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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataacttgtttaaaagtagtatgtgcaaaaaatggtatcagagataagagatggagtagaaatataatgttgatctatctgtaacttagGTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAGAAGGAAGCCAAGTTCCAAGCTTTTAGTGGTAAAAAATATTCATTGAGGGGTTGAACCA

Basic information

species Arabidopsis thaliana
transcript AT4G38930.2
intron # 9
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|125291931|gb|EL306016.1|EL306016
EST:     AACTTGTGTTCGGTTCAAATGTAGAGCGGTCTACTAAAGAGACAACAAAG                         GTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAG
genomic: AACTTGTGTTCGGTTCAAATGTAGAGCGGTCTACTAAAGAGACAACAAAGgtaaataact ... tgtaacttagGTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAG
EST: gi|163968615|gb|ES191625.1|ES191625
EST:     AAAGAGACAACAAAG                         GTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAGAAGGAAGCC
genomic: AAAGAGACAACAAAGgtaaataact ... tgtaacttagGTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAGAAGGAAGCC
EST: gi|124836870|gb|EH921309.1|EH921309
EST:     AACTTGTGTTCGGTTCAAATGTAGAGCGGTCTACTAAAGAGACAACAAAG                         GTTGGAGCTGGGAAAGATAGAAAG
genomic: AACTTGTGTTCGGTTCAAATGTAGAGCGGTCTACTAAAGAGACAACAAAGgtaaataact ... tgtaacttagGTTGGAGCTGGGAAAGATAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcagagataagagatggagtagaaatataatgttgatctatctgtaacttagGTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAGAAGGAAGCCAAGTTCCAAGCTTTTAGTGGTAAAAAATATTCATTGAGGGGTTGAACCA
                                            ctgtaac  putative branch site (score: 3)
                                       tctatct  CT-rich tract
                      tagaaatataatgtt  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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataacttgtttaaaagtagtatgtgcaaaaaatggtatcagagataagagatggagtagaaatataatgttgatctatctgtaacttagGTTGGAGCTGGGAAAGATAGAAAGCAAGAGGAAGAGGCTGAGAAGGAAGCCAAGTTCCAAGCTTTTAGTGGTAAAAAATATTCATTGAGGGGTTGAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT