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'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgccgtttttccctttcctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG

Basic information

species Arabidopsis thaliana
transcript AT5G63960.2
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 28
gtatgctgccgtttttccctt----tcctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG
||| | |      | ||  |     |    | |      ||   | |   ||     ||| | |   |||    | | ||||  ||||||| ||   | | ||||||||||| ||||| |||||||||||||| |||||||| |||||||| || ||  | ||||| ||
gtacgatatatcctctcaataagggtttactgggtctcctggcgtttgattactggctga-attaatgttaacgtctgcagTTTCTGAGCTGGAGATGCTCTTTGGGAGGCTCTGGACGCAGTGCCAGGAGTGCCAAGGCTCCCTTCATCAGGACGTTCTCTGCACAAG

upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 12
---------------------gtatgctgccgtttttcccttt---cctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG
                      |       | || | || ||     |  ||  ||| |      | |  | | |  | | | ||| | |   ||   ||||  |||| || ||   | | ||||||||||| |||||||| ||||||||||| ||||| ||||| || || || ||  | ||||| ||
gtacgtgctgtacactctgaaatgcatctacattatgcctttggaagcactatgctcctgagctaaccactgacagatcaaaattttgct---ttccgcagTTTCTGACCTGGAGATGCTCTTTGGGAGGCTATGGACACAATGCCAGGAGTGCCAAGGATCTCTGCACCAGGACGTTCTCTGCACAAG

upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA06G16110.2 (Glycine max), 3'ss of exon 28
---------------------------gtatgctgccgtttttccctttcctatagactctttgatatatctataaaatttgatactttcgttgtgttatt-cagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG
                            | | |   ||||||    |     || |   |     | | | |||   ||   | |  |  || |||| | | ||||| ||||||| ||   | ||||||||||| ||||||||||||| |||||||| ||||| || |||||||| |||||  | ||||||||
gtaggcatctcttgagctctctgttcaatttccaatcgttttgttgtactggatggttccagatgtttttttattggataaaacaagtg-gtggtgtgactgcagTGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACCAG

upper sequence: AT5G63960.2 (Arabidopsis thaliana), 3'ss of exon 28
lower sequence: GLYMA04G38800.2 (Glycine max), 3'ss of exon 12
---------------------------gtatgctgccgtttttccctttcctatagactctttgatatatctataaaatttgatactttcgttgtgttatt-cagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG
                            | | |   | ||||    |     || |   |     | | | |||   ||   | |  |  || ||||   | ||||| ||||||| ||   | ||||||||||| ||||||||||||| |||||||| ||||| || |||||||| |||||  | ||||| ||
gtaggcatctcttgagctctctgttaaatttccaatcattttgttgtactgcatggttccagctgtgt-tttattggataaaacaagtg-gtggtgtggctgcagTGTCTGAGCTGGAGATGCTTTTTGGGAGGTTGTGGACACAGTGTCAGGAGTGCCAAGGTTCACTTCATCAGGATGTTCTCTGCACAAG

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|163983210|gb|ES114600.1|ES114600
EST:     GAAGAGAAGCCGAGTTATATTGC-AAAACGTGTCTCAAG                         TGGCTGAGCTTGAAGAGGTTTTTGGGAGGCCTGTGGACACAGTGCCAGGAG
genomic: GAAGAGAAGCCGAGTTATATTGCAAAAACGTGTCTCAAGgtatgctgcc ... tgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGC-TGTGGACACAGTGCCAGGAG
EST: gi|164187325|gb|ES169661.1|ES169661
EST:     GAAGAGAAGCCGAGTTATATTGCAAAAACGTGTCTCAAG                         TGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGT
genomic: GAAGAGAAGCCGAGTTATATTGCAAAAACGTGTCTCAAGgtatgctgcc ... tgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG
                            atttgat  putative branch site (score: 5)
           tttgatatatctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgccgtttttccctttcctatagactctttgatatatctataaaatttgatactttcgttgtgttattcagTGGCTGAGCTTGAAGAGGTTTTTGGGAGGCTGTGGACACAGTGCCAGGAGTGTCAAGGCTCTCTTCATCAAGATGTCTTGTGCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG