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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaataaaaacagtatttccctgggttgcatttttgtttgtatatgctgatcttaaaccatgaatctgtatttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAAATGTCAGCAAAGGACAT

Basic information

species Arabidopsis thaliana
transcript AT1G09150.1
intron # 6
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|164085171|gb|ES001513.1|ES001513
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGC
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGC
EST: gi|125326184|gb|EL340264.1|EL340264
EST:     AAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCT-CACCAAA
genomic: AAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|116478254|gb|EG520846.1|EG520846
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|125207790|gb|EL222744.1|EL222744
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAGGGCCAGTG                         GCCATATATGCAGAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAA
EST: gi|164007529|gb|ES198601.1|ES198601
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACAT
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACAT
EST: gi|124837179|gb|EH921618.1|EH921618
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAA
EST: gi|164205287|gb|ES091206.1|ES091206
EST:     CTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: CTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|164013820|gb|ES004040.1|ES004040
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTC
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTC
EST: gi|124993560|gb|EL065829.1|EL065829
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATNTGCAGAAGGAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAA
EST: gi|124854092|gb|EH938529.1|EH938529
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         -CCATATATGCAGAAGGAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAA
EST: gi|124780972|gb|EH870915.1|EH870915
EST:     ATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: ATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|125073969|gb|EL138100.1|EL138100
EST:     TCCCCGGGAGGCGTTCTGGATCAAGTAAGTTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTT
genomic: TCCCCGGGAGGCGTTCTGGATCAAG-AAG-TCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTT
EST: gi|86061004|gb|DR356761.1|DR356761
EST:     CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: CATCCCCGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|124998999|gb|EL071268.1|EL071268
EST:     CTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: CTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
EST: gi|125162356|gb|EL189126.1|EL189126
EST:     CGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTG                         GCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA
genomic: CGGGAGGCGTTCTGGATCAAGAAGTCGAGGCTGAAAGGCCAGTGgtatgaataa ... atttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcatttttgtttgtatatgctgatcttaaaccatgaatctgtatttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAAATGTCAGCAAAGGACAT
                    tgctgat  putative branch site (score: 3)
                                              tttgttt  putative PPT
     atttttgtttgtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaataaaaacagtatttccctgggttgcatttttgtttgtatatgctgatcttaaaccatgaatctgtatttgtttagGCCATATATGCAGAAGGAAAGCAACATGCCTTAGCAATAGGCTTCACCAAAATGTCAGCAAAGGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG