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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT

Basic information

species Oryza sativa
transcript LOC_Os01g72340.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 1
-gtagctctcttctgtca-actgtc--atatctgaagacatttcgtattactatctctttggctcgtttt--tttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
   |      | |||||| | ||    | || | |||   |||   || |  ||||||||||   | |||  |  |   ||||||     ||||| |  | || || ||| |||||||||||||| ||| |||||||||| |||||||| || |||||||||||||| |||||||| || || || ||||||||||||||| | |||||||||||||| ||||
gtcaagatcttcctgtcatattggagaacattttaag-tttttaacataataatctctttggtctgatttaatcatatgcccagg-----ttcagattcttacaatatatctatttgtgacagGACCTGATTTTGATGAGGCAAAACAATATCAATGCTGTTAGAAATAGCCATTACCCACAGCACCCAAGGTGGTATGAGTTATGTGACATTTTTGGTCTTT

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 8
gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
|||   ||  ||| |       | |   | || |  | |    |||  ||      |||    |  | |||       | | |||| ||  | |||  |||  | |  ||   ||||||| |||| || ||||  |||||||| ||||||||||| || |||||||||||||||||||||||| | ||||||||||| |||||  | |||||  | |
gtactgctaatctttttttccccttcaataaaaaattgttagtttatgat------ggccaaatgctattt-------gtttttttaagacactaataattgctgtgctt---acagGATTTGGTCTTAATGAAGCAAAACAATATTAATGCTGTGAGGAACAGCCATTATCCCCAACATCCACGTTGGTATGAGCTATGTGATTTGTTTGGCATGT

upper sequence: LOC_Os01g72340.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 3'ss of exon 8
--gtagctctcttctgtcaactgtcatatctgaagacatttcgtattactatctctttggctcgtttttttttctcccaggctgttttc-aggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
  | | |   ||  |||    |||  | | || | |        ||   | | | ||  | |  | ||  |||     |   | || || || | || | || |   |    |   ||||||| ||||| | ||||  |||||||| || |||||||| ||||||||||||||||||||||||||  | ||||| ||| |||||||  | |||||  | |
gtgcaacctcctcttgt----tgttctctttggatat------catctttgtgtgttaagttaatgttggtttgattgatcatattgtcgagatcttcattactctctggcat---acagGATTTGGTTCTAATGAAGCAAAACAATATCAATGCTGTGAGAAACAGCCATTATCCCCAACATCCTCGATGGTACGAGTTGTGTGATTTGTTTGGCATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttctcccaggctgttttcaggtattaactatttatttatttgtgacagGATCTGGTTTTGATGAGACAAAACAACATTAATGCTGTTAGAAACAGCCATTATCCCCAACATCCAAGGTGGTATGAGCTGTGTGACATTTTTGGACTTT
                            tattaac  putative branch site (score: 1)
                                         tttattt  putative PPT
                    ttttcaggtattaact  TA-rich tract