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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcatgaaacatcactaattttcttgattctttgctatgattttgcatggttgccttgtttagaattaacagtttcttgtcatatactcttttctcagGTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTTGTGCTTGCAGAAAGTTTTGGCCATTCTGTTTTTAAAGAGTCACTCCAAC

Basic information

species Oryza sativa
transcript LOC_Os08g36994.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g36994.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0045g00540.t01 (Vitis vinifera), 3'ss of exon 3
-atatcatgaaacatcactaattttcttgattctttgctatgattttgcatggttgccttgtttagaattaacagtttcttgtcatatactcttttctcagGTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTTGTGCTTGCAGAAAGTTTTGGCCATTCTGTTTTTAAAGAGTCACTCCAAC
   ||   ||        |||| ||      | |    || | || |  ||||   | | |||| |||  |    || | ||   | | || | ||  ||||| || ||||||||  | ||  ||||||| ||||| ||||| ||||| ||||||||||| ||||||||||||||| | |||||||  || || ||  |||
ggcatgcggaggtggatttaatattaagatctatggcttacgcttgttgatggacac-tggttttgaaagatgttttgcatgcttttttctttatttccagGTGGGGGTTGCTGAACTTAAAATTGCAGTTGAGAGAACTGGAGGAATTGTTGTGCTTGCTGAAAGTTTTGGCCATGCAGTTTTTAGGGACTCTCTTAAAC
















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|29622673|gb|CB627684.1|CB627684
EST:     TTGTACATCAAGGCCATGTGCTTGATTTATTTGCATGTGCACTTGACCAG                         GTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTT
genomic: TTGTACATCAAGGCCATGTGCTTGATTTTTTTGCATGTGCACTTGACCAGgtttgctgct ... cttttctcagGTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTT
EST: gi|396941631|gb|HO188288.1|HO188288
EST:     TTGTACATCAAGGCCATGTGCTTGATTTATTTGCATGTGCACTTGACCAG                         GTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTT
genomic: TTGTACATCAAGGCCATGTGCTTGATTTTTTTGCATGTGCACTTGACCAGgtttgctgct ... cttttctcagGTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatggttgccttgtttagaattaacagtttcttgtcatatactcttttctcagGTTGGTGTTGCTGAGATGAAGGTTGCAGTGGAGAGGACTGGGGGAATAGTTGTGCTTGCAGAAAGTTTTGGCCATTCTGTTTTTAAAGAGTCACTCCAAC
                    aattaac  putative branch site (score: 2)
                                       tatactcttttctc  putative PPT
            ttgtttagaattaa  TA-rich tract