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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGGTTGATTCTTCAGCTCCTGTTGTTGTTGATCCTAATCAGTATCATGCGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctcttagatccatttcttatgtgtattcagattaaaggaattgatgatttcaacaataaggaatgtttggttgtgtgttgatttgatatgattttcttcag

Basic information

species Arabidopsis thaliana
transcript AT3G54620.2
intron # 1
splice site 5'
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|86058664|gb|DR354421.1|DR354421
EST:     CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
genomic: CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
EST: gi|86058666|gb|DR354423.1|DR354423
EST:     CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
genomic: CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
EST: gi|124934606|gb|EL011663.1|EL011663
EST:     CTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAG
genomic: CTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAG
EST: gi|164067120|gb|ES144091.1|ES144091
EST:     GCTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
genomic: GCTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
EST: gi|86058665|gb|DR354422.1|DR354422
EST:     CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
genomic: CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA
EST: gi|86058659|gb|DR354416.1|DR354416
EST:     CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGT                         GTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCNNNNN
genomic: CGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctct ... ttttcttcagGTGGGAACTGTGAAACCGGAAGATTCGAGTGCTTCAGCTAGCAATCAAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGGTTGATTCTTCAGCTCCTGTTGTTGTTGATCCTAATCAGTATCATGCGATTCTTAAGAGCAAGCTCGAGCTTGCTTGCGCTGCTGTTGCTCGTCGTgtacgtctcttagatccatttcttatgtgtattcagattaaaggaattgatgatttcaacaataaggaatgtttggttgtgtgttgatttgatatgattttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT