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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccag

Basic information

species Oryza sativa
transcript LOC_Os04g52710.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52710.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T01 (Zea mays), 5'ss of exon 6
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccag------------------------------------------------------------------
|| ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| |                                                                   
CTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag

upper sequence: LOC_Os04g52710.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G094255_T02 (Zea mays), 5'ss of exon 5
-------------------------------------CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgc-ttcagatcaaatttccatccagt--gttggatcattattacaagagtgctgtttggcactgaata-aattgcatcc-ctagttgaacataagagtca-atctttgcttttcctccag------------------------------------------------------------------
                                     || ||||||||||| ||||||||| | ||||| |||||||||||||| ||||||||||||||||||||||||||| | |  ||| ||||||||  | || |    | ||||||| |  |||||   |  |    |||| |   || |||   ||   || | ||| ||||||    | ||  |||  ||| ||| |                                                                   
CTTACAGAAAAGTTTCATTTATTCGTTTTGGTCCCAGCTGGTTGAGCACTTCTTCCAATCTGTGGTGAACACATCTGGGATGACTCTTCACATCCGTCAGgtacatattgctgtccgctcaaatcaaattctcctcaaaacagctggatcagtgatacaattttagtcacgggcattttgtagaatcatattgactggctgagcataaggccaagatggttgagttttctctattttttatagcgaatttgcatgaccccgtccctatcacctgatctcgctccatactgtcttttgaag

upper sequence: LOC_Os04g52710.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G22425.1 (Arabidopsis thaliana), 5'ss of exon 5
-------------------------------------CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgctt-ttcctccag
                                      | || |||||||||||||| ||  | |||||||| ||||| ||||| ||||||||||| ||||||| |  || ||    ||    ||||     |   | |  || |      || || ||||  | ||     ||   |    ||    ||   ||  | |  ||  | ||| |||| || || |  |||
AGTGTTGCCAAAAATTGTTTAACCTTTCGATTTGTAGTTGGTGGAGCACTTTTTCCAGTCGTTGGTGAATACTTCTGGTATGACTCTTCACATCCGGCAGgtactttgtgattcaaatctt-ccaaaagctaacaaaatcatgca-----gtttcatgagt-ttcttctatcctctgt---ctgtggacc--atttcataacagttttaatatttgtttgttacaacag

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

upper sequence: LOC_Os04g52710.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 5'ss of exon 6
CTAGTTGAGCACTTTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattgctttgcttcagatcaaatttccatccagtgttggatcattattacaagagtgctgtttggcactgaataaattgcatccctagttgaacataagagtcaatctttgcttttcctccag
 | || |||||||||||||| ||| | |||||||| || || |||||||||||||| || |||||| |    |  || | | | ||  |  ||  | | | |  |   || |      || | |  ||||        || |||   |||| | | |  |   |                           
TTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgagagtttcctaacattta--ttgtagcaaatagtaactcctc---caaatattcttgttaatttagaaagaaaacacatctccattcaatggtcttc-----------------------

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|38477762|gb|CF961895.1|CF961895
EST:     TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAG                         TTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTT-G
genomic: TTTTCCAATCTCTTGTGAATACATCTGGGATGACACTTCACATCCGTCAGgtacatattg ... tttcctccagTTAAGCGAGCTAAGAAGTACGTATATCATACCTGAGCCTGCCTTTTCTTTG