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

gtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttgtgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG

Basic information

species Arabidopsis thaliana
transcript AT3G14350.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 14
-----------gtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttg-----tgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG
           ||  | ||    ||    || | ||  ||     || |   |     |  || || | ||  || |||   | |     ||  ||||||        |   ||||||| ||||| ||||||| || || || |||||  |||||||||||||||| || || || |||||||| ||||  |||||||||||||| ||  | ||||||
gtgaattaatggttttctttatgtctgc-tctcacgtttttgagcaatattctgcagattttgaaattatgcaca-aataataatgttgtctcctgattgcaaaacattccatgacagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG

upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 16
--------gtacttttacaatccatat-ccctcgccttcctaaaaaa-acttaagagtgatgcaaatgtgttcaga-attgaagtaagtcctggtgattgttg-----tgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG
         |  ||||    |   | | | ||| | ||  | |  || | |    ||  ||  |||| | |  ||| ||   | |     ||  ||||||        | ||| ||||| ||||| ||||||| || || || |||||  |||||||||||||||| || || || |||||||| ||||  |||||||||||||| ||  | ||||||
gtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaat-tatgtagatataataatgttgtctcctgattgcgaaacattctgtaacagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG

upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
gtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtga--tgcaaatgtgttcaga-attgaagtaagtcctggtgattgttgtg-------tgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG
       ||  ||  |||| |||     |   | || |  || |   | |  || | |    |||| | ||| | |          ||||||||          |   ||||| ||||| | || || || ||  | |||||  |||||||||||||||| || || || || ||||||||||  |||||||||||||| ||  |  |||| 
------gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA

upper sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 14
-----------gtactttta-caatccata---tccctcgccttcctaaaaaaacttaagagtgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttgtgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG
           | |||  || | |||||     ||| |  ||||  |  || |    | ||        |     ||    | | |  ||| |  |  || |     | | ||||||| | ||||| ||||| || ||||| |||||  ||||||| || ||||||||||| ||||| |||||| |||  |||||||||||||| || |||||||||
gtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactatta-tgttaacattttctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCTTCATGACATCGATGCTCTGGCTAAAATGGTTGATCCGGCACTCAAAGGG

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|164227395|gb|ES168829.1|ES168829
EST:     TAGTGATGCTCGAGCTTTTAACCCGAAG-AAACCATTCGACAG                         CACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCT
genomic: TAGTGATGCTCGAGCTTTTAACCGGAAGAAAACCATTCGACAGgtacttttac ... tgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCT
EST: gi|164010351|gb|ES050759.1|ES050759
EST:     GAAGAAAACCATTCGACAG                         CACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCT
genomic: GAAGAAAACCATTCGACAGgtacttttac ... tgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttgtgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG
                  aattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtgatgcaaatgtgttcagaattgaagtaagtcctggtgattgttgtgtgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC