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'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG

Basic information

species Arabidopsis thaliana
transcript AT3G13870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 5
gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
||||||  || |   |  | ||    | |||    || |   |   |          |||  |   |    | |   || |    ||| |     |||||||||||||| |||||| | ||||| || || || ||||||||||| |||||||| ||||||
gtaagttctgctgaatgatgtg----cgttggacctattgtttcctaaattggacagtgcaatgagtgaacttttaattat----tttcttccatagGTGGTGTCATGACATTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 3
gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG----
||||||    ||  | |     |  |  |||   ||     ||    |  ||  | |  || | |  | || | |  |  |  | |||    |  |||||||||||||| |||||  | ||||| || ||||| || |||||||| |||||||| ||||||    
gtaagtttgtttagtgaagcgatcgttgttggacttgg--aatcttggacctattatccccttgtgcaactcaaaattcttttgttttcctgtatagGTGGTGTCATGACATTGGCAGAGAACAGGCTGCAAACAAGCCTCTTTTGAAGACTGTTTTCCAGGCAA

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------gtaagtggtgttctttactttgttttctttgatattaatagataacagga-cttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
                                                                                |||| || ||| |||  |||||||||  |   | ||  ||  | | |    |||  |||||    || |||||   ||  ||   |||  |  |  |||||||||||||| |||||||| |||||||| |||||||| || |||||||| |||||||| |||
gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtactt--ctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctccccttt-attatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatc--ttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
                           ||| | |  ||||  |  || | || |  | ||   ||   |    | |  |||||    || | |     | |||||||   |    | |  |  ||||||||||||||||||||||| || || || |||||||| |||||| | || ||||| ||||||
gtaagttttattacaaaacaaggcatataacttggattctacagattatgtt-tcagttaaacatgttttgaggtatctctttaatggtttatgcgagtaatatcttgaagcgaattttgtttagGTGGTGTCATGATATTGGTCGTGAGCAGGCTGCAAATAAGCCTCTTCTGAAAACTGTATTCCAG

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ31796 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatcttatatcttc-tcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
                                                 | || || |      |      | ||| ||| || |   | |  |  ||||||||||||||||||||||| || || ||||| || |||||| |  | ||||| || || |||
----------------------------------------------gtaagttgttgtagtacttcgtctgtttatgttcgtcagtactttcgtaaagGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAG

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ38064 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtggtgttctttactttgttttctttgatattaatagataacaggacttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
                                              | |   || |    | || |    |||| | |  || |   | |  |  ||||||||||||||||||||||| || || ||||| || |||||| |  | ||||| || || |||
--------------------------------------------gtaagttgtcgtagtacttcgtctgtttatgt-tcgtcagtactttcgtaaagGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAG

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|164109402|gb|ES085428.1|ES085428
EST:     CACTTGCAGTCTCAGACATAGTTCTTATAAACAT                         GTGGTGTCATGATATTGGTCGGGAACAAGACAGCAAATAAACCTCTTTTAA
genomic: CACTTGCAGTCTCAGACATAGTTCTTATAAACATgtaagtggtg ... tgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAG-CAGCAAATAAACCTCTTTTAA
EST: gi|116444534|gb|EG487126.1|EG487126
EST:     CAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACAT                         GTGGTGTCATGATACTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAA
genomic: CAGAGTGCTCTTTTTGCACTTGCAGTCTCAGACATAGTTCTTATAAACATgtaagtggtg ... tgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAA
EST: gi|164028597|gb|ES214154.1|ES214154
EST:     CACTTGCAGTCTCAGACATAGTTCTTATAAACAT                         GTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTT-AAA
genomic: CACTTGCAGTCTCAGACATAGTTCTTATAAACATgtaagtggtg ... tgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAA
EST: gi|124976365|gb|EL049787.1|EL049787
EST:     TGCAGTCTCAGACATAGTTCTTATAAACAT                         GTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAA
genomic: TGCAGTCTCAGACATAGTTCTTATAAACATgtaagtggtg ... tgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaggacttcttttgccgtctttatcttatatcttctcggatttgtaatgcagGTGGTGTCATGATATTGGTCGGGAACAAGCAGCAAATAAACCTCTTTTAAAGACTGTGTTCCAG
 agataac  putative branch site (score: 3)
                      tttatcttatatctt  TA-rich tract