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

GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactcgcaatatttcggtttttgtagtttgattttatcggtgtatctcaaggtttttttgcttgctttctacag

Basic information

species Arabidopsis thaliana
transcript AT5G43810.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G38770.1 (Glycine max), 5'ss of exon 16
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactcgcaatatttcggtttttgtagtttgattttatcggtgtatc--tcaaggtttttt--tgcttgctttctacag---------------------------------------------
||||||| |||||||||||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||| || || |||||||| || |||||| |||| |||     |||||  |  ||||  || ||| ||| |     |  ||   || |||||||||  || ||| |||| |                                                
GTTTAGTATGTGCTCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTTGGCAAGACCCTGTTCGTGGCACAGTTAGTGGTGGCATGATCCGgtactaat----aatat--caattttactattttaattctgaatattaattgttctaggttttttgatgattggtttcaattatattatatcttagtttataattttcatgtgtccttttatgtgcag

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA20G28970.1 (Glycine max), 5'ss of exon 16
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgta------ataactcgcaatatttcggtttt---tgtagtttgatttta-tcggtgtatctcaaggtttttttgc-ttgctttctacag----------------------------------
|||| || || || |||||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||| || || |||||||| || |||||| ||||      ||| ||   | |||||   || |   | |   ||| | |   | | ||| |    || ||   ||   || | || ||                                     
GTTTGGTATGCGCCCAAGCTCATAGGCAGGAACTTATACAAGATTTGTACAAAACTTGGCAAGACCCTGTTCGTGGCACAGTTAGTGGTGGCATGATCCGgtactaataatatcttttactattttaattctgaatattaattgttctaggttgttgtgtgatgagtttcaattatattacattgtattttagtttataattttcatgtgccctttttgtgcag

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G00530.1 (Glycine max), 5'ss of exon 7
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactcgcaatatttcggtttttgtagtttgatt-ttatcggtgtatctcaaggtttttttgcttgctttctacag-------------------------------------------------------
||||||| |||||||||||||| || || ||||| |||||||||||||| ||||  ||||| || |||||||| ||    || ||||| ||||||||| |||||||   |   | || |    |  | |  | | ||| |||  | ||| | |    ||    |     | |||  |||                                                        
GTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGTGGCACGACCCTGTTCGTGGCTTAGTCAGTGGTGGTATGATCCGgtaata---caagaaatatgaactcctattttctaattcttaatgttgtttttggttgtgagatgatgggattttcacaatataattttcattttcctcctgtatctaaatattgttttttgtccttttttgcag

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA02G00510.1 (Glycine max), 5'ss of exon 15
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgta--ataactcgcaatatttcggtttttgtagtt--------tgattttatcggtgtatctcaaggtttttttgcttgctttctacag---------------------------------------------
||||||| |||||||||||||| || || ||||| |||||||||||||| ||||  ||||| || |||||||| ||    || ||||| || |||||| ||||  | ||     |  |  ||  ||||| || ||        || ||||    |||   |    || ||||     | |  | | ||                                              
GTTTAGTGTGTGCTCAAGCTCATAGACAGGAACTCATACAAGATTTGTACAAAATGTGGCACGACCCTGTTCGTGGCTTAGTCAGTGGTGGCATGATCCGgtattacaagaaatatgacctccttttttctaattctcaatgttgtttttggttgtgggacgatgggattttgacaatacaattttcactttcctcctgtatctaaatattgttttttgtatccttttttgcag

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 5'ss of exon 13
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactcgcaatatttcggtttttgtag-tttgattttatcggtgtatctcaaggtttttttgct-----tgctttctacag------------------------------------------
| || ||||||||||| |||||||| || ||||| ||||||||||| || || |||||||| ||||||||||| || || |||||||| || |||||  ||||  |     |     |  | ||| | | |  ||   | | |  ||| || |  |  ||||| | ||     | | || |   |                                          
GATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACATGGCATGATCCTGTTCGTGGCACAGTTAGTGGTGGCATGATTCGgtataaggattcttctctatgttttatctggactttcctgtgtgtgtgcatgtgcatatttttatactgtatgtacattttttggttctagtatttagatttctttttcctcttgctttctatgcag

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: EFJ19862 (Selaginella moellendorffii), 5'ss of exon 15
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgt-aataactcgcaatatttcggtttttgtagtttgattttatcggtgtatctcaaggtttttttgcttgctttctacag
|| |||| || |||||||||||||| |||||  | || |||||||||||||||||||||   ||||||      || ||  | | |||||||||||| |||| | || |    | | ||| | |||   || | || |   ||  |   |  | |                         
GTCTAGTCTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACATGGGTTGATCCTCAGAAGGGAACCATGAATGGCGGTATGATAAGgttagtagcggtgagttttttgttttacttattgtgctaacatacgcaaactttag------------------------

upper sequence: AT5G43810.2 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: EFJ19863 (Selaginella moellendorffii), 5'ss of exon 15
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgt-aataactcgcaatatttcggtttttgtagtttgattttatcggtgtatctcaaggtttttttgcttgctttctacag
|| |||| || |||||||||||||| |||||  | || |||||||||||||||||||||   ||||||      || ||  | | |||||||||||| |||| | || |    | | ||| | |||   || | || |   ||  |   |  | |                         
GTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACATGGGTTGATCCTCAGAAGGGAACCATGAATGGCGGTATGATAAGgttagtagcggtgagttttttgttttacttattgtgctaacatacgcaaactttag------------------------

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|47828868|gb|CK118552.1|CK118552
EST:     AAAACATGGCAAGATCCTGTTCGCGGTACTGGTAGTGGCGGTATGATCAG                         GGACCTTCTTATCTCATTTAGAAA-GCA-CAGGG
genomic: AAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactc ... ctttctacagGGACCTTCTTATCTCATTTAGAAAAGCAACAGGG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACATGGCAAGATCCTGTTCGCGGTACTGTTAGTGGCGGTATGATCAGgtaataactcgcaatatttcggtttttgtagtttgattttatcggtgtatctcaaggtttttttgcttgctttctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA