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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtttcgattaggttcgatttggttatttttacctgtgaattgatctcgattcgttgtattaacgtctctttgtgtttttttattctgtttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTCAGACGAGAGCATCAGAGGATCACAAATGGTCTACTGTTGCAACGAAGCT

Basic information

species Arabidopsis thaliana
transcript AT3G27090.1
intron # 1
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|152034258|gb|BP823391.2|BP823391
EST:     CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAG                         CCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
genomic: CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAGgtctctctcg ... tttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
EST: gi|301503164|gb|HO208704.1|HO208704
EST:     CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAG                         CCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
genomic: CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAGgtctctctcg ... tttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
EST: gi|86024217|gb|DR319970.1|DR319970
EST:     CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAG---AACAACAACAAAAG                         CCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
genomic: CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAGgtctctctcg ... tttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
EST: gi|125093772|gb|EL151311.1|EL151311
EST:     CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAG                         CCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAG
genomic: CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAGgtctctctcg ... tttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAG
EST: gi|86024210|gb|DR319963.1|DR319963
EST:     CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAG---AACAACAACAAAAG                         CCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC
genomic: CCGCCGGATTTCGAGGAAACGAAGAAGAAGAAGAACAACAACAACAAAAGgtctctctcg ... tttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgattcgttgtattaacgtctctttgtgtttttttattctgtttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTCAGACGAGAGCATCAGAGGATCACAAATGGTCTACTGTTGCAACGAAGCT
              tattaac  putative branch site (score: 1)
                                tttttttattctgttt  putative PPT
                                tttttttattctgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtttcgattaggttcgatttggttatttttacctgtgaattgatctcgattcgttgtattaacgtctctttgtgtttttttattctgtttatgctagCCTTTTGAGATATGGACAGCTTCTGGCAATTAGGTGATGAGCTACGAGGTCAGACGAGAGCATCAGAGGATCACAAATGGTCTACTGTTGCAACGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- ggtttcg
- - - - - - - - - gatttgg