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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA

Basic information

species Arabidopsis thaliana
transcript AT5G42270.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 4
gtagt-ttacaactgaaactgtactggttttgatttacaagagtagt--cttcgagtgttaa-acaatgtttattgtgtt----tcacctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
||  | || |  |  |  |||| |   | |  ||     |  || |   || ||  | || |   | |||    |||  |    |    |   | |||||||| || ||||||||||||||  | || || |||||||| ||||| || || || |||||||||||||| || || ||  | || ||||| || |||
gtgctctttctgcatactctgttcatttctgcatcattgactgttgctgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcagGGTTGCTGAGGAGGTGATCTTTGGCCAAGACAACGTGACAACAGGAGCTTCCAACGACTTCATGCAAGTGTCACGTGTCGCAAGGCAGATGGTCGAAAGA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 3
-gtagtttacaactgaaactgtactggtttt-gatttacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcac----ctatggta-----gGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
 || |  ||    |  || | |   | | |  |||  | |    |   ||| ||   || || | | | |      || ||     |||||| |     ||||||| |||||||| || |||||  | || ||||| || ||||||||||||||||| ||||||||||| || || |||||  | || ||||||||||||
tgtgggatatggttataattttgtagatgtgagatgcagagttttgtgctttgaagtttgaatattatctgacaaattccatgtctctatggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATCAAATGACTTCATGCAAGTTTCACGAGTGGCAAGGCAGATGGTTGAGAGA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 3
--------gtagtttacaactgaaactgtactggttttgatttacaagagtagtcttcgagtgtta----aacaatgtttattgtgtttcacctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
         | |   |    ||  | | |   | |||   |||       |    || || | |||     ||||  |  || || | |     |    |||||||| |||||||| || |||||  | || ||||| || |||||||||||||| || ||||||||||| || || |||||  | || ||||||||||||
tttgcattatgggacatggttgttattttgtagatttgagttttgtgctttgaagtttgaatattatcctgacaaattccat-gtctctatggcaaaacagGGTTGCCGAAGAGGTTATTTTTGGCCAGGAAAATGTCACCACCGGAGCATCAAACGACTTCATGCAAGTTTCACGAGTGGCAAGGCAGATGGTTGAGAGA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 3
-------gtagtttacaactgaaactgtactggttttgatttacaagagt--agt-cttcgagtgttaaacaa--tgtttattgtgtttcacctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
        || |   |   |  |  ||   |||  ||      ||| | |  | | | || | |   |||  |    | | |||    ||||  |||  ||||||||||||||||| || |||||||| || ||||| ||||| || ||||| ||||| || |||||||| || ||||||||  | || ||||| ||||||
tcctattatattgggcttgttcagttgatatggggttacccatcaacaatctattacctcaattaacaaaagaatcatctcttggtcatcactaatg-cagGGTTGCAGAAGAGGTAATATTTGGAGAGGATAATGTAACAACAGGGGCATCCAATGACTTTATGCAAGTTTCACGGGTGGCCAGGCAGATGGTGGAGAGA

upper sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ37923 (Selaginella moellendorffii), 3'ss of exon 3
gtagtttacaactgaaactgtactggttttgatttacaagagta-gtcttcgagtgttaaacaatgtttattgtgtttcacctatggt---agGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
                                         ||| ||  || | | ||   | || ||  |||  ||   | |  | |   ||  | || || ||||||||||| ||   |||||| || || |||||||| ||||| ||||||  ||||||||||||||| || ||||| ||||| ||| ||
-----------------------------------------gtacgtgatctaatcttc--ccattttctttgctttaagcgtgcgattccagAATCGCGGAGGAGGTGATCTTCGGCCCCGAGAACGTCACCACCGGAGCTTCAAACGATTTCCAGCAAGTGTCGCGGGTTGCACGCCAGATGGTGGAGCGA

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|125017651|gb|EL089920.1|EL089920
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCG
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCG
EST: gi|125212703|gb|EL227657.1|EL227657
EST:     ATAGCAGAAGCTACCTTGAGAACCAAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACG
genomic: ATAGCAGAAGCTACCTTGAGAACC-AAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACG
EST: gi|125189404|gb|EL204358.1|EL204358
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAAT
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAAT
EST: gi|124889013|gb|EH967915.1|EH967915
EST:     TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGG
genomic: TATAGCAGAAGCTACCTTGAGAACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGG
EST: gi|125034754|gb|EL107023.1|EL107023
EST:     ATAGCAGAAGCTACCTTGAGTAACCAAATGGCTGTTGCACTTGGTGGAAG                         GGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAG
genomic: ATAGCAGAAGCTACCTTGAG-AACCAAATGGCTGTTGCACTTGGTGGAAGgtagtttaca ... cctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaagagtagtcttcgagtgttaaacaatgtttattgtgtttcacctatggtagGGTTGCAGAAGAGGTGATCTTTGGAGACGAGAATGTGACAACCGGAGCATCAAATGATTTCATGCAAGTGTCGCGGGTGGCTCGCCAAATGGTTGAGAGA
                                        tttcacct  CT-rich tract
                     ttaaacaatgtttatt  TA-rich tract