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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttctttccttcgtatcatctagctttaatgtttgattcatcattaaagttggggctacatatatctttgtcgatattattgtgtggcctcggtc...

Basic information

species Oryza sativa
transcript LOC_Os03g02150.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G700148_T01 (Zea mays), 5'ss of exon 6
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttctttccttcgtatcatctagctttaatgtttgattcatcattaaagttggggctacatatatctttgtcgatattattgtgtggcctcggtc-
||| ||||||||||||||||| |||||||||||  | |||||||| |||||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||  ||||| | |  || ||| |        | || ||| || | ||||||| || ||  |  ||    |    |   | ||   |    |    | 
TTGTCTTCCAAAATGTGTAAGAATATTGGAGAGATTAGCAAGAAATCAAGATATTCCACAAGAGTACACTTATTATGGAATTCCATCTCCTTGGCTTCAGgtacttccctttcatgc-cattatccattcaaccagcttcatttattagtaaagttaggcctttacttagtagtcattaggctgttaccttctattaagct

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 7
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttctttccttcgtatcatctagctttaat---gtttgattcatcattaaagttggggctacatatatctttgtcgatattattgtgtggcctcggtc
||| ||||| |||||||| || |||||||||||| | |||||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||||||||||| | |   |  | ||| | |||||   | || ||   | |||||  |||| |||| || || ||| |||| | |||    |  |  |  |  ||||      
TTGTCTTCCTAAATGTGTGAGAATATTGGAGAGGTTAGCAAGAAATCAAGATATTCCACAAGAGTACACTTACTATGGAATTCCATCTCCTTGGCTTCAGgtacgtacttccctttcatgtcatcatccattcatccagcttgatctatcagtaaaattagg-ctagatatgtatttaattac-tggtcattaggccgttac-

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 6
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgt------gcttttctttccttcgtatcatctagctttaatg-tttgattcatcattaaagttggggctacatatatctttg-tcgatattattgtgtggcctcggtc---------------------------------------------------------------------
||| ||||| || ||| | |  || || ||  || | || || ||||| ||||||||||||||||||||||| || || || |||||||| |||||||||||        |||||||| | ||  || || |  || || ||  |||  |  |    | | ||  |  | |   | |    | | | | |||||| |   |    ||                                                                      
TTGTCTTCCTAAGTGTATCAAAATTTTAGAACGGCTTGCTAGGAACCAGGATATCCCACAAGAATACACTTACTACGGTATCCCATCTCCCTGGCTTCAGgtttgtgaatttttcttttcatcaaat-atatttctgtattggcttgggttttaggaagatttttgaatgctactcttacagcttgcttttattgagaaccaaaagtgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttaatgtag

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 6
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttcttt-----ccttcgtatcatctagctttaatg------tttgattcatcattaaagttg--gggctacatatatctttgtcgatattattgtgtggcctcggtc------------------------
||| ||||| || ||| | |  || || ||  || | || || ||||| ||||||||||||||||||||||| || || || |||||||| |||||||||||   |   |||       ||  |     |||   |||         ||| ||| |  |  |||  ||  |  ||| || | |  || || |     ||        |  ||                         
TTGTCTTCCTAAGTGTATCAAAATTTTAGAACGGCTTGCTAGGAACCAGGATATCCCACAAGAATACACTTACTACGGTATCCCATCTCCCTGGCTTCAGgtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtag

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 5'ss of exon 6
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttctttccttcgtatcatctagctttaatgtttgattcatcattaaagttggg--gctacatatatctttgtcgatattattgtgtggcctcggtc
||| || ||||| ||||| | |||  |||||||| | || || || || ||| | ||||||||||||||||| ||||| || ||| |||| |||||||||||   | |      ||  | |  |  | |  ||| ||   ||        |||         | | ||  |    |    | |   ||||   |||  |   
TTGTCTCCCAAAGTGTGTTAAGATTCTGGAGAGGCTTGCTAGGAATCAGGATGTTCCACAAGAATACACTTACTATGGTATCCCAACTCCCTGGCTTCAGgtttgtgtgcccattttctttacttaatccctaaagtaatatgggctgaaaaaaaaaaataacaagatgaaaaaataa-aaaacctttgttcagccaggca-

upper sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 5'ss of exon 6
TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttctttccttcgtatcatctagctttaatgtttgattcatcattaaagttggggctacatat-atctttgtcgata--ttattgtgtggcctcggtc
|||  | |||||||||||| ||||  | ||  |  || | ||    |||||||| ||||||||||||||||| ||||| || || ||||| ||| | |||||| |||  | | | |  | |||  |||  ||| ||||  ||  |    |  || ||    |  || |   ||||   | ||  | ||  ||| |    ||  
TTGTGTACCAAAATGTGTACGGATCCTAGAACGCCTGACCAGGGGTCAAGATATTCCACAAGAATACACTTACTATGGCATCCCCTCTCCTTGGTTGCAGgtgatttcttattcatt-tgtcagttagaatta-tgttgcatataattgtggagctgct-ttgtatgttgactttccaggtagctaatcatgttgatggggaa

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: 65 (upstream exon), 61 (downstream exon)
Score: 25

TTGCCTTCCAAAATGTGTAAGGATATTGGAGAGGATGGCAAGAAACCAAGATATCCCACAAGAATACACTTATTATGGAATTCCATCTCCATGGCTTCAGgtgcttttct ... ctatatacagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG




<











<


<