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

GAACATTGTAAGGATTAAGCTTCTTCGGAACAAACCTGACCATGCCCTTGTCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccatgtccctttatttgtgcatttgagattgtacttgggacaagttccgagttacaaagatgtgaaatggaattgttaatttatgcaaagttttgtttcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G43190.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA16G27970.1 (Glycine max), 5'ss of exon 12
GAACATTGTAAGGATTAAGCTTCTTCGGAACAAACCTGACCATGCCCTTGTCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtc-catgtccctttatttgtgcatttgagattgtacttgggacaagttccgagttacaaagatgtgaaatggaattgttaatttatgcaaagttttgtttcttttgcag
||||||||| || ||||| ||||| || || || || || ||||| ||| |||||||||| |||||||||||||||||| | ||||||||||| || |||||||||  | ||| |   |  |  |  || |     | |  ||   | | ||     |||| |  | |||    |  ||||||    |   |  || | |||            
GAACATTGTCAGAATTAAACTTCTCCGAAATAAGCCAGATCATGCACTTATCCAAATGGGAGATGGTTTCCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttcttgtgctccttatactagatcttgtgatatctttacta-atgtgaaaggttatattgttgtttgttataattgt-ggctggagataattgttg------------

upper sequence: AT1G43190.3 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA02G08870.2 (Glycine max), 5'ss of exon 8
GAACATTGTAAGGATTAAGCTTCTTCGGAACAAACCTGACCATGCCCTTGTCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtc-catgtccctttatttgtgcatttgagattgtacttgggacaagttccgagttacaaagatgtgaaatggaattgttaatttatgcaaagttttgtttcttttgcag
||||||||| || ||||| ||||| || || || || || ||||| ||| |||| ||||| |||||||| ||||||||| | ||||||||||| || |||||||||  | ||| |   |  |  || ||       | |  ||   || | |    |     |  | |||    |  ||||||   |  |   | | | | ||           
GAACATTGTCAGAATTAAACTTCTCCGAAATAAGCCAGATCATGCACTTATCCAGATGGGAGATGGTTTTCAAGCTGAATTGGCAGTACATTTTCTGAAGgtttgtttcttgtacaccttatgctggatcatgtgatatcttt---actaatgtgaaaggttattgttgtttgttataattgtgcctgaagatatattatggt-----------
















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|124886066|gb|EH964968.1|EH964968
EST:     TGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAG                         GGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
genomic: TGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccat ... tcttttgcagGGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
EST: gi|125316060|gb|EL330145.1|EL330145
EST:     CGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAG                         GGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
genomic: CGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccat ... tcttttgcagGGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
EST: gi|47829251|gb|CK118935.1|CK118935
EST:     TCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAG                         GGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
genomic: TCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccat ... tcttttgcagGGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTTCTCAAAGCATCCA
EST: gi|125245165|gb|EL259250.1|EL259250
EST:     TCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAG                         GGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTT
genomic: TCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccat ... tcttttgcagGGAGCAATGCTGTTTGGTAAGCGGTTAGAAGTAAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATTGTAAGGATTAAGCTTCTTCGGAACAAACCTGACCATGCCCTTGTCCAAATGGGCGATGGTTTCCAAGCTGAACTTGCAGTACATTTCCTCAAGgtttgtccatgtccctttatttgtgcatttgagattgtacttgggacaagttccgagttacaaagatgtgaaatggaattgttaatttatgcaaagttttgtttcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA