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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taataacaagatttgaatccttgatagatttaggatttcacaggattccaacacacttaccattctctatgtttgttcatgttctgttgtgaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATGGAAACTACTGAGAGTGCTTCAGCTTTCAAACCTGTTCTAATAACATGAA

Basic information

species Arabidopsis thaliana
transcript AT5G59613.2
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|164217706|gb|EL992843.1|EL992843
EST:     GTTTGTCCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
genomic: GTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
EST: gi|19799281|gb|AU230571.1|AU230571
EST:     AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
genomic: AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
EST: gi|86082122|gb|DR377881.1|DR377881
EST:     AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCTGAAGCGTTCTTATG
genomic: AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
EST: gi|125208773|gb|EL223727.1|EL223727
EST:     AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTC
genomic: AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTC
EST: gi|164142940|gb|ES154622.1|ES154622
EST:     AGAACTCCAAGTTTGTCCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTACGAAGCTGAGAAGCCGAAG
genomic: AGAACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGT-CGAAGCTGAGAAGCCGAAG
EST: gi|164200813|gb|ES091144.1|ES091144
EST:     AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCG                         GTGATCCACTGACGTGAGTTGTCGAAGCTGAGAAGCCG
genomic: AGGAAGACGCCAAGAACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCG
EST: gi|164033508|gb|ES033232.1|ES033232
EST:     TCCAAGTTTGTCCAACAACACAGGCG                         GTGATTCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTAT
genomic: TCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGA-TCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTAT
EST: gi|164104243|gb|ES133338.1|ES133338
EST:     AACTCCAAGTTTGTCCGACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
genomic: AACTCCAAGTTTGTCCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
EST: gi|125019417|gb|EL091686.1|EL091686
EST:     CCAACAACACAGGCG                         GTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG
genomic: CCAACAACACAGGCGgtaatgtctt ... gaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaacacacttaccattctctatgtttgttcatgttctgttgtgaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATGGAAACTACTGAGAGTGCTTCAGCTTTCAAACCTGTTCTAATAACATGAA
        cacttac  putative branch site (score: 2)
                      tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taataacaagatttgaatccttgatagatttaggatttcacaggattccaacacacttaccattctctatgtttgttcatgttctgttgtgaaatctcagGTGATCTACTGACGTGAGTTGTCGAAGCTGAGAAGCCGAAGCGTTCTTATGGAAACTACTGAGAGTGCTTCAGCTTTCAAACCTGTTCTAATAACATGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - aacaaga
- - - - - - -tgaatcc
- - - - - - - - - - - - - gatttag
- - - - - - - - - - - - - - - - - - - - - - - -ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt