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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag

Basic information

species Arabidopsis thaliana
transcript AT1G45332.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 11
TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatattt-ttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag
||| ||||||||||| || || || ||||| || ||||| || ||||||||||| |||||||| |||||    ||  | || ||||||||||||||||| ||| ||      |  |||  |  |  || ||    |||||   |    ||   |   | |   ||||    || | ||||    |||| |       
TACAGATGGATCAGTGAAATATACCATGACTTCCATGAATGTCCCTGAACCTGTGATGTCCTTGGCTGTCTCCCCTATATCTAAAGATTCTGGAGGACAAgtatct------acttttctattttcaagaatgctatattaactttaataccatacatgtgacaaataattaattaaaataacatttcag-------

upper sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G056393_T02 (Zea mays), 5'ss of exon 11
TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag
|||||||||| |||| || || || ||||| || ||||| || ||||||||||| |||||||| || |||  |||  | || ||||| |||||||||||||||  | || |      | ||   |  || ||  | |||   |  |||  |       || ||  |    |    ||||  |  |  |  | | ||
TACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcatatttttcatcaaaagggtacgactgc-tatacatagtttgtt---acccta-gatgtcctaagtgaaaatacacctatccctttcag

upper sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA01G14800.1 (Glycine max), 5'ss of exon 6
TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag---
||| || || ||||| || ||||| ||||| || ||||| |||||||| || || ||||| ||||| || || |||||||| |||||||||||||| || || | | || |    | || | |     ||||  |     |    || ||    ||| ||  |  |    || || | |    | |    || |     
TACTGACGGTTCAGTTAAATACACAATGACTTCTATGAATGTTCCTGAGCCAGTGATGTCATTAGCCGTACAGCCGGTTTCTAAAGATTCTGGAGGGCAAgtgagtaatttattttatgtaac-atgtcaacccctgccctagatttgaaaaacgttgtatcacct----aattggatttctctgtgaattgcttacag

upper sequence: AT1G45332.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA11G16460.1 (Glycine max), 5'ss of exon 11
TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag---
||| || || ||||| || ||||| ||||| || ||||| |||||||| || || ||||| |||||||| || || || || |||||||||||||| || || | | || |    | || | |     ||||  | |   |    || ||    ||| ||  |  |    || || | | | |  |    || |     
TACTGACGGTTCAGTTAAATACACAATGACTTCTATGAATGTTCCTGAGCCAGTGATGTCATTAGCTGTACAGCCAGTCTCTAAAGATTCTGGAGGGCAAgtgagtaatttattttatgtaac-acgtcaaccccctgcctagatttgaaaaaagttgtatcacct----aattgga-tttctcctgaattgcttacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACGGATGGATCAGTCAAGTACACGATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCGGTTTCAAAAGATTCTGGAGGACAGgtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaatctattttccggtgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA