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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctcctctctctctctctctctctctctctcttctcttctctcatcactcaccatcttcttgtcttctctctctcctctcatccttttgtgcaatgcagGGATTGTGGCAAGCAGGTCTATTTGG

Basic information

species Oryza sativa
transcript LOC_Os04g55560.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174784_T04 (Zea mays), 3'ss of exon 1
ctctcctctctctctctctctctctctctctcttctct-tctctcatcactcaccatcttcttgtcttctctctctcctctcatcct-tttgtgcaatgcagGGATTGTGGCAAGCAGGTCTATTTGG--------------------------------------------------------------------------
     ||||||||  |||| ||| | | || | ||||| |||||| ||   | |  |||   |  || | |  |  |||||  |  |  ||||||||||||||||||| |||||||||||||||||||                                                                          
--tctctctctcttgctctgtctgtgtgtcccctctctctctctcctcctcctctctctctctcactcccccatgccctctgcttgtgcttgtgcaatgcagGGATTGCGGCAAGCAGGTCTATTTGGGTAAGTTTCGTTCATGTCCATGCATACACATCCGTACTTGGGAGAGAGGTGGGTGACTGCCCCAATCCGAGGCG

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G174784_T01 (Zea mays), 3'ss of exon 1
ctctcctctctctctctctctctctctctctcttctct-tctctcatcactcaccatcttcttgtcttctctctctcctctcatcct-tttgtgcaatgcagGGATTGTGGCAAGCAGGTCTATTTGG
     ||||||||  |||| ||| | | || | ||||| |||||| ||   | |  |||   |  || | |  |  |||||  |  |  ||||||||||||||||||| |||||||||||||||||||
--tctctctctcttgctctgtctgtgtgtcccctctctctctctcctcctcctctctctctctcactcccccatgccctctgcttgtgcttgtgcaatgcagGGATTGCGGCAAGCAGGTCTATTTGG
















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|29644662|gb|CB649669.1|CB649669
EST:     CGCGGCGTCACGTTCTACCGCCGCACCGGGCGATGGGAATCGCACATATG                         GGATTGTGGCAAGCAGGTCTATTTGG
genomic: CGCGGCGTCACGTTCTACCGCCGCACCGGGCGATGGGAATCGCACATATGgtaagcatcc ... tgcaatgcagGGATTGTGGCAAGCAGGTCTATTTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactcaccatcttcttgtcttctctctctcctctcatccttttgtgcaatgcagGGATTGTGGCAAGCAGGTCTATTTGG
 cactcac  putative branch site (score: 2)
       ccatcttcttgtcttc  CT-rich tract