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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatatttttttttttttattactatattatatactctttgtaaacgaaagatgttctgttcttgattctcaattttttttttttgttgaaaacagAGGAGATTTGGGATTTTGTAGTAGAGAGTGCAGAGAAAGTCAGATGTTGATTGATGATAGAAAAGAACTAGAGGCTTCGACGAAGATGATGTTGGCTTCG

Basic information

species Arabidopsis thaliana
transcript AT1G53903.1
intron # 1
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|19878688|gb|AU239519.1|AU239519
EST:     CATCTCTGCAATAAACAACTCCATCAAGACAAAGATGTTTACATGTACAG                         AGGAGATTTGGGATTTTGTAGTAGAGAGTGCAGAGAAAGTCAGATGTTGAT
genomic: CATCTCTGCAATAAACAACTCCATCAAGACAAAGATGTTTACATGTACAGgtacgatatt ... ttgaaaacagAGGAGATTTGGGATTTTGTAGTAGAGAGTGCAGAGAAAGTCAGATGTTGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacgaaagatgttctgttcttgattctcaattttttttttttgttgaaaacagAGGAGATTTGGGATTTTGTAGTAGAGAGTGCAGAGAAAGTCAGATGTTGATTGATGATAGAAAAGAACTAGAGGCTTCGACGAAGATGATGTTGGCTTCG
                   tcttgat  putative branch site (score: 4)
                         ttctcaattttttttt  CT-rich tract
                        attctcaatttttttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatatttttttttttttattactatattatatactctttgtaaacgaaagatgttctgttcttgattctcaattttttttttttgttgaaaacagAGGAGATTTGGGATTTTGTAGTAGAGAGTGCAGAGAAAGTCAGATGTTGATTGATGATAGAAAAGAACTAGAGGCTTCGACGAAGATGATGTTGGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG