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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagagtctttgtgttttctttctttcttgcattatcttgatttgttgttcctggttttgattatatgttgtttctttgttaaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G27350.1
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|124958436|gb|EL033181.1|EL033181
EST:     ACCGCCAGAGATTCGGTCTCTTGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAG
genomic: ACCGCCAGAGATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAG
EST: gi|125227521|gb|EL241606.1|EL241606
EST:     ACCGCCAGAGATTCGGTCTCTTGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
genomic: ACCGCCAGAGATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
EST: gi|125225414|gb|EL239499.1|EL239499
EST:     ACTCAGGTAGAAGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTAGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGG
genomic: ACTCAGGTAGAAGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGG
EST: gi|124848234|gb|EH932671.1|EH932671
EST:     AGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTTGTAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATA
genomic: AGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTTG-AGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATA
EST: gi|124768096|gb|EH858226.1|EH858226
EST:     TCAGGTAGAAGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTTGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
genomic: TCAGGTAGAAGAAAAACCGGTTCACCGCCAGAGATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
EST: gi|125246063|gb|EL260148.1|EL260148
EST:     AAAAACCGGTTACACCGCCAGAGATTCGGTCTCTTGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
genomic: AAAAACCGGTT-CACCGCCAGAGATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
EST: gi|124940175|gb|EL016646.1|EL016646
EST:     GATTCGGTCTCTTGAG                         CTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA
genomic: GATTCGGTCTCTTGAGgtaagtcaga ... aaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatttgttgttcctggttttgattatatgttgtttctttgttaaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAAG
                   ttttgat  putative branch site (score: 4)
                   ttttgattatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcagagtctttgtgttttctttctttcttgcattatcttgatttgttgttcctggttttgattatatgttgtttctttgttaaaccaatagCTGTTTCATAAGTAATGCTAAAACTCAAGATCAGAACCAGAGCAGGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG