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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaactattcaatttgtattttattgatatttgttgacccttcttgctttgtgtaatattattgtggcaccatttggcctaatatcttcaccaaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
aaactattcaatttgtattttattgatatttgttgacccttcttgctttgtgtaatattattgtggcacc-atttggccta-atatcttcaccaaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC
   |   | || |||  ||   ||       |   ||  | || ||    | |  | ||     || ||  ||||| || | | ||           | |||||||| || |||||||| || ||||||   || || || |||||||||||||| |||||| | |||||||||||| | || || || || ||||| ||
--gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
















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|33804193|gb|CF327971.1|CF327971
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGGTAA-GATGCACTGGCAGAATCTGATAAGATTACATTGGAAA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGG-TAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAA
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGAT
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtgtaatattattgtggcaccatttggcctaatatcttcaccaaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC
                              gcctaat  putative branch site (score: 3)
                                      tcttcacc  CT-rich tract
     tgtaatattattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaactattcaatttgtattttattgatatttgttgacccttcttgctttgtgtaatattattgtggcaccatttggcctaatatcttcaccaaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA