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

AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag

Basic information

species Oryza sativa
transcript LOC_Os01g62420.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacata-gagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcct-ggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag--
| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||  ||||| |   | ||||||| ||  || ||||      ||   | |||||          | || |    ||   | ||     | | |||   |   |||||||   |    | | || |    |    ||||||| |  |  | || |||||| || ||||||  |||    
AAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAGgtatagcttcttatgcacgagcaataactgcatgatt------ttttttccacat----------cgtaga----tagttgcttccatttgtgtctcccggtattcttgatttacatatcgatatcaatgttcttaattctgctt-tgtgtatcatttgagatgtgcatggtattgtag

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G04290.1 (Glycine max), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| ||||||| | | |  | ||   |  |  |||  || |||    || |      | | ||   |||| | ||  |   | |   ||| |   |  || | ||   | ||                                                                      
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGgtatgcttgcctatattttgtta--acagtacaattgttttggt----gaaaacttgcttgccac-tatgctgttttttttttgtgtgtgaattttattgttctcac--------------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttcccttcacatttatctgcctcataaaccaatatgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| ||||||| | |    | ||   |  |  |||  || |||    || |     |    |   |    |  | |    || |  |  ||||  | | ||| |  | ||                                                                        
CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAGgtatgcttgtctatattttgtta--acagtactattgttttggtgaaaacttgctcgccattatggtgattatatttttgaattttattgt-tctcacatatt------------------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttccct-tcacatttatctgcctcataaaccaatatgggttttttc-ctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
|   | |  |  | ||| | ||||||||  | || ||||||||||| ||||||||||||||||| ||||| || | ||| || || ||||| || |||     |     || | ||| || ||       || | |||| | | |     | || |       ||||||||   | |||  |  | | | ||  | || ||  ||| |                                                                
ATCGGGTGACAAACTGGTCAAATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGAAgtaagtggttctcgat-gcgcagttgcactg----taacgtgttgcatatggtcatgatttaataggaaaaccaatgctgttttccttacgagagcttgtttcgtttatgaacag--------------------------------------------------------------

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 6
AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttctaacatagagcaattacatcacgattagcatgttccctt-cacatttatctgcctcataaaccaat-atgggttttttcctatatctaatgtctttcttgaccgatgcctggtacctgattctgcaattctgttcattcgaattatttgaaatatgcatgacattag
| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| |||   ||       ||  | | ||        |||| || |   | ||   |    |      | |||   || | || | |        || ||||||                                                                             
AAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAAgtaagtctgggttgttattgaatttgtcatttcattaacaaggatctttatgctggaaagcatgttatagttcagttattgttaaaccggaatctctaat-----------------------------------------------------------------------------

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|27576926|gb|CA999620.1|CA999620
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTG
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTTTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG                         GTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT
genomic: TTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGgtattccttc ... atgacattagGTTCATGATGGTCTGAGAAAGTGGCTTGTGACTAATGTTAGTCCTGCAGTT