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'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctcttaaatgaatcctatgatgcgaggctgatacagagaatgatattttag

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G16170.1 (Glycine max), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatt--tgtaaattctcttaaatgaatccta-tgatgcgaggctgatacagagaatgatattttag----------
 || |||||||||||||||||||| |||||||| ||||| ||||| || || ||||||||||| || || ||  | || |||||||| || ||  ||||||| ||      ||    ||  || | ||   ||||    | | || |   |   |   |  | | | | ||   |          
AAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACGTGTTATATGAATTCTCTACTCCAAACCTTGTATCATATTCCTTATTTTAGAAAGgttagaacggtttgtcttattttgttttgcctgaagttcacttatccattgaaaagtaatgggaagttgttcctggacatttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 1
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggcta-aatttgtaaattctcttaaatga-atcctatgatgcgaggctgatacagagaatgatattttag-----
 |||||||| ||||| |||||||| || || |||||||| |||||||| || ||||||||||| ||||| ||  | ||||| ||| | || ||||||||||| |  |   |   | |||| | | | |  |   ||  | | ||  |    |    ||   |   || |||| |     
AAAAAAGGAAACTGGTTATGTTGGACTGAAAAATCAAGGAGCTACATGTTATATGAATTCTCTGCTTCAAACATTGTACCACATTTCTTATTTCCGAAAGgttacccagtagcatataaactttgtaaggtcttatttttttataaggaaatagctcatgtataaatttttttgttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaattt--------gtaaattctctt----aaatgaatcctatgatgcgaggctgatacagagaatgatattttag--------------------
 ||||||||||||||||||||||| |||||||| || || |||||||| || ||||||||||| ||||| ||  | ||||||||||| || || |||||||| ||||    |||        ||   ||  |||    |  |  ||  | | |   ||   ||||   ||   |   ||||  |                    
AAAAAAGGAGACTGGCTATGTTGGACTTAAGAACCAGGGAGCTACATGTTATATGAATTCTCTACTTCAAACTTTGTACCATATTCCTTATTTTCGAAAGgtcaggcattgtttctcttattgttgttttccttctgaagttttatttttttactggatagtgatgaggaagtttggatttgggtcctggatgtcatatttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G11300.1 (Glycine max), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatt--tgtaaattctcttaaatgaa--tcctatgatgcgaggctgatacagagaatgatattttag---------------
||| |||||||||||||||||||| |||||||| ||||| ||||| || || ||||||||||| ||||| ||  | ||||||||||| || ||| ||||||| ||      ||    ||  || | ||   ||||  ||  |||      |     ||  | |||   | ||   |               
CAAGAAGGAGACTGGCTATGTTGGGCTTAAGAACCAAGGAGCTACCTGTTATATGAATTCTCTACTTCAAACCTTGTACCATATTCCTTATTTCAGAAAGgttagaactgtttgtcttattttgttttgcctgaagttcacatgtccattgaaaagtaatgggaagtttgttcctggatattacatttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggc---------taaatttgtaaattctcttaaatga---atcctatgatgcgaggctgatacagagaatgatattttag--------------------
 ||||||||||||||||||||||| |||||||| || || |||||||| || ||||||||||| || || ||  | ||||||||||| || || |||||||| || |             ||| |   |||  | | | |    ||  | | |   || | ||||   ||   |   ||||  |                    
AAAAAAGGAGACTGGCTATGTTGGACTTAAGAACCAGGGAGCTACATGTTATATGAATTCTCTACTCCAAACTTTGTACCATATTCCTTATTTTCGAAAGgtcagccattgtttctcttgttttttttttccttcagaagttttatttttttactggatggtgatgaggaagtttggatttgggtcctggatatcatatttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggc-taaatttgtaaattctcttaaat----gaatcctatg-------atgcgaggctgatacagagaatgatattttag-------------
 ||||| |||||||| | |||||| || ||||| ||||| || |||||||||||||||||||| || ||||| || ||||| || || |||||| ||||||| ||   ||   ||||   |||  | |  |     ||| | |||       ||   |  ||    | || ||    |||||               
TAAAAAAGAGACTGGTTTTGTTGGACTCAAGAACCAAGGTGCAACATGCTACATGAATTCTCTCCTACAGACACTATACCACATACCTTACTTCAGAAAGgtaagatatattcttgttttttccttcagtttgttaaattccatgggttctcattgaatccttgaccggacaactgaattttgcatgttgcttgtag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctcttaaatgaatcctat-gatgcgaggctgatacagagaatgatattttag--------------
 || ||||||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||||||||||| || ||||||||||| |||||| |||||||  ||  |   |  |   | ||| |  |    |   || |||   |   ||  | | || |  | ||||                 
AAAGAAGGAGACTGGTTATGTTGGACTGAAGAACCAAGGAGCTACCTGTTACATGAATTCCCTTCTTCAGACACTCTACCATATTCCTTACTTCAGAAAGgttgggaaattctcttttttcctcctttacttgtttcattgatattat-ttgcaagaaagcactacatttggaactgtgtatttcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctct--------taaatgaatcctatgatgcgaggctgatacagagaatgatattttag--------------
 |||||||||||||| | |||||| || ||||| ||||||||||| || ||||||||||||||  | || || || ||||||||||| || ||| ||||||| |||   |  || ||  ||   |        | | |   |  |   ||| |   || | |   |  |   |||||| |              
AAAAAAGGAGACTGGTTTTGTTGGACTGAAGAACCAAGGGGCTACTTGTTACATGAATTCTCTCTTACAAACTCTCTACCATATTCCTTATTTCAGAAAGgttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcag

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctcttaaatgaatcctatgatgcgaggctgatacagagaatgatattttag---------------------------------
 || ||||| || || | ||||||  | ||||||||||| ||||||||||||||||||||||| || |||||  | || ||| | || |||||||| ||||| |   |     ||| ||| |    |||| |    | || |  ||  ||  |      ||     ||| ||                                 
GAAGAAGGAAACAGGATTTGTTGGGTTAAAGAATCAAGGAGCTACATGCTACATGAATTCTCTCCTCCAGACATTGTATCATCTGCCTTACTTCCGGAAGgttatttt---cctgtcaatacag--aaatcatggttgtggttagaaccttttttcagcaactcagtttcaggagtctcggattctctttcggttcagtacttta

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgagg---ctaaatttgtaaat--tctcttaaatgaatcctatgatgcgaggctgatacagaga-atgatattttag-----------------------
 || || ||||| || ||||||||  | ||||||||||| || |||||||||||||||||||| || |||||| | || ||  | || ||||| || ||||| |     ||    |   | ||  | ||| || |  || ||   || |   ||  || ||| |  | ||   | ||                        
GAAGAAAGAGACAGGTTATGTTGGATTGAAGAATCAAGGAGCGACATGCTACATGAATTCTCTCCTCCAGACGTTGTATCACCTGCCCTACTTTCGGAAGgttatttccctgccatcacagatcatttctgaattacattctgcaattcagtgc-aattcagtgccaggaggctctatccagttttcggtttattgtgtct

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ13603 (Selaginella moellendorffii), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctcttaaatgaatcctatgatgcgaggctgatacagagaatgatattttag
 || ||||||||||| |  |||||  | |||||||| || || || ||||||||||| || || ||||||||||||||||| ||||| |||||||| ||||| |   | |  |  ||     |      |   ||  |   |      ||  ||                  
GAAGAAGGAGACTGGTTTCGTTGGGTTGAAGAATCAGGGTGCGACCTGCTACATGAACTCACTACTTCAGACGCTTTACCACATTCCTTACTTCCGTAAGgtaactattatctcttatcccttgactgttcggtctcacagttaagttcttgtaattcag------------

upper sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ19227 (Selaginella moellendorffii), 5'ss of exon 5
CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaaatttgtaaattctcttaaatgaatcctatgatgcgaggctgatacagagaatgatattttag
 || ||||||||||| | ||||||  | |||||||| || || || ||||||||||| || || ||||||||||||||||| ||||| |||||||| ||||| |   | |  |  ||   || ||| | ||  | |  |    |      | |   | || | |        
GAAGAAGGAGACTGGTTTTGTTGGGTTGAAGAATCAGGGTGCGACCTGCTACATGAACTCACTGCTTCAGACGCTTTACCACATTCCTTACTTCCGTAAGgtaactattatctctta---tcccttgactg--ttcggtctcacagttaagttcttgtgattcag-------

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|58666754|gb|CK055440.1|CK055440
EST:     ACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAG                         GCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGAAGCATC
genomic: ACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaa ... gatattttagGCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGGAGCATC




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 60 (downstream exon)
Score: 29

CAAAAAGGAGACTGGCTATGTTGGCCTTAAGAATCAAGGGGCTACATGCTACATGAATTCTCTTCTTCAGACGCTTTACCATATTCCGTACTTCCGAAAGgtgaggctaa ... gatattttagGCTGTATACCATATGCCAACTACAGAGAATGATACACCTTGCGGGAGCATCCCTTTGGCTTTGCAAAGTCTTTTCTGCAAACTTCAGCATAGTGACAATA




<











<


<