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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacatccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G39280.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G101463_T01 (Zea mays), 3'ss of exon 9
gtatcctctagttattaagaatcttggttttcagctttccatggag-gctttaaggatatcta-attatacatccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                  || |  |||      |      || ||     |||  | | |||  ||||    ||| |   || ||| || |||  || | ||   ||| | | | | |    ||||||||||||||| |||||  |||| |||||||| ||||| |||||||| ||||| ||||| || || || || ||||
-----------------ggatttctgggccattgtaacatatagattatattactgctttctggattaagagtccctgcattcctaatt-ttgcatgtttttg--ctgctgctt-tgc----cagCTTCTGGAATTTCGATGCACTGTTTCAGCCTCAACAGCATCCTGCTCGGGATTCACATGATACATTTTTCCTGAAAG

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G12530.1 (Glycine max), 3'ss of exon 8
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacatccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                  | ||       | ||    |  |  ||   || ||  |||| || || |  |  ||   | |   || | ||  ||    |  || || |  || ||     |||||||||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||| || |||||| |  || 
-----------------tgcattgcaacat-cacaaatgaagtgacatttaaaaaatatatattttttaaatct---catatcatatattttcttgcttgtatgtgct--atttaattggcagCTTCTGGAACTTTGATGCCTTGTTCCAGCCCCAACAACACCCAGCCCGTGATTCACATGATACATTCTTTTTGGAAA

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G04730.1 (Glycine max), 3'ss of exon 8
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaag-gatatctaattatacatccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                      |||| || |  |  | | ||  |   |||| | |||||  |||   |||   | |   |    | |        || |  |||||| |  | ||     |||||||||||| |||||||| ||||||||||| || || ||||| || |||||||| ||||| || |||||| |  || 
----------------------cttgcttatatg--tcctatttactatttaggtgatattgaatccaacaggttatatgtctgctctcgccttaaatttacatctgaatgttttaattggcagCTTCTGGAACTTTGATGCCTTGTTCCAGCCCCAACAACACCCAGCCCGTGATTCACATGATACATTCTTTTTGGAAA

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G34950.1 (Glycine max), 3'ss of exon 10
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacat-ccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
              | ||       ||||||   |  |   || ||    |   |  |  ||     ||||  ||  |||  |  |   ||        |  |||||| |  | |      |||||||||||| || ||||| ||||||||||| || || ||||| ||||||||||| ||||| || || |||||  |||
--------------tgaatccaacaggttttactcactgtgtgtagcaact---ggcaagtagcagcacatgtctgctctcaccctaaatt-------ttacatctgaatgttttgattggcagCTTCTGGAACTTCGATGCCTTGTTCCAGCCCCAACAACACCCAGCTCGTGATTCACATGATACATTTTTTCTGGAAG

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv03s0063g02560.t01 (Vitis vinifera), 3'ss of exon 9
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacatccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
        |   | |  ||    |||  | | | |   | ||      ||||  | |  |  ||         |||| ||||| || | |   | |||    | |||| | |  ||  | |||||||||||||||||||||  |||||||||| || || ||||||||||||||||| ||||| |||||||| ||  |||
-------atgcatttccagggctttgaatgttaacccactat------tttagtggtgaccgata--------tttttttgctcttagatt-ttaatccctttatgatgc-tccaccttccagCTTCTGGAATTTTGATGCACTGTTCCAGCCACAACAACACCCTGCTCGTGATTCACATGATACCTTCTTCCTGCAAG

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S358_20V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------gtatcctctagttattaagaatctt----ggttttcagct---ttccatggaggctttaaggatatctaattatacatccttttcttgctat-ttgttg-gctgatcttaatctgattcatatac----------------gctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                       |||  |||  |||||   | |  |       ||||   |   || |||| |     || | || | | |   | || ||| |||     || |||||| | | | | |  |||  | |  |||                   |  |||||||||||||| |||||  ||||||||||||| ||||| || || ||||| |||||||||||||| ||  | || |
gtacttggaacgcatcaatcacctattttcttcttatttgcatttattcgaaactttcccttagattgcatgaaattaatacgcatgtttgagactgcaccctcttcggtacatgttgttgagttaagcgttttctagtactcatattgttttgttcgtgggaattgtagCTTCTGGAATTTCGATGCACTGTTCCAGCCTCAACAGCATCCAGCCCGTGACTCTCATGACACCTTTTTCTTGAAGG

upper sequence: AT4G39280.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ30485 (Selaginella moellendorffii), 3'ss of exon 9
gtatcctctagttattaagaatcttggttttcagctttccatggaggctttaaggatatctaattatacatccttttcttgctatttgttg-gctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                                                                      | ||| |||||  |    ||| |  ||  |||| |  |||  | |   | | |||||||||||||| ||||| ||||||||||| |||||||| ||||| || || || || ||||| |||||  ||||| 
---------------------------------------------------------------------gtacttgtcttgacaacaattgcgtcgagtttaagc--atttgtctttacgatagCTTCTGGAATTTCGATGCCTTGTTCCAGCCGCAGCAGCATCCTGCCCGGGACTCACACGACACATTCTTCTTAAAAA

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|164208897|gb|ES026766.1|ES026766
EST:     GCCAACAAACAACTATGTGGAGAGCAG                         CTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGA
genomic: GCCAACAAACAACTATGTGGAGAGCAGgtatcctcta ... tacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catccttttcttgctatttgttggctgatcttaatctgattcatatacgctacagCTTCTGGAATTTTGATGCTTTGTTCCAGCCTCAGCAGCACCCTGCTCGTGATTCTCATGACACCTTCTTTCTAAAAG
                                      attcatata  TA-rich tract