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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataaatgaagataatgatgtgctttttgctcttgtttctctttattaatgaataatgagtcatagggcactactcatcttgcctcactgttgattgaattcatgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGCCTCTCAAATTCCACAGGAGAGTGAAGACAAGGAACATAAAGAGACTCCT

Basic information

species Arabidopsis thaliana
transcript AT5G13560.1
intron # 6
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|116478203|gb|EG520795.1|EG520795
EST:     TTTGCCCAAAATGCCATCACAGGGTTGAAGATTAATGCTGAAATGCTGAG                         AATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGC
genomic: TTTGCCCAAAATGCCATCACAGGGTTGAAGATTAATGCTGAAATGCTGAGgtgataaatg ... atgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGC
EST: gi|164052182|gb|ES113310.1|ES113310
EST:     CACAGGGTTGAAGATTAATGCTGAAATGCTGAG                         AATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGC
genomic: CACAGGGTTGAAGATTAATGCTGAAATGCTGAGgtgataaatg ... atgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGC
EST: gi|116478208|gb|EG520800.1|EG520800
EST:     TTTGCCCAAAATGCCATCACAGGGTTGAAGATTAATGCTGAAATGCTGAG                         AATTGATGCTGAAGCTTTTGATTTGAGAAAGAAACTCGAAAAGATGAATGC
genomic: TTTGCCCAAAATGCCATCACAGGGTTGAAGATTAATGCTGAAATGCTGAGgtgataaatg ... atgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtcatagggcactactcatcttgcctcactgttgattgaattcatgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGCCTCTCAAATTCCACAGGAGAGTGAAGACAAGGAACATAAAGAGACTCCT
                                              tgttttc  CT-rich tract
                                    attgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataaatgaagataatgatgtgctttttgctcttgtttctctttattaatgaataatgagtcatagggcactactcatcttgcctcactgttgattgaattcatgttttcagAATTGATGCTGAAGCTTCTGATTTGAGAAAGAAACTCGAAAAGATGAATGCCTCTCAAATTCCACAGGAGAGTGAAGACAAGGAACATAAAGAGACTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA