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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagctaatcactttgttcttactgtaaattcaagaatatctagtcttttgcctttgacaacaaagattttaagatttcgtataatttatgctctctttttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCA

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
intron # 4
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|125039477|gb|EL111746.1|EL111746
EST:     TTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTTGAGCCCATACTAGAAGCACTACCCAAACTA
genomic: TTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAG-TTGAGCCCATACTAGAAGCACTACCCAAACTA
EST: gi|125218948|gb|EL233033.1|EL233033
EST:     GAAGTCATGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCC
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCC
EST: gi|124792372|gb|EH882051.1|EH882051
EST:     CTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: CTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|124868450|gb|EH952887.1|EH952887
EST:     CGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: CGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125307684|gb|EL321769.1|EL321769
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCG
EST: gi|124863148|gb|EH947585.1|EH947585
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125040335|gb|EL112604.1|EL112604
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAG
EST: gi|125017495|gb|EL089764.1|EL089764
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAG
EST: gi|124862398|gb|EH946835.1|EH946835
EST:     TCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: TCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125258036|gb|EL272121.1|EL272121
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCAC
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCAC
EST: gi|125246797|gb|EL260882.1|EL260882
EST:     CAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: CAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125187527|gb|EL202481.1|EL202481
EST:     TGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: TGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125213423|gb|EL228255.1|EL228255
EST:     GCTTCGATGTTGTTTATGATATCAACG                         GGAGGGGAGGCCGAAGAAGTTGAG-CCATACTAGAAGCACTACCCAAACTA
genomic: GCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGA-GGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTA
EST: gi|116412032|gb|EG454624.1|EG454624
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125002089|gb|EL074358.1|EL074358
EST:     CTTTCAGCAGAAGGCTTCGATGTTGTTTACGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: CTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125100739|gb|EL156087.1|EL156087
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAG
EST: gi|125008009|gb|EL080278.1|EL080278
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAAGAAGTTGAGCCCATACTAGAAGCACTACCC
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAA-GAAGTTGAGCCCATACTAGAAGCACTACCC
EST: gi|164226909|gb|ES086149.1|ES086149
EST:     GATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAAC
genomic: GATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAAC
EST: gi|116412031|gb|EG454623.1|EG454623
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125263216|gb|EL277301.1|EL277301
EST:     TGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: TGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|124941309|gb|EL017678.1|EL017678
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAG
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAG
EST: gi|124867224|gb|EH951661.1|EH951661
EST:     TTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: TTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|124947840|gb|EL023647.1|EL023647
EST:     CTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: CTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
EST: gi|125165514|gb|EL191765.1|EL191765
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACC
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACC
EST: gi|124858704|gb|EH943141.1|EH943141
EST:     GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATA
genomic: GAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATA
EST: gi|125169805|gb|EL193623.1|EL193623
EST:     AAGGCTTCGATGTTGTTTATGATATCAACG                         GGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG
genomic: AAGGCTTCGATGTTGTTTATGATATCAACGgtaacagcta ... tttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgacaacaaagattttaagatttcgtataatttatgctctctttttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCA
 ctttgac  putative branch site (score: 4)
                                tttatgctctcttttt  putative PPT
         aaagattttaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagctaatcactttgttcttactgtaaattcaagaatatctagtcttttgcctttgacaacaaagattttaagatttcgtataatttatgctctctttttttctcagGGAGGGAGGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA