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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatatatatatatcgctatgtttatcttactttttttcccagtggcttaactttatttttgtatcctgatttttttccatgccatcaactgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAATTCTTGAGAACAATAAGTGCTTTTTGGTCGACTGTGGGTCTGATTTATTT

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 12
-----------------tatatatatatatatcgctatgtttatcttactttttttcccagtggcttaactttatttttgtatcctgatttttttccatgccatcaactgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAATTCTTGAGAACAATAAGTGCTTTTTGGTCGACTGTGGGTCTGATTTATTT
                 ||  |||||| ||||  | ||  || | ||     ||| | ||       ||||||||| || |||  | | ||||| |             | |||||| || | ||| || ||| | |||||||||||||| ||||| |||||||||||| | ||||| |  || ||||||||  | ||||||||| ||||  |||||
cagaactgctagcctactacttatataaatattccaataattttattcgccgtttcctcaaaaa---aactttattctt-tattgttaatttttac-------------gtttgcagTATTAGTAACGGCCAACTGAAGTTAGAAGACACTGTTCTTACAAAATCAATTTTGGAGAATACCAAATGCTTTTTACTTGACTGTGGGGCTGAGCTATTT

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 7
-tatatatatatatatcgctatgtttatcttactttttttcccagtggcttaactttatttttgtatcctgatttttttccatgccatcaactgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAATTCTTGAGAACAATAAGTGCTTTTTGGTCGACTGTGGGTCTGATTTATTT
 |  | |  |||  |   |||    || |       ||||  || |    |  | | |       || || ||| ||     |    |    || |||||| |||| ||| || ||| | |||||||||||| | || || |||||||||||| | |||||||  |||||||||||  | ||||| ||| ||||  |||| 
ctgcaaacctattaactactacaaatacccccaacattttttcaatattgtttcctcaaaaaataattct-attcttcattgttaattgttgtgtttgcagTATCAGTAACGGCCAACTGAAGTTAGAAGACGCTGTCCTTACAAAATCAATTTTGGAGAACACCAAGTGCTTTTTACTTGACTGCGGGGCTGAGCTATTC
















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|58668298|gb|CK056984.1|CK056984
EST:     CGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAG                         CATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT
genomic: CGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAGgtatgatttt ... ctgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT
EST: gi|11442605|gb|BF430508.1|BF430508
EST:     ATATGTGACGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAG                         CATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT
genomic: ATATGTGACGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAGgtatgatttt ... ctgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT
EST: gi|58670145|gb|CK058831.1|CK058831
EST:     ATATGTGACGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAG                         CATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT
genomic: ATATGTGACGATGATGTTGTTCTTGAAACCACAGCCCCCAAGCTTTACAGgtatgatttt ... ctgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttaactttatttttgtatcctgatttttttccatgccatcaactgcttgcagCATCAATAATGGTCAATTAAAGTTAGAAGACACAGTTCTGACAAAATCAATTCTTGAGAACAATAAGTGCTTTTTGGTCGACTGTGGGTCTGATTTATTT
                    tcctgat  putative branch site (score: 3)
     aactttatttttgtat  TA-rich tract