Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccggctagccgccccccatattcttgtttctgtgttgatcggagctcgatggctggggtgctctgggctcgtcgtcgtcggtcgatcgtcatggcttgcttcgtttcttgcagCTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTCCGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGCCGGGCTCGGG

Basic information

species Oryza sativa
transcript LOC_Os04g42800.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42800.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G051952_T03 (Zea mays), 3'ss of exon 1
gtagccggctagccgccccccatattcttgtttctgtgttgatcggagctcgatggc---tggggtgctctgggctcgtcgtcgtc--ggtcgatcgtcat-ggcttgctt-----cgtttcttgcagCTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTCCGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGCCGGGCTCGGG------
   |   | ||||| || || |    ||||||||||   | ||| | ||           |||   ||||| |  || |  || ||  |||  | || ||  ||| ||||       |  | | |  ||   | |||||| || |||||| |||||||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||||| |  ||| |||      
---gtaaggtagccaccgcc-accagcttgtttctg--ctcatcagcgcgtagcaaaccatggctagctcttgagtccttatcatccgggtgaaccggcaccggcctgctcatgcgtgcatgtcgtcgccgcagCTCCATTGCGAAGATACGGAGTGAGGTCCTCTCCCCGTTCCGGTCGGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGGCACGCTGGGGGGCCTC

upper sequence: LOC_Os04g42800.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G051952_T02 (Zea mays), 3'ss of exon 1
gtagccggctagccgccccccatattcttgtttctgtgttgatcggagctcgatggctggggtgctctgggctcgtcgtcgtc--ggtcgatcgtcat-ggcttgctt-----cgtttcttgcagCTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTCCGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGCCGGGCTCGGG------
||||||  |  ||| ||  |  | ||  || |  |  |    | | |   | |||||| |    |||| |  || |  || ||  |||  | || ||  ||| ||||       |  | | |  ||   | |||||| || |||||| |||||||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||||| |  ||| |||      
gtagccacc--gccaccagct-tgtttctgctcatcagcgcgtagcaaacc-atggctag----ctcttgagtccttatcatccgggtgaaccggcaccggcctgctcatgcgtgcatgtcgtcgccgcagCTCCATTGCGAAGATACGGAGTGAGGTCCTCTCCCCGTTCCGGTCGGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGGCACGCTGGGGGGCCTC
















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|29639238|gb|CB644247.1|CB644247
EST:     TCGGCGGCGAACAAGCCTTCTCCTTCCACCGCTCCGGGCACCGAGGTAAG                         CTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTC
genomic: TCGGCGGCGAACAAGCCTTCTCCTTCCACCGCTCCGGGCACCGAGGTAAGgtagccggct ... tttcttgcagCTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctctgggctcgtcgtcgtcggtcgatcgtcatggcttgcttcgtttcttgcagCTCGACCTCCATGGCAAAGATAAGGAGTGAGGTGCTGTCCCCGTTCCGCTCCGTGCGGATGTTCTTCTACCTCGCGTTCATGGCCAGCGCCGGGCTCGGG
                                    cttgcttcgtttctt  CT-rich tract