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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacacacacgctaactcttcttctggtttcattcttcaaatccttccaaatcattaagtaaaatcaatcctcttttttttttgttttgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTACGCGATAAGCAGAGAACAAGCGAACGATAAAGGAGAGAAAATGTATATCC

Basic information

species Arabidopsis thaliana
transcript AT1G20020.3
intron # 7
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|86074562|gb|DR370319.1|DR370319
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCATTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|86065482|gb|DR361239.1|DR361239
EST:     CTTGGTTGTTCTTGGGTGTACSAACCACTAGCTCATTGSTCTACSAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCSCGAGAACTTCAGGGTGGATTAC
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|124757280|gb|EH847410.1|EH847410
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAG
EST: gi|116472061|gb|EG514653.1|EG514653
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|163974241|gb|ES169483.1|ES169483
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCATTGCTCTACCAAGAG                         GAGTTTGATAAGATAGAAAG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGAT-GAAAG
EST: gi|125253621|gb|EL267706.1|EL267706
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTT
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTT
EST: gi|125264174|gb|EL278259.1|EL278259
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAG
EST: gi|86081707|gb|DR377464.1|DR377464
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCATTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|124788603|gb|EH878282.1|EH878282
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGG
EST: gi|125244961|gb|EL259046.1|EL259046
EST:     CCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: CCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|124732290|gb|EH823692.1|EH823692
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAG
EST: gi|124929428|gb|EL006973.1|EL006973
EST:     GGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: GGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
EST: gi|125020654|gb|EL092923.1|EL092923
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCCAGGGTGGATTA
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTC-AGGGTGGATTA
EST: gi|124951093|gb|EL026496.1|EL026496
EST:     TCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTA
genomic: TCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAG-TTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTA
EST: gi|124877315|gb|EH956752.1|EH956752
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATG
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATG
EST: gi|124767511|gb|EH857641.1|EH857641
EST:     TTGTTCTTGGGTGTACCAACCACTAGCTCTTTGTCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCC
genomic: TTGTTCTTGGGTGTACCAACCACTAGCTCTTTG-CTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCC
EST: gi|125074820|gb|EL138620.1|EL138620
EST:     CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCC
genomic: CTTGGTTGTTCTTGGGTGTACCAACCACTAGCTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCC
EST: gi|124852586|gb|EH937023.1|EH937023
EST:     GTTGTTTCTTGGGTGTACCAACCACTAGCCTCTTTGCTCTACCAAGAG                         GAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC
genomic: GTTG-TTCTTGGGTGTACCAACCACTAG-CTCTTTGCTCTACCAAGAGgcacacacac ... tgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccaaatcattaagtaaaatcaatcctcttttttttttgttttgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTACGCGATAAGCAGAGAACAAGCGAACGATAAAGGAGAGAAAATGTATATCC
                      tcaatcctcttttttt  CT-rich tract
                             tcttttttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacacacacgctaactcttcttctggtttcattcttcaaatccttccaaatcattaagtaaaatcaatcctcttttttttttgttttgaaaatcagGAGTTTGATAAGATGAAAGCAAAGGCCCCCGAGAACTTCAGGGTGGATTACGCGATAAGCAGAGAACAAGCGAACGATAAAGGAGAGAAAATGTATATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA