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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacatttccttattaacattcatactcaccatttacttgaacaagatatatgccaagtgtgagtgatgtaaatgttgtaacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACATCTTTTGTGAATCTTGTGCTATATGTTTTAAAATGCTGTAGAGTTATTTA

Basic information

species Arabidopsis thaliana
transcript AT5G58340.1
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|116430323|gb|EG472915.1|EG472915
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTT
EST: gi|116430318|gb|EG472910.1|EG472910
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430333|gb|EG472925.1|EG472925
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430327|gb|EG472919.1|EG472919
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACGT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430324|gb|EG472916.1|EG472916
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAAC
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAAC
EST: gi|116430332|gb|EG472924.1|EG472924
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430336|gb|EG472928.1|EG472928
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430320|gb|EG472912.1|EG472912
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
EST: gi|116430321|gb|EG472913.1|EG472913
EST:     GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAG                         GTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT
genomic: GGAAAGATATAAAGAATGGAAACCCTACAGTATTTGCGGAGAGGACAGAGgtgaacattt ... aacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgaacaagatatatgccaagtgtgagtgatgtaaatgttgtaacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACATCTTTTGTGAATCTTGTGCTATATGTTTTAAAATGCTGTAGAGTTATTTA
                                         ttgtaac  putative branch site (score: 2)
         aagatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaacatttccttattaacattcatactcaccatttacttgaacaagatatatgccaagtgtgagtgatgtaaatgttgtaacttggtagGTGGATTTGAAAGATAAATGGAGGAACTTAGTCGGTGGGTAGAGGTAACATCTTTTGTGAATCTTGTGCTATATGTTTTAAAATGCTGTAGAGTTATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG