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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcag

Basic information

species Arabidopsis thaliana
transcript AT5G03540.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 11
CGCAA-TGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttac-tgcgaaggcttttctaatatttgattgaaa--tgtaaaaaaacctaaatgagat-tttaacctatgatcgatgcag
 |    ||| | |||||||| || |||||  | ||||||||||||||||| ||||||||| |  | |||||||| || ||||| ||||| || |||||||||||    |||        || |||| ||  ||   | |  ||||   ||    |      |||  || |||  ||    | || || || |  |        
-GTGGCTGGTCTGTTCCAGATACGGAGTTGCGTGAGTCACTAAGACTTGCAGTTGCTGAAATCCTGTTGCCTGCATACAGATCTTTCCTAAAGCGCTTTGGgtatgtttctttgaaacttcattacatgtaaataatatattaatgcatggacaaggaccataactaatcctttattttctattcaaactctcctgctcat--

upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os04g58870.1 (Oryza sativa), 5'ss of exon 10
CGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcag-----------
 | | |||   ||||| |||| ||| ||| |||| || ||||  |||    |||||||| |||| || |||||||||||||| ||||| |||| |||||||||     |   || ||||  ||  | |||    | || || |  || ||  |  |    || |   |          |||   |||| |    |              
TGAACTGGGGTGTTCCTGACAGAGATTTACGAGATTCCCTAATTCTTATGATTGCTGAAATATTGTTACCTGCTTATAGATCTTTCCTGAAACACTTTGGgtactttccaatttgctctggtt-ttacgact-ttgttttatttctttatcaagctcctcaagacatttctcctttggttatgttatggttatcgttttcatcatgtag

upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 11
CGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatg--taaaaaaacctaaatgagattttaacctatgatcgatgcag----
| |||||||||||||| ||||| |||||  ||||||| || || ||||| ||||||||||| || |||||||| |||||||||||  ||||||| |||||||       ||   | |   || | | | || | | || |   ||||   | ||  |  | |||  |  |  || | |  | |     | ||  |||||     
CTCAATGGACAGTTCCTGACACTGAGTTGCGAGAGTCTCTTAGGCTTGCAGTTGCTGAAGTCTTGTTGCCTGCCTATAGATCATTTGTCAAACGATTTGGgtttg---ttctcattttggttcatttccaacgttattatgtcatttctatcaagggagttaaagtatgttcatcaaacatgagtagtttat-aatgcaagtct

upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 11
CGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttactgcgaaggcttttctaatattt----gattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcag-
|||||||||||||||||||| | |||||  |||| || || || || || ||||||||||| || |||||||| |||||||| ||  ||||||| |||||||       ||   | | | || ||| | || | | || |   ||||    ||||   || ||   |     ||    |  |||  ||  |    ||   |  
CGCAATGGACAGTTCCAGACTCCGAGTTGCGAGAATCTCTTAGGCTAGCAGTTGCTGAAGTCTTGTTGCCTGCCTATAGATCGTTTGTCAAACGATTTGGgtttg---ttctcatttttattcacttcaaacgttattatgtcatttaggggattattatctatggatgtgaaataatgtgtttgtcccctttgtgacaaaaa

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|124947015|gb|EL022886.1|EL022886
EST:     GTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGG                         GCCTTTGGTTGAGAGTGGGAAGAAT
genomic: GTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatct ... atcgatgcagGCCTTTGGTTGAGAGTGGGAAGAAT
EST: gi|124813810|gb|EH898676.1|EH898676
EST:     TTCCTCAAACGCTTTGG                         GCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGC
genomic: TTCCTCAAACGCTTTGGgtaaaaatct ... atcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA