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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagttattttccagaatattgctgttggtctttatcgatatctcagctttgtttagtatctttgtggcattgtggctgatcgtcctcctttttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGAGTCCGAACATCTCGTAACTCTCCTTGCAGTTGTTCCGAAGTATTCCCAA

Basic information

species Arabidopsis thaliana
transcript AT1G12840.1
intron # 5
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|124842801|gb|EH927238.1|EH927238
EST:     GCCATT-ACCGAAAGCAAAGTGGAAG                         CTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGA
genomic: GCCATTAACCGAAAGCAAAGTGGAAGgtaattcttt ... tttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGA
EST: gi|125230858|gb|EL244943.1|EL244943
EST:     AACTCAATGCCATTAACCGAAAGCAAAGTGGAAGG                         CTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCG
genomic: AACTCAATGCCATTAACCGAAAGCAAAGTGGAA-Ggtaattcttt ... tttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCG
EST: gi|164035646|gb|ES192485.1|ES192485
EST:     GGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAG                         CTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGA
genomic: GGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAGgtaattcttt ... tttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgtttagtatctttgtggcattgtggctgatcgtcctcctttttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGAGTCCGAACATCTCGTAACTCTCCTTGCAGTTGTTCCGAAGTATTCCCAA
                            ggctgat  putative branch site (score: 4)
                                  tcgtcctcctttttgt  CT-rich tract
      tttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagttattttccagaatattgctgttggtctttatcgatatctcagctttgtttagtatctttgtggcattgtggctgatcgtcctcctttttgtctcagCTTAGCTGTTCGTGACCTCTCAAACTTGGTTAAGCCAGAAGATATTGTCGAGTCCGAACATCTCGTAACTCTCCTTGCAGTTGTTCCGAAGTATTCCCAA

- - - - - - - - - - - - - - - - - - - -atctcag
- - - - - - - - - - - - - - - - - - - - - - - - -tgtttag