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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactaaatatatccaacattttgaattaccttcttcaaagaatatatataccatagatctatttcttatgcatgcatacacgctttttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCTCGTGTGTTCGAGAATACAAAAGCATTCTAACATCAAAAAGCACTGAAGA

Basic information

species Arabidopsis thaliana
transcript AT3G11680.1
intron # 2
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|116404273|gb|EG446865.1|EG446865
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404278|gb|EG446870.1|EG446870
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404286|gb|EG446878.1|EG446878
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404475|gb|EG447067.1|EG447067
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATCTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404282|gb|EG446874.1|EG446874
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAA
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAA
EST: gi|116404280|gb|EG446872.1|EG446872
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCC
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404444|gb|EG447036.1|EG447036
EST:     TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAG                         GATTCGAGGGTGAATATTTTCAACCGGAGAAGATCTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
EST: gi|116404279|gb|EG446871.1|EG446871
EST:     TCACAAGATGATTGCTAACAACATTAACAATCTTGCTAAGTACCTAGAAG                         GATTTGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT
genomic: TCACAAGATGATTGCTAACAACATTAACAAACTTGCTAAGTACCTAGAAGgtgactaaat ... tttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatataccatagatctatttcttatgcatgcatacacgctttttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCTCGTGTGTTCGAGAATACAAAAGCATTCTAACATCAAAAAGCACTGAAGA
                                        cgcttttt  CT-rich tract
                                           tttttataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactaaatatatccaacattttgaattaccttcttcaaagaatatatataccatagatctatttcttatgcatgcatacacgctttttataaaagGATTCGAGGGTGAATATTTTCAACCGGAGAAGATTTCAAAGGAGACAAGCTCGTGTGTTCGAGAATACAAAAGCATTCTAACATCAAAAAGCACTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA