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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctcaaaatcgtaaaaccctaaatcaaaatctaaacaaataaatggtcaaaaccctgaattcaattgttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCATTCAGATCAAAAGAGCAGAGGGTGAAGCAGAGTCAAAGTACCTGTCGGG

Basic information

species Arabidopsis thaliana
transcript AT3G01290.1
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|116437518|gb|EG480110.1|EG480110
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
EST: gi|125232934|gb|EL247019.1|EL247019
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGC
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGC
EST: gi|86083495|gb|DR379254.1|DR379254
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCWGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
EST: gi|116437519|gb|EG480111.1|EG480111
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
EST: gi|124819415|gb|EH904281.1|EH904281
EST:     GTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
genomic: GTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
EST: gi|301501545|gb|HO207085.1|HO207085
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAAGAGGCTGAAAAAATC
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCA-GAGGCTGAGAAAATC
EST: gi|125034696|gb|EL106965.1|EL106965
EST:     AACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
genomic: AACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCA
EST: gi|124790142|gb|EH879821.1|EH879821
EST:     CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCG                         CGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGG
genomic: CATTGAGCCTGATCAACAGGTTAAACGTGCCATGAACGAAATCAACGCCGgtaagtcctc ... gttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaaaatctaaacaaataaatggtcaaaaccctgaattcaattgttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCATTCAGATCAAAAGAGCAGAGGGTGAAGCAGAGTCAAAGTACCTGTCGGG
       atctaaa  putative branch site (score: 3)
     aaatctaaacaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctcaaaatcgtaaaaccctaaatcaaaatctaaacaaataaatggtcaaaaccctgaattcaattgttgttacagCGGCGAGGATGAGAGTGGCAGCGAGCGAAAAAGCAGAGGCTGAGAAAATCATTCAGATCAAAAGAGCAGAGGGTGAAGCAGAGTCAAAGTACCTGTCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC