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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctttctacatttgagcttgctttctatgaactttcttgctcgtcacttaaactacgagtttcttggtgtaaaacatggtaactcttttgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTACACTTTGGATATGTCTAAAGATTTTATTCCTATGAATGTTTTCTGTGAGT

Basic information

species Arabidopsis thaliana
transcript AT3G52270.1
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|116394554|gb|EG437146.1|EG437146
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394574|gb|EG437166.1|EG437166
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394553|gb|EG437145.1|EG437145
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTTGCTCGAGCTGACTCTGGAAACATGCCGATGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394622|gb|EG437214.1|EG437214
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCG
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCG
EST: gi|116394463|gb|EG437055.1|EG437055
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTC
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTC
EST: gi|116394469|gb|EG437061.1|EG437061
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACT
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACT
EST: gi|116394477|gb|EG437069.1|EG437069
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAA
EST: gi|116394462|gb|EG437054.1|EG437054
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394578|gb|EG437170.1|EG437170
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394459|gb|EG437051.1|EG437051
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394620|gb|EG437212.1|EG437212
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAA
EST: gi|116394611|gb|EG437203.1|EG437203
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGA
EST: gi|116394473|gb|EG437065.1|EG437065
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394476|gb|EG437068.1|EG437068
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394602|gb|EG437194.1|EG437194
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAA
EST: gi|116394608|gb|EG437200.1|EG437200
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394621|gb|EG437213.1|EG437213
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394468|gb|EG437060.1|EG437060
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGCCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
EST: gi|116394585|gb|EG437177.1|EG437177
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACT
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACT
EST: gi|116394579|gb|EG437171.1|EG437171
EST:     AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAA                         TTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA
genomic: AAGTCATCCTCGGCGTCGATCCTCTGGCTCACGAGGACGAAGGGACCCAAgtatgctttc ... tgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttaaactacgagtttcttggtgtaaaacatggtaactcttttgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTACACTTTGGATATGTCTAAAGATTTTATTCCTATGAATGTTTTCTGTGAGT
                                 tggtaac  putative branch site (score: 2)
                                       ctcttttgccttgc  CT-rich tract
                          taaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctttctacatttgagcttgctttctatgaactttcttgctcgtcacttaaactacgagtttcttggtgtaaaacatggtaactcttttgccttgcagTTCGTAATGGAATTAGCTCGAGCTGACTCTGGAAACATGCCGAGGCGTTACACTTTGGATATGTCTAAAGATTTTATTCCTATGAATGTTTTCTGTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - cttaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaca