ||        |||| |  |  ||| ||       |||||||| || |||||||| |||||||| ||||| || || || ||||| || || || || || ||||| || |||||||||||||| || ||| |  | ||
gatgaatgggtttaatgcaattcagattgtttagaattgttggcatgttatctacacttagctgcatagtttttcgt--gtaaatatattcatgtctt-------acagTTGAGGAATACGAGAGGTCATGGGAACAAAATGAAGAATTAGGTCTGAATGATATAGACACCTCTTCTGCCGATGCTGCTTATGAATCAACAAATACTAC

upper sequence: AT5G37340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv01s0011g01690.t01 (Vitis vinifera), 3'ss of exon 15
ctgtataatgaaatcgac-ttgaattaggagtgaatatgtcaattaga-actggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC
||| || |      |    || ||  |  | | | | |   |   ||  | |    | ||    ||         |||  |||  |||      | || ||||||| || |||||||| ||||||||||| || |||||| ||||||| || || || || ||||||||||| ||||| || ||  | |             
ctgcattagattgcctctattaaaacatcattcactctagtatccagttattactattttttcttttgttgtgataatactgtattgtcacc--atctccagTTGAGGAATACGAGAGGTCATGGGAGCAGAATGAGGAGCTGGGTCTTAATGATATGGACACTTCTTCAGCAGATGCCGCATACAACTGA-----------

upper sequence: AT5G37340.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S83_162V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------------------------------------ctgtataatgaaatcgacttgaatta---ggagtgaatatgtcaattagaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC
                                                                  || ||||| ||    ||  ||   |    |  | |   || |    |   | |  |  |  |  |    |  ||  |||  | | | ||     |   | |||  ||||| || ||  |  |||  |||||||||||||| |||||||| || ||||| ||||||||| | || |||| |||||||||        |      
gtgcgtatctgccttctttctcaacattttatggatgccatctggctttttcctgttatgtaaggactctataacgatgatgatgtggggtgcttgatgggtccattttgggtgttaatt-atacacgatgcatgaaaaattaattatatggagtggaacattttgcagCGGAAGAATATGAACGTACATTTGAGCAAAACGAGGATTTGGGTCTTAATGACATGGATACTTCTGCTGCAGATGGTGCTTATGACAATTAGTATTTGTT

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|116485281|gb|EG527873.1|EG527873
EST:     TTTTATTTCACCAGTAACAGATGATATCAAAGATGATCATCAGCTCACAT                         TTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACG
genomic: TTTTATTTCACCAGTAACAGATGATATCAAAGATGATCATCAGCTCACATgtaagttact ... taaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC
                    aagtaac  putative branch site (score: 2)
                                      tgtttttt  putative PPT
                                   ttgtgttttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtataatgaaatcgacttgaattaggagtgaatatgtcaattagaactggagtcttggggttcaagtaacaaatgttgttgtgttttttaaactacagTTGAAGAGTACGAGAGATCATGGGAGCAAAACGAGGAGTTGGGTCTCAACGACATTGATACTTCTTCAGCTGATGCTGCTTATGAGTCCACAGAGCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT