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

CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag

Basic information

species Oryza sativa
transcript LOC_Os04g52710.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag
                                     || ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
-------------------------------------CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag

upper sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T02 (Zea mays), 5'ss of exon 5
CTTAGACAGCTATTG-ATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccagtta----agcgagctaagaag--tacgtatatcatacctgagcctgccttttctttgctcttatgaag
|||| | |    ||  ||||||||  |||| |  |||||| ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| | ||     |||||  |   | |    |||   |   |||||| |  ||    |  |   |||| |||||
CTTACAGAAAAGTTTCATTTATTCGTTTTGGTC-CCAGCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactg--tcttttgaag

upper sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22425.1 (Arabidopsis thaliana), 5'ss of exon 5
--CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgctt-ttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
    | | ||   |||| || |     || |||    || | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| ||||||| |  || ||    ||    ||||     |   | |  || |      || || ||||  | ||     ||   |    ||    ||   ||  | |  ||  | ||| |||| || || |  |||                                                              
AGTGTTGCCAAAAATTGTTTAACC--TTTCGATTTGTAGTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgattcaaatctt-ccaaaagctaacaaaatcatgca-----gtttcatgagt-ttcttctatcctctgt---ctgtggacc--atttcataacagttttaatatttgtttgttacaacag--------------------------------------------------------------

upper sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22425.2 (Arabidopsis thaliana), 5'ss of exon 6
CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgctt-ttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
                                      | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| ||||||| |  || ||    ||    ||||     |   | |  || |      || || ||||  | ||     ||   |    ||    ||   ||  | |  ||  | ||| |||| || || |  |||                                                              
-------------------------------------TTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgattcaaatctt-ccaaaagctaacaaaatcatgca-----gtttcatgagt-ttcttctatcctctgt---ctgtggacc--atttcataacagttttaatatttgtttgttacaacag--------------------------------------------------------------

upper sequence: LOC_Os04g52710.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 5'ss of exon 6
CTTAGACAGCTATTGATTTATTCACTTTGATGACCAGCTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccagttaagcgagctaagaagtacgtatatcatacctgagcctgccttttctttgctcttatgaag
                                      | || |||||||||||||| ||| | |||||||| || || |||||||||||||| || |||||| |    |  || | | | ||  |  ||  | | | |  |   || |      || | |  ||||        || |||   |||| | | |  |   |                                                                                         
-------------------------------------TTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgagagtttcctaacattta--ttgtagcaaatagtaactcctcc---aaatattcttgttaatttagaaagaaaacacatctccattcaatggtcttc-------------------------------------------------------------------------------------

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|88846550|gb|CI373318.1|CI373318
EST:     ATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: ATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|89186200|gb|CI048069.1|CI048069
EST:     TGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|58666132|gb|CK054818.1|CK054818
EST:     TTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|86504503|gb|CI147136.1|CI147136
EST:     TTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: TTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
EST: gi|89182904|gb|CI045662.1|CI045662
EST:     GACACTTCACATCCGTCAG                         CTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT
genomic: GACACTTCACATCCGTCAGgtacatattg ... tcttatgaagCTTGCTGGAAAAAACTCACACCATATTATTGAGGCAACTTTCAAAGCATTT