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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaattgtagtttctttatagcattacttcttcaattaactttggaaaggaccagt...

Basic information

species Oryza sativa
transcript LOC_Os01g67340.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G346132_T01 (Zea mays), 5'ss of exon 5
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaattgtagtttctt--tatagcattacttcttcaattaactttggaaaggaccagt-
||||  | |||||||| |||||||||||||||||||||||||||||||| ||  ||||||| ||||||||  ||||||||||||| |||||||||||||||||||||  |||  | ||   |    |  |  ||| || ||  || | ||||  |||| |  | | ||||   || |   ||||| ||| ||   |  |||  
CAAAGATAGCAGACTTTAATCTCTCAAATCAGGCTCCAGATATGGCTGCCCGGTTGCATTCAACTCGTGTCTTGGGAACCTTTGGATATCATGCTCCAGAgtaaaaacccttttcttaaagta-actatatgttacttaac--tttagttgtgctttcctgcttttgcatgggttgtctcattaattttcgagttggtcagca

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 6
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaatt--gtagtttctttatagcattacttcttcaattaactttggaaaggaccagt
| ||  | || ||||| || || || |||||||| || || |||||||| ||||| ||||| ||||||||| ||||||| ||||||||||||||||||||||||   |    | | |  |      | |  ||||| |     ||   ||   || || ||||  |    ||    | | || |  | |   |||||     
CCAAGATAGCTGACTTTAACCTTTCTAATCAGGCCCCTGACATGGCTGCACGTCTTCATTCAACTCGTGTATTGGGAACTTTTGGTTATCATGCTCCAGAgtaagcttcgagaacctgctagcatttaatttttatatctacatttgctttcatatttcctttgaattcatatgcatgctatcatgtattacaaggaagg--

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G44210.1 (Glycine max), 5'ss of exon 6
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaatt--gtagtttctttatagcattacttcttcaattaactttggaaaggaccagt
| ||  | || ||||| || || || |||||||| || || |||||||| || || ||||| ||||||||| ||||||| ||||| ||||||||||||||||||   ||   | | |  |  ||  | || ||||| |     ||   ||   || || ||||       |     | | ||    | |   |||||     
CCAAGATAGCCGACTTTAACCTTTCTAATCAGGCCCCTGACATGGCTGCACGCCTTCATTCAACTCGTGTATTGGGAACTTTTGGGTATCATGCTCCAGAgtaagctttgagaacctgcta-gtatttaattttatatctacatttgctttcatatttcctttgagttcatgtgcatgctatcttgtattacaaggatttt-

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 5'ss of exon 4
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaattgtagtttctttatagcattacttcttcaattaactttggaaaggaccagt
| ||  |||| ||||| ||||| || ||||| ||||| ||||||||||||||||| ||||| ||| | ||  |||| ||||| ||||||||||| |||||||||| || ||| | | |||    | |     || | ||  |  | | |    |      | || | ||   | | ||                      
CCAAGATTGCTGACTTTAATCTTTCCAATCAAGCTCCTGATATGGCTGCTCGTCTTCATTCCACTAGAGTTTTGGGGACCTTCGGTTATCATGCACCAGAgtaaatatgctt-caacattgatagctcggaattttcttgattcttagtaactgaaagaatgtaactttgggtttgcag---------------------

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G59350.1 (Arabidopsis thaliana), 5'ss of exon 3
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattcttaccatattctgtgatgaactttattttactgttcaattgtagtttctttatagcattacttcttcaattaactttggaaaggaccagt
| ||  | || || || ||||| || || ||  |||| ||||||||||||||||| ||||||||  | ||  |||||||||| ||||| || || |||||||||  | |  | |   | |   |  |  |    |   || |  |  |     |     || || |  ||| | |||  |    |   |           
CCAAGATCGCTGATTTTAATCTATCGAACCAATCTCCTGATATGGCTGCTCGTCTTCATTCTACCAGAGTTTTGGGAACCTTCGGTTACCACGCACCAGAgtaatgaatgcttctgaaata-atagttgatcacacagtatt-cttgaggaaggaaagattgtaactgtacattttcgct--gttgcag-----------

upper sequence: LOC_Os01g67340.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 5'ss of exon 5
CAAAAGTTGCAGACTTCAATCTCTCAAATCAGGCTCCAGATATGGCTGCTCGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattct-taccatattctgtgatgaactttattttactgttcaattgt-----agtttctttatagcattacttcttcaa--ttaactttggaaaggaccagt
| ||  ||||||| || ||||| |||||||||||||| || ||||||||||| || ||||||||||| || ||||| |||||||| |||||||| |||||||||  ||||| || | |||| |    ||    ||    || | ||   || |     | ||  ||  ||  |||| || |  ||  ||  |||     |        
CCAAGATTGCAGATTTTAATCTTTCAAATCAGGCTCCTGACATGGCTGCTCGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattctgtaacttattttcctttgtttctttgactattattatcttatgagttaattgtttggtaaaattatttttataagattgccttcttgta--------

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|29644034|gb|CB649041.1|CB649041
EST:     CGTCTGCATTGTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGA                         GTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
genomic: CGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattc ... aactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
EST: gi|88830237|gb|CI076493.1|CI076493
EST:     TGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGA                         GTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG
genomic: CGTCTGCATTCTACTCGTGTACTGGGAACCTTTGGTTATCATGCTCCAGAgtaaaaattc ... aactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGG