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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G179308_T01 (Zea mays), 5'ss of exon 6
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| | || |||    |  | | ||  ||||    | |  |   || || ||    ||  |   ||| |   |  ||   ||   | || | |  |     |||| |||  ||||||| |||| | |         | |  ||||||| |||||| | ||||| |    ||||||||||
GGACCAAGCTTATATGATTTTCTGCGGGAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGATTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttcttcctattatcgctcctgc-actataatgcatatacattagtt-tttttttgcaatatatgtgcagcattgtagcctatcattaatccatattactactcatgctta-aggaatatctaacatca--------tgggatgtttatgtatttaccctctctctgtaatgtgttgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G063792_T04 (Zea mays), 5'ss of exon 6
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgc-ttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||||||||||||| ||||||||| |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||| |||| | |  |    |||||  ||    || || |||| | ||    |   |   |||||   | |||    |   | || | ||  |     |  | ||    ||| || |||| | |  |  || |      |||| | |||||| | ||||| |    ||||||||||
GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttctttctattacccctcct---gcacta--taatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatc--atgtgat------gtttttgtatttaccctctctctgtaatgtgttgcag

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G02740.1 (Glycine max), 5'ss of exon 5
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatt-tatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| ||||||||| ||||||||||||||||||||||    | || |||    ||  ||| ||      ||| ||      || | |  |||   |  |  |||          |  | | |  |    ||| | |   |     || || | || | |   |  |   |  |    |  ||| | ||    ||  |||||| |    ||| ||        
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAAACAACTATTGGAATGTATAGCATgtgtgta-gtatttacttgaactag-cttctttttgagctatttc----ttccatac-atttcactttggattatcattaactaataat-ggcaatacatgttgtagatctaatatactgtcag-actctgttgtttttgtctctgtgggttagctttctaatagtatctttttatgaatttgcag-----

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G13440.2 (Glycine max), 5'ss of exon 5
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttcttt-gcttcatccttttaggaatacctaatacctaacctgctttgtttg-tttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| || |||||| ||||||||||||||||||||||    | || |||    ||  ||| ||      ||| ||     ||  |  | | | |        ||  || |  | | | | | || || ||| | | || | | |  |   |  |   |     |  |   |       |  ||| | ||| ||  | |||||| |    ||| ||        
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTATTGGAATGTATAGCATgtgtgta-gtatttacttgaactag-cttctttttgagctatttcttccatacatttcacttt-------gttttatcc--ttaactgataatggc-gatacgtgctgtagatctaatatactgtcagactgtgttgtttttgtcagtgggttaggtttctaactgtatctttttatgaatttgcag-----

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G18530.1 (Glycine max), 5'ss of exon 5
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgt-catca--gttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||||||| || ||||| || ||||  || || || ||| ||| |   ||||| ||||||||| ||||||||||||    | || |||     | | |  ||   |   || ||     || |  |||  | ||   |  ||  |||  ||| ||  |  |||  || | ||                                                                                           
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTATTGGAATGTGTAGCATgtgtgta-gtatttacttgaacaagtttctttttgat-ttatttcatctatttccattcctattttgtgcatatcattatgtacaatactgtttttaacaga-------------------------------------------------------------------------------------------

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G36360.1 (Glycine max), 5'ss of exon 5
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||||||| || ||||| || ||||  || || || ||| ||| |   ||||||||||||||| ||||||||||||    | ||   |     |   || ||       || ||     || |  |||  | ||   |  |||      |   || | |||  || | |||                                                                                          
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAGTTATCGTTCATTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTGTTGGAATGTGTAGCATgtgtgta-gtattttacttgaacaagtttctttttgatttatttcatctatttccattcctgttttgtgcattattatatccaatactgtttttaacagat------------------------------------------------------------------------------------------

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||| ||| |||||||| ||| |||  ||||| || ||| ||| || |||||||||||||||| ||||||||||||     |||  || || |  |  | |  |      ||  |   |||    |   ||||   |  |  ||| | | | | |  ||  |   |||    ||                                                                                      
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt-gttatttgtgctgtttatttatctttttcaa--acttgatggtaacagttctagtaggagatgc-ttcagccttttgtctagctctgggattt--------------------------------------------------------------------------------------

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 6
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag
|||||||||||||| |||||||| |||||||||| ||| |||||||| || ||||  || || || ||| ||| || |||||||||||||||| ||||||||||||    |  | ||| || || | || ||  ||  | |  ||     | |        |||   |  ||| |||    |   | |||||  |   |   ||| |                                                                                   
GGACCAAGCTTATACGATTTTCTACGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgta-gtaaatacttttgctagtttttttttcaatcca--taatgcgtttg------ccttttgtgtattccatctcttatactgttgaatgtctactatttgtaa---------------------------------------------------------------------------------

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|86900381|gb|CI296424.1|CI296424
EST:     AATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCAT                         TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTC
genomic: AATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTC