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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAGTCTTCGTCATCGTCTCCAAAGTCTTTGAAATCGAAGGTTTATCGTTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttactctgatcccgtttcgatatttgttctcagttttttaaaacgaattcgtttgcgttggcttgatctgtttgattttctcactagtttaagg...

Basic information

species Arabidopsis thaliana
transcript AT4G11220.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G11220.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv02s0025g00640.t01 (Vitis vinifera), 5'ss of exon 1
AAGAAGTCTTCGTCATCGTCTCCAAAGTCTTTGAAATCGAAGGTTTATCGTTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttactctgatcccgtttcgatatttgttctcagttttttaaaacgaattcgtttgcgttggcttgatctgtttgatttt-ctcactagtttaagg----
    |      |  |||||||||     |||| ||| | |||||||||||  | ||||| || || |  |||||||| |||||||||||||| |||||||||| ||  | | |   ||      ||| ||| || |   ||||||        ||  | || | | ||| |         ||    ||    |   |  |     
TCCGACAACGAGAAATCGTCTCCCTCAGCTTTCAAAGCCAAGGTTTATCGGATCTTCGGCAGGGAAAAGCCTGTTCACAAGGTTCTCGGCGGTGGAAAACgtacgtaaagtgtacaccatcgatgatcttttttttttttttttt-----ttttttttgtgtggttgctaggaaaaaaaaatgcggcttgagaaaatgggaattc
















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|86046426|gb|DR342181.1|DR342181
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046427|gb|DR342182.1|DR342182
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046442|gb|DR342197.1|DR342197
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046433|gb|DR342188.1|DR342188
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046443|gb|DR342198.1|DR342198
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|116471761|gb|EG514353.1|EG514353
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046434|gb|DR342189.1|DR342189
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046428|gb|DR342183.1|DR342183
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046425|gb|DR342180.1|DR342180
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046444|gb|DR342199.1|DR342199
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046437|gb|DR342192.1|DR342192
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGWCAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046424|gb|DR342179.1|DR342179
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046439|gb|DR342194.1|DR342194
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046441|gb|DR342196.1|DR342196
EST:     TTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAA-TGTCANGAGGTGTATTTK
genomic: TTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGG-CGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|301501948|gb|HO207488.1|HO207488
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046440|gb|DR342195.1|DR342195
EST:     TTTGTTCGGAAGAGANAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046430|gb|DR342185.1|DR342185
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046438|gb|DR342193.1|DR342193
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046435|gb|DR342190.1|DR342190
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|116471630|gb|EG514222.1|EG514222
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046429|gb|DR342184.1|DR342184
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|124864373|gb|EH948810.1|EH948810
EST:     CGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: CGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
EST: gi|86046432|gb|DR342187.1|DR342187
EST:     TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAAC                         CGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG
genomic: TTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttac ... ttaattgcagCGGCAGATATATTTATGTGGAAGGACAAGAAAATGTCAGGAGGTGTATTTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAGTCTTCGTCATCGTCTCCAAAGTCTTTGAAATCGAAGGTTTATCGTTTGTTCGGAAGAGAGAGACCTGTTCATAAGGTTCTCGGCGGCGGAAAACgtatgtttactctgatcccgtttcgatatttgttctcagttttttaaaacgaattcgtttgcgttggcttgatctgtttgattttctcactagtttaagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcacta