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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtaggaatagtcttcatgatcccttttttgccactgtttcttgatttcgacgggataatgtttgaaaggagatgtgatatattatatctgttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAGAAATACAAGCATATGATTGGAGGTCCTTCTCTTCAGGTTGATGTGCACA

Basic information

species Arabidopsis thaliana
transcript AT3G04090.1
intron # 1
splice site 3'
intron type U2

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|116485953|gb|EG528545.1|EG528545
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485960|gb|EG528552.1|EG528552
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTATATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAAAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485956|gb|EG528548.1|EG528548
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485961|gb|EG528553.1|EG528553
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116468028|gb|EG510620.1|EG510620
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485957|gb|EG528549.1|EG528549
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485972|gb|EG528564.1|EG528564
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485968|gb|EG528560.1|EG528560
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485976|gb|EG528568.1|EG528568
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|116485955|gb|EG528547.1|EG528547
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
EST: gi|164124786|gb|ES163997.1|ES163997
EST:     GTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAAGAATTACCTGCTCAG                         GCAATTGGTGCTG
genomic: GTCCCCGGAGATACTCTTTTCTCCTTGGCGATTA-GA-TTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTG
EST: gi|86073834|gb|DR369591.1|DR369591
EST:     GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAG                         GCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG
genomic: GTGTCCCCGGAGATACTCTTTTCTCCTTGGCGATTAGATTACCTGCTCAGgttttctaaa ... gttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgacgggataatgtttgaaaggagatgtgatatattatatctgttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAGAAATACAAGCATATGATTGGAGGTCCTTCTCTTCAGGTTGATGTGCACA
                                              ttattcc  CT-rich tract
                              tgatatattatatctg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaggaatagtcttcatgatcccttttttgccactgtttcttgatttcgacgggataatgtttgaaaggagatgtgatatattatatctgttattccagGCAATTGGTGCTGCAGGAGGTGCATTGGCGATCATGGAGTTCATACCAGAGAAATACAAGCATATGATTGGAGGTCCTTCTCTTCAGGTTGATGTGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaga