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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtgtgattggtttcatcttgataataagaagcattgttattgtctcttgttagaaactcaagtcacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG

Basic information

species Arabidopsis thaliana
transcript AT3G25520.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 5
---gtatgttgtgtgattggtttcatcttgataataagaagcattgttattgtctcttgttagaaactcaagtcacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
     || | |    ||   |    |  |  |||||       |||   | || |  | ||    ||     ||      |  ||||||||||||| || ||||| || ||||||||| |||||   ||||| ||||||||||||||  | |||||||| ||||||||||| |||||||| |||||||
gtaaaatttggccaaatatataatcttattttaatatctgatgttgcattggtttggtatttctgac--ggttctttttgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTG

upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 5
gtatgttgtgtgatt-ggtttcatcttgataataagaagcattgttattgtctcttgttagaaactcaagtcacac-----aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
       ||   ||| || |  || | |||  ||        || | |    | | ||| |  | | |  |            |  ||||||||||||| || ||||| || ||||||||| |||||   ||||| ||||||||||||||  | |||||||| ||||| ||||| ||||| || |||||||
-------gtaaaatttggctaaatttcgatcttattttttgctgatgtcacat-tggttgggcatttatattgtttcttttcgttcatcagGCCACTGGTGAGGACTTCTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTG

upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 5
gtatgttgtgtgattg----gtttcatcttgataataagaagcattgttattgtctc----ttgttagaaactcaagt-cacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
|||| || ||   |||    | |   | |   |      ||    ||   || ||||    ||||||   | |    |  |  |  |  ||||||| |||||||| |||| ||| || || ||  ||||    ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||| || |||||||
gtat-ttatgaatttgctatgctgtgtgtgtgtgtgtgcaactgctgcctttctctcagttttgttaattaattggttgtatccttttcatcagGCTACTGGAGAGGACTATTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTG

upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 5
gtatgttgtgtgattggtttcatcttgat-----aataagaagcattgttattgtctctt--gttagaaactcaagtcacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
|||| || || | ||| | |  | ||  |     |   ||   | || || | |     |  | ||   | |    ||  |   |   |||||| |||||||| || | |||||| || ||  ||||    ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||| || |||||||
gtat-ttatgagtttgctatgctgtttgtgccccagcgagtgcctttcttttggctgtgtaagctaatgagttgtatcttattttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

upper sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 5
gtatgttgtgtgattggtttcatcttgat-----aataagaagcattgttattgtctctt--gttagaaactcaagtcacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
|||| || || |  || | |    ||  |     |   ||   | || ||   |     |  | ||   | |    ||  |   |   |||||| |||||||| || | |||||| || ||  ||||    ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||| || |||||||
gtat-ttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTG

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|164048039|gb|ES203625.1|ES203625
EST:     TGAGGGAAAACGTTGAG                         GCCACTGGAGAGGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: TGAGGG-AAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|124942201|gb|EL018488.1|EL018488
EST:     TTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: TTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|125270568|gb|EL284653.1|EL284653
EST:     TATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: TATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|164165069|gb|ES033006.1|ES033006
EST:     TGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAGGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: TGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|124728441|gb|EH819843.1|EH819843
EST:     ATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: ATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|164072194|gb|EL982875.1|EL982875
EST:     CGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAGGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: CGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|124949905|gb|EL025417.1|EL025417
EST:     TGTTGG-AATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATT
genomic: TGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATT
EST: gi|164006650|gb|EL971289.1|EL971289
EST:     AGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAGGACTTCTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: AGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|124910228|gb|EH984308.1|EH984308
EST:     AGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: AGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
EST: gi|125255909|gb|EL269994.1|EL269994
EST:     ATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAG                         GCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC
genomic: ATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtg ... aatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagaagcattgttattgtctcttgttagaaactcaagtcacacaatgaatcagGCCACTGGAGAAGACTTTTCCGTTGAGCCAACTGATTCAAGGAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACCACAACAGGAAACCGTG
         attgttatt  TA-rich tract