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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatggttacaatgtagttgaacatgataatatattttagacagagacaggcttcaataacctccatatattcacttatgggccttgcgtatttcgcagGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATCCAGCATCGTGATACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGC

Basic information

species Oryza sativa
transcript LOC_Os04g11880.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11880.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 12
---------catatggttacaatgtagttgaacatgataatatattttagacagagacaggcttcaataac----ctccatatattc-acttatgggccttgc---gtatttcgcagGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATCCAGCATCGTGATACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGC
            | |  | |||| ||| ||   ||   ||  ||  ||  |||| |  | | || |  ||      |||||||  || |||||    | ||      ||||   ||| ||||||||||||||||| |||| | ||||||||| ||  ||||| ||||||| ||||||||||  || |||||  |||||||||| |  ||| ||||||
gtatcaaaatggaggagtccaatttagctgctaatacaaagttacattctacagtggtatgttttagaaaaagcattccatatcctcgacttaaacactttttttaatattcttcagATTGTCAATCTTATGATAGTGGACAATAAAAGAACAGTTCACCTACTGATCCAACATCGTGATATCATTCCCCCATATGAAGTTGTGGAGCAGCTGTTGC
















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|58675059|gb|CK063746.1|CK063746
EST:     TATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG                         GTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATC
genomic: TATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAGgtatggttaa ... tatttcgcagGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATC
EST: gi|66914272|gb|CX101120.1|CX101120
EST:     TATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAG                         GTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATC
genomic: TATTCGAATTTATTGAGAAGCACAACTTGCATGATGCCATTCATGACAAGgtatggttaa ... tatttcgcagGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacaggcttcaataacctccatatattcacttatgggccttgcgtatttcgcagGTTGTCAATCTTATGATATTGGATAGTAAAAGAACTGTAAACCTATTGATCCAGCATCGTGATACGATCCCCCCGAATGAAGTTGTAGGACAGTTGTTGC
          caataac  putative branch site (score: 2)
                     atatattcacttat  TA-rich tract