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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggatggtttctcttttggtctcctactcttcacaggtatatatgtacatgctaacttgtgtaattttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGTGACTGGAATGGCTAAAGCAAAGGACAAGTCATCTGCTGCAAATCAAAAC

Basic information

species Arabidopsis thaliana
transcript AT3G42790.1
intron # 3
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|86069053|gb|DR364810.1|DR364810
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATAATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86069050|gb|DR364807.1|DR364807
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86069049|gb|DR364806.1|DR364806
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATAATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86069051|gb|DR364808.1|DR364808
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATAATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86069052|gb|DR364809.1|DR364809
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGNGGTTGTTCAACATGATCAATAATGTTCCTACTATATTTGAAGNAGN
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|164148636|gb|EL996131.1|EL996131
EST:     TCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTAATATTTGAAGTAG
genomic: TCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTA-TATTTGAAGTAG
EST: gi|124983514|gb|EL056240.1|EL056240
EST:     TTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|124962185|gb|EL036627.1|EL036627
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAG
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAG
EST: gi|164062938|gb|ES036091.1|ES036091
EST:     AAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAG
genomic: AAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAG
EST: gi|86069046|gb|DR364803.1|DR364803
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86059812|gb|DR355569.1|DR355569
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|86069047|gb|DR364804.1|DR364804
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|125023834|gb|EL096103.1|EL096103
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACA
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACA
EST: gi|164109340|gb|ES082286.1|ES082286
EST:     CACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: CACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
EST: gi|116471935|gb|EG514527.1|EG514527
EST:     TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAG                         GAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT
genomic: TCTGTCTCGTTTTACTTTGGCTCAAGGTTTTCTTTCCACAAGGAAGAGAGgtaatggatg ... attttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctcctactcttcacaggtatatatgtacatgctaacttgtgtaattttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGTGACTGGAATGGCTAAAGCAAAGGACAAGTCATCTGCTGCAAATCAAAAC
                               tgctaac  putative branch site (score: 1)
                                              ttttttc  putative PPT
                                      ttgtgtaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggatggtttctcttttggtctcctactcttcacaggtatatatgtacatgctaacttgtgtaattttttcagGAAGCGTTTGTTCAACATGATCAATGATGTTCCTACTATATTTGAAGTAGTGACTGGAATGGCTAAAGCAAAGGACAAGTCATCTGCTGCAAATCAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC