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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttcttcctcacattactctttactcttaaggccaatctggtttttgatttgtcggaaaaatgaaaatatcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACACATACAAGACGCAAATGCTATATTCTCATTGGTATTGGATGAAGAAGATG

Basic information

species Arabidopsis thaliana
transcript AT2G27680.1
intron # 8
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|124973733|gb|EL047339.1|EL047339
EST:     GTACTAGATCAG                         CAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC
genomic: GTACTAGATCAGgtatttgttc ... atcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC
EST: gi|125223097|gb|EL237182.1|EL237182
EST:     AACGTGGAGTCTCTATACCAACAGTGGCTGTGAGATATGTACTAGATCAG                         CAAGGAGTTGGTGGATCAA
genomic: AACATGGAGTCTCTATACCAACAGTGGCTGTGAGATATGTACTAGATCAGgtatttgttc ... atcatctcagCAAGGAGTTGGTGGATCAA
EST: gi|124938232|gb|EL014888.1|EL014888
EST:     TGAGATATGTACTAGATCAG                         CAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGACGGAACA
genomic: TGAGATATGTACTAGATCAGgtatttgttc ... atcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAG-CGGAACA
EST: gi|86075241|gb|DR370998.1|DR370998
EST:     AACATGGAGTCTCTATACCAACAGTGGCTGTGAGATATGTACTAGATCAG                         CAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC
genomic: AACATGGAGTCTCTATACCAACAGTGGCTGTGAGATATGTACTAGATCAGgtatttgttc ... atcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC
EST: gi|125031971|gb|EL104240.1|EL104240
EST:     TGGCTGTGAGATATGTACTAGATCAG                         CAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC
genomic: TGGCTGTGAGATATGTACTAGATCAGgtatttgttc ... atcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttaaggccaatctggtttttgatttgtcggaaaaatgaaaatatcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACACATACAAGACGCAAATGCTATATTCTCATTGGTATTGGATGAAGAAGATG
                   ttttgat  putative branch site (score: 4)
                                              tcatctc  putative PPT
                                 aaaaatgaaaatatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgttcttcctcacattactctttactcttaaggccaatctggtttttgatttgtcggaaaaatgaaaatatcatctcagCAAGGAGTTGGTGGATCAATGATTGGAGTGAGACTCGGGTTAGCGGAACACATACAAGACGCAAATGCTATATTCTCATTGGTATTGGATGAAGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG