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

gtcagtcgtataagcattttctaattgtttgagattcttttcttaacaactgctaaaatttgtaaccttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
gtcag---tcgtataagcattttctaattgtttgagattcttttcttaacaactgctaaaatttg--taacct-tttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC
|| ||   | || | | | ||  |  ||      |  ||  |||  |      ||   |||       ||  | |||||||| |||||||| || || || |||||||||||||| |||||||||||||| ||   
gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtcagtcgtataagcattttctaattgtttga-gattcttttcttaacaactgctaaa-atttgtaaccttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC
    |    |||||| ||| |  ||  |   |  || || ||   | |    ||     ||| |||| |||   |||||||| |||||||| || || ||||| ||||||||||||||||||||| | |  ||  |
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataattatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtcagtcgtataagcattttcta-attgtttgagattcttttcttaacaactgctaaaatttgtaaccttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC
                   |  |  || |   | |||| | |||| ||| | |    |    ||  | ||||| ||| | ||     ||||||| |||||||| || || || ||||| ||||||||||||||||||   |||||  |
gtatgtaatttacaatgagctttgttaaatatactttcgatattgattgtgttatcatgtacaagtaatgctataatatata----cttcagGTCATGGACATGCTTGGTCCGAGTCTCTGGGATGTTTGGAATTCTTCGGGGCAATC

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|29629024|gb|CB634035.1|CB634035
EST:     GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTG                         GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG
genomic: GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTGgtcagtcgta ... accttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTG                         GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG
genomic: GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTGgtcagtcgta ... accttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG
EST: gi|58661787|gb|CK050467.1|CK050467
EST:     GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTG                         GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG
genomic: GTATACCCTGGGTTCACTACAAAGGCCGGCAGGGGGACTATTATGTTCTGgtcagtcgta ... accttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaattgtttgagattcttttcttaacaactgctaaaatttgtaaccttttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC
                                        ttgtaac  putative branch site (score: 2)
                                              ccttttc  CT-rich tract
                                  taaaatttgtaa  TA-rich tract