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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgcagaacccaatctcgtttcaatttctgtgttaattttgaggctcgcggttttagatctgtgttatcttccttgtttgattatgattatcgtattgggtgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGGAAGTTCGAACTTGAGCTTGATGTTGGGATCTAGCGGATCGAGATCTTGT

Basic information

species Arabidopsis thaliana
transcript AT3G57440.1
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|116376518|gb|EG419110.1|EG419110
EST:     TCCTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376528|gb|EG419120.1|EG419120
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376722|gb|EG419314.1|EG419314
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376709|gb|EG419301.1|EG419301
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGCGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376723|gb|EG419315.1|EG419315
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376526|gb|EG419118.1|EG419118
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376708|gb|EG419300.1|EG419300
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGCGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
EST: gi|116376721|gb|EG419313.1|EG419313
EST:     TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAG                         GTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG
genomic: TCGTCTCTTCTTCTCCTTTCCTATGGACCAGTGTTCTTCTCACCTAAAAGgttcgcagaa ... tgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatctgtgttatcttccttgtttgattatgattatcgtattgggtgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGGAAGTTCGAACTTGAGCTTGATGTTGGGATCTAGCGGATCGAGATCTTGT
                    gtttgat  putative branch site (score: 5)
                     tttgattatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgcagaacccaatctcgtttcaatttctgtgttaattttgaggctcgcggttttagatctgtgttatcttccttgtttgattatgattatcgtattgggtgattattagGTCGGAATCTGTAGAGGAATCGAGCTATGTGAGGAAGTGGTGTCACGAAGGAAGTTCGAACTTGAGCTTGATGTTGGGATCTAGCGGATCGAGATCTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC