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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGATTCTCTGATCAGTACACTCTCACCATCGACAGTGCTGATCCAAAATCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctctcggcatctttcttacaattgctcgctctgttttccttacatgagtctcattagatggtttctctgtgtgtttttcag

Basic information

species Arabidopsis thaliana
transcript AT2G39960.1
intron # 4
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|86023934|gb|DR319687.1|DR319687
EST:     TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCT
genomic: TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCT
EST: gi|163969403|gb|ES038693.1|ES038693
EST:     AAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGA
genomic: AAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGA
EST: gi|124961803|gb|EL036287.1|EL036287
EST:     TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAG
genomic: TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAG
EST: gi|86023936|gb|DR319689.1|DR319689
EST:     TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAGGGNNTATTCTGGGAAGACGTAGA
genomic: TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGA
EST: gi|86076622|gb|DR372379.1|DR372379
EST:     TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGA
genomic: TCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGA
EST: gi|125002564|gb|EL074833.1|EL074833
EST:     GCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAA
genomic: GCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAA
EST: gi|86023937|gb|DR319690.1|DR319690
EST:     CAATCTCAGCTGGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATG                         GTTCACGAAAGATGGAGTTCTTTGTTGAGGGTTTA
genomic: CAATCTCAGCTGGG-AAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctct ... tgtttttcagGTTCACGAAAGATGGAGTTCTT-GTTGAGGGTTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGATTCTCTGATCAGTACACTCTCACCATCGACAGTGCTGATCCAAAATCAATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGgtctctctctcggcatctttcttacaattgctcgctctgttttccttacatgagtctcattagatggtttctctgtgtgtttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA