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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag

Basic information

species Arabidopsis thaliana
transcript AT3G05530.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G100873_T01 (Zea mays), 5'ss of exon 2
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaagacagaactc----ttaatgatttga--gctttatgattgtgtagtttggtctgttttttaaggtgg--ggttctctgttgttgtgtttgtgtgttcag-------------------------------------------
 || ||  | || || ||||||||||| ||||| ||||| |||||||| ||||| |||||||| || |||||| | ||||| || || ||||| |||||||| |      |    |||    |  | |||| ||     || |  |||  |   | | |   || |   |    |  ||||   | |||   ||||  | | |                                               
CGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTGTAGAAGCTGGCATGCTCGCTCTACGGCGGGATGCTACAGAGgtgagccttccgctcctccatatgcacgattcgattatattttccttgcatcaatagatggattctgacatcccgtaggttgattattgacttgttgatttttctttttgtgatgattgcgatttcctaacctgatttttctttgcacag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 9
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga--cagaactcttaatgatttga--gctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag
||| || ||||| || || ||||||||||||||||||||||| ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || |||||          |   |     |   | || |  |||| |  ||    |  |       ||    |||  |    |  |   |  | |    | | |  |   
TGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttcttccagatatgcagcaacttaatagcttaaacatcaatttataaaaaaagtaaaataa--taccatgattcatcctaggagatatttactgg-

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 9
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaag---acagaactcttaatgatttgagcttta---tgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag
||| || ||||| || || ||||||||||||||||| || || ||||| || || ||||| ||||| |||||||| ||||| ||||||||||| || |||||           ||  |     ||  | || |   | |   |  |     |   |   |    |  | |     ||     | |   || ||| |  | |    
TGAAGAACTTGCCCGGTCCACAGATGATTTCAATGGCGCACAACTGAAGGCTGTCTGTGTTGAGGCTGGCATGTTGGCTCTACGCCGTGATGCAACTGAGgtttgttttcttccaagatatgcaacaacttaaatatcaatttattaaaaaaaaattaacaccatgatgaatccaggagagatatcactg-gttggcattt----

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 9
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaa---------aaagacagaact-cttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag
||| ||  | || || || |||||||||||||||| ||| || || ||||| || ||||| ||||| |||||||| || |||||||||||||| || |||||            | | |   |||  || ||| |||  |   | |||| |    |  | | | |   ||    | | |   | ||||||    | ||| | |      
TGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttcttctagatatgcaacaactaaataattaaaatatcatgacta---atctagctttaaattactggattgtcatttctgtttggatctttcttt------

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 9
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaagacagaactcttaatgatttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag--
||| || || || ||||| ||||||||||||||||| || || |||||||| || ||||||||||| || ||| | |||||||| |||||||| || ||||||          | | |         |   | |     | ||| | | || |   |      || | |    |       |  | ||      ||     
TGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTGTAGAGGCGGGAATGCTGGCTCTTCGTCGTGATGCAACTGAGgtactctctctctaccccacctcctcctacccctctccctcgtgca-tgtgctgaatgaaactagcttgccagccaccccatctttttaacagatttgaag

upper sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 9
TGAGGAGCTTGCACGATCAACAGATGATTTCAATGGAGCTCAGCTGAAAGCAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaagacagaactcttaatgatttgagctttatgat-tgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtgttcag
||||||| | || || ||||||||||| || || ||||||||  |||| || |||||| | ||||| || ||||| || ||||||||||||||||| || ||||   |  ||     | |  | ||   |   |  |  | | |  |  ||  | |  | ||  |      ||       |||||  ||  ||  |    
TGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTATTGAGGCCGGAATGTTGGCGCTTCGCCGTGATGCCACGGAAgtaagttattcaaggagcattttcatactatgctagtcttgtatcaatcttaattttctgttcgattgaaagtcaatcaatgttgaattgttgcatcatc

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|164233584|gb|ES108850.1|ES108850
EST:     CAGTGTGTGTAGAGGCTGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAA
genomic: CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAA
EST: gi|124918842|gb|EH992643.1|EH992643
EST:     CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAG
genomic: CAGTGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAG
EST: gi|124837257|gb|EH921696.1|EH921696
EST:     TGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGG
genomic: TGTGTGTAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGG
EST: gi|125216401|gb|EL230484.1|EL230484
EST:     TAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAG                         GTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAG
genomic: TAGAGGCAGGCATGTTAGCTCTTCGCCGTGATGCCACAGAGgtaaaaaaga ... gtgtgttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAG