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'   		20  
 5'  3'   
21  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa...

Basic information

species Oryza sativa
transcript LOC_Os03g18310.2
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgatttt----ccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
|||||||||||||| |||||||| || || |||||  |||||||||||||||| || |||||||||||||||| |||||||||||||||||||||||  |||||| |||| |     | |||| | ||      | |     | |  ||| |   |     | || ||    |  |    |||  ||         
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct----

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgttttgtttttttcat-tgaagc--tatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa---------------------------------------
||||||||||| ||||||||||| ||||| |||||  | |||||||||||||||||||| ||||| ||||| |  |  || || || |||||||| |   |||  |  |  || |  ||| | |   |||   | ||  ||   |  ||  | |    |||  || |  ||| |  ||| ||  | ||| | |  ||                                        
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgt-aatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttggg--agcaca-atgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 30
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgttttgtttttttc-attgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa-------------------------------------------------
||||||||||| ||||||||||| ||||| || ||  | |||||||||| ||| ||||| ||||| ||||| |  |  || || || || ||||| |   |||| |  |  ||||  ||| | |   |||   | | | ||   |      |      |     |   || ||  |  || || |||   |  ||                                                  
ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGAgtatgtcacaaacttgt-aatttgtcttatttccagttgaatgctactggtacatcagataaaaaaaaccagtgcgtg-gtgggagcacgtgctgtttaaaaatgttttaaacacttttgttattttattttattttgccttttctattgcag

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg----caaattcattgattttccttttgtttt---gtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaag--taaa-------------------------------------------------------
||||||||||||||||||||||| ||||| || ||  | |||||||| ||||| || |  ||||| |||||||  |  || || || |||||||| |    || | |  |  ||||  || || |||    |||   | ||   ||  |  |   |     |   |  |  || | ||   | | |  |     |  || |                                                       
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgt-aatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 21
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgtttt---gtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa----------------------------------------------------------
 |||||||||||||||||||||| |||||||| ||  | |||||||| ||||| ||||  ||||| |||||||  |  || || || |||||||| |   |||| |  |  ||||  || || |||    ||| | | ||   ||  | |||  |  |  |   |  |  || | ||   | | |  |     |  ||                                                          
-TACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAGtatgttgcaaacttgt-aatttctctcttatttgcaagttgtatgcaactaatatgtctgataataaagaagcacaatgtgaaacttcttttggttttggggtaagaagatgctgtttaaattccgtaattattatttccctcccctcttattttgttacaga

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 25
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTA-TGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttca-ttgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
||||||||||||||||||||||| |||||||| ||  | |||||||| ||||| ||  |  ||||| |||||||  |  || || || |||||||| |    ||    || ||    ||| | |  | |||   | |||||   | ||  | | |||                                     
ATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGgtatgacataacgcagaaatcaagaaaaacatgccagaggagtatgagtatg----tttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcag------------------------------------

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgt---tgcatttgttctttgagtaa-gcccatgtcctgccaagtaaa-
||||||||||||||||||||||| ||||| |||||  | |||||||| ||||| ||||| || |||||||| |  |  ||||| ||||| ||||| |   |||  ||     |   |||      ||||  | ||  ||  | ||||   |   | ||  || |  | |  ||     |||  | || ||  | |  
ATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcatttttta----tttgtttaagaaattttcatgatgtaatttttcttccatgcatacacatgatgatagcttattagacata-cttgtcatattaca

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|29643803|gb|CB648810.1|CB648810
EST:     GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA                         ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
genomic: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA