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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatataatcccgttttcttttgctatgtttcattaagaagattgttgatgaatttttctcactaatctggtgaactcctgcaaaacctattcaaagCCAAAAGATTCGTGGAAGTCTGAGTTACGCGACTTTAATAGCAACAATGGTTTTGAGCTCAATAGAAATGGAGATAGTGGACCACTCCTTCTCGATGTTC

Basic information

species Arabidopsis thaliana
transcript AT3G55000.1
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|19877291|gb|AU238122.1|AU238122
EST:     GGGCACAACTTAATCACACGCTCATAGTTTATCAACCTGAAAGCAATTTG                         CCAAAAGATTCGTGGAAGTCTGAGTTACGCGACTTTAATAGCAACAATGGT
genomic: GGGCACAACTTAATCACACGCTCATAGTTTATCAACCTGAAAGCAATTTGgtaatcaata ... ctattcaaagCCAAAAGATTCGTGGAAGTCTGAGTTACGCGACTTTAATAGCAACAATGGT
EST: gi|124711409|gb|EH802811.1|EH802811
EST:     GGCACAACTTAATCACACGCTCATAGTTTATACAACCTGAAAGCAATTTG                         CCAAAAGATTCGT
genomic: GGCACAACTTAATCACACGCTCATAGTTTAT-CAACCTGAAAGCAATTTGgtaatcaata ... ctattcaaagCCAAAAGATTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgatgaatttttctcactaatctggtgaactcctgcaaaacctattcaaagCCAAAAGATTCGTGGAAGTCTGAGTTACGCGACTTTAATAGCAACAATGGTTTTGAGCTCAATAGAAATGGAGATAGTGGACCACTCCTTCTCGATGTTC
                  cactaat  putative branch site (score: 2)
                                            cctattc  putative PPT
      atgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaatataatcccgttttcttttgctatgtttcattaagaagattgttgatgaatttttctcactaatctggtgaactcctgcaaaacctattcaaagCCAAAAGATTCGTGGAAGTCTGAGTTACGCGACTTTAATAGCAACAATGGTTTTGAGCTCAATAGAAATGGAGATAGTGGACCACTCCTTCTCGATGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA