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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G53520.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaacta--ttgtggcttat-atctatgcag
||  | |||||||| |||||||| |||||||| ||  ||||||| || |||||||| ||||| ||||| || |||||||||||||||    |    | | | |   |    |    |||| |  || |   ||  |    || | ||| |     |  || |   | || |||  || ||
GTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAGgttcgtttaacacgt-accgctattttattaacttttggttacacatttgcgctgtcaatatgaaattctgagtttatacatgattatcattgtag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgttta-gctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacaga-actattgtggcttatatctatgcag
|| |||||||| || || |||||||||||||| ||  | |||||  | ||||||||||| |||||||| ||||| || || |||||||  | |  || || |   |||              | |  |||  | ||  ||          |   ||||||   | |      | | |||
GTGAGAATTGCGCGAATATTCAACACATATGGCCCTCGTATGTGTTTAGATGATGGGCGAGTTGTTAGCAACTTCGTCGCTCAGgtttgtgttaatttatgattctaatcctttggaaaagagaaataagtatatttgaagtttagcattacttactattaaagatgcctcatttccag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G347717_T01 (Zea mays), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag------
|| |||||||| || || || ||||||||||| ||  |||||||  | |||||||| || |||||||| ||||||||||| |||||||  |||  |     |     |  ||      || |   | ||  || | | |  |||    ||   ||  |   | |   ||   | ||       
GTGAGAATTGCACGCATATTTAACACATATGGCCCTCGAATGTGTTTAGATGATGGCCGAGTTGTTAGCAACTTTGTTGCACAGgtttgtctcagtttgtgattctgatgca------ttggagaagaggattatcatagaacttcagcactgct--taaagttggcattgcttcatttctag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag
||  | ||||| ||||||||||| |||||||| ||  | |||||||| || ||||| ||||| || || || |||||||| |||||||   | || |||     || |||| |    | |    |      |||   |  || |   |||    |||  | |      ||  |||||
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatat---tatagactatttttcttagttgtgatattt---atgcatttaaacatccatatgatcg------tccttgcag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G05260.1 (Glycine max), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag
||| | |||||||| ||||||||||||||||| ||| | |||||  | |||||||||||||||||||| || |||||||| |||||||  ||   |  ||   ||  |      |  | | ||  | |||  ||||       ||| | |   |||||       |||| | | |||
GTTCGTATTGCTCGAATTTTCAACACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTTGTTAGCAATTTTGTTGCACAGgtttgactttcttgtccttatttaatttgtcattattgtggagagcaatttg----tgttcttata---ctatttatttacatatgtttccag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G19640.1 (Glycine max), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag
||| | |||||||| |||||||| |||||||| ||| | |||||  | |||||||||||||| ||||| || |||||||| |||||||   |   |  ||   ||         |  | | ||  | ||    |||       ||| | |  | |||  |   |||| | |  ||||
GTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAGgtttgattttcttgtccttattttttttgtcattattgtggagaggaacttg----tgttcttatacta-tatatttatttatgttt--gcag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 5'ss of exon 5
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacat----------------aaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag-----
||  | || || || |||||||| |||||||||||  | |||||  |||||||||||||||| ||||| || |||||||| |||||||     | | |   |  |                ||| ||||         | | |  | |||| | ||   ||| | ||   | ||     ||||| |||||        
GTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAGgtttgatctcctgacttattttccttacagttctgccaaacacaatgaaccgaatcttagacatttttataa-gttctaa-agtttttttaactgttatagctatgttttgcag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S120_29V6.1 (Physcomitrella patens), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctcc-------ttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacag-----aactattgtggct-tatatctatgcag---------------------------------------------------------------
||| | |||||||||||||| ||||| ||||| || || |||||| | ||||||||  | |||||||||||||| ||||| |||||  || |||         |||||   | ||    |  |||| | | |  |    |   | ||| |    | |      |||| || ||  | | ||| |    |                                                                
GTTCGCATTGCTCGTATTTTTAACACTTATGGACCAAGGATGTGCATCGATGATGGCAGGGTTGTTAGTAACTTCGTTGCTCAGgtg-agttccacacatgcccatcagtttgaaattgat-gcttccattttgaatactc-aataactccggaataatgagaaactgttatgattgtctatttgacaaaaatcctgttctggtaacttaactgttaaagttctgacaagtccactttttccttaattttcag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S120_28V6.1 (Physcomitrella patens), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataa-agccttttgaaaacactctgacagaactattgtggcttatatct-atgcag-------------------------------------------------------------------
||| | || || || ||||||||||| ||||| || ||||||||| ||||||||||  | ||||| |||||||||||||| |||||     |  |  || |   |       ||| | ||   | || | || |||| |     |   ||  | |  ||||  || | | || ||  |                                                                    
GTTCGGATCGCCCGCATTTTCAACACTTATGGACCAAGAATGTGCATTGATGATGGTAGGGTTGTCAGTAACTTTGTTGCTCAGgtgagattgatctataattcttgcactcacctccttgaaacaatatccgtttgtatg---ttcaacttagcacttgtaactgacaactgatatacgaatgaggaagtatccatgttgaccgtgatggatagtattgacaaactcgttgcgtattttgtccag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataa----agccttttgaaaacactc--tgacagaacta----ttgtggcttatatc-tatgcag--------------------------------------------------------------
||| | ||||||||||||||||| || ||||| || ||||||||  ||||||||||  | ||||| || ||||| || || |||||     |    |||  |||| |     ||   | | || | |    |   ||  | ||  | ||  ||  |  ||||      |  | ||   || ||||||                                                               
GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag
|| || || ||||||||||||||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || ||||||||  |    | ||     | |  | |       |  ||| |  |  ||||||    |  |||  |||                          
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatc-----ccttgaaaagcttcttcccgttttcattcttttg----ctttctcgcag--------------------------

upper sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ30517 (Selaginella moellendorffii), 5'ss of exon 5
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag
|| || || ||||||||||||||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || ||||||||  |    | ||     | |  | |       |  ||| |  |  |||||    ||  |||  |||                          
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatc-----cgttgaaaagcttcttcccgttttcattctttt----actttctcgcag--------------------------

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|125192778|gb|EL207732.1|EL207732
EST:     CAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCTAG                         ACCATTCGCAAACACCCAATGA
genomic: CAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCC-AGgtttagctcc ... atctatgcagACCATTCGCAAACACCCAATGA