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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcattcttcctcactcaatctggattcttctctttagctttttgaaattcagatctcttatcatttacttgtttctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAGATGGCCGTACTTTGGCTGACTACAACATCCAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52590.1
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|164085444|gb|ES028176.1|ES028176
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGC
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGC
EST: gi|163974037|gb|ES156365.1|ES156365
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAG
EST: gi|47832020|gb|CK121704.1|CK121704
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|116446032|gb|EG488624.1|EG488624
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125020801|gb|EL093070.1|EL093070
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGC
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGC
EST: gi|125219449|gb|EL233534.1|EL233534
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGG
EST: gi|125049334|gb|EL121603.1|EL121603
EST:     CACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: CACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125318881|gb|EL332966.1|EL332966
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGAT
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGAT
EST: gi|47831890|gb|CK121574.1|CK121574
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|116474135|gb|EG516727.1|EG516727
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|47828414|gb|CK118098.1|CK118098
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125223123|gb|EL237208.1|EL237208
EST:     GTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|124965309|gb|EL039507.1|EL039507
EST:     CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAA
genomic: CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAA
EST: gi|86077140|gb|DR372897.1|DR372897
EST:     GAGCAGCGATMCCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|124922227|gb|EL000537.1|EL000537
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAA
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAA
EST: gi|125255531|gb|EL269616.1|EL269616
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTT
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTT
EST: gi|116439570|gb|EG482162.1|EG482162
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCGGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|124996428|gb|EL068697.1|EL068697
EST:     CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|164164816|gb|EL999222.1|EL999222
EST:     TCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: TCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|164212428|gb|EL988999.1|EL988999
EST:     TCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGACCGGAAAGCAGCTCGAA
genomic: TCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCG-CCGGAAAGCAGCTCGAA
EST: gi|125229696|gb|EL243781.1|EL243781
EST:     CCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCCCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGA
genomic: CCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGAT--CAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGA
EST: gi|124947220|gb|EL023076.1|EL023076
EST:     GTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAAGCTCGAA
genomic: GTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCA-GCTCGAA
EST: gi|164059131|gb|ES087910.1|ES087910
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTT
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTT
EST: gi|47828471|gb|CK118155.1|CK118155
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|164057339|gb|ES054227.1|ES054227
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAG
EST: gi|125233317|gb|EL247402.1|EL247402
EST:     TCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: TCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125168227|gb|EL193029.1|EL193029
EST:     CAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTC
genomic: CAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTC
EST: gi|125271189|gb|EL285274.1|EL285274
EST:     CACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: CACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125248280|gb|EL262365.1|EL262365
EST:     CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGA
genomic: CGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGA
EST: gi|124844137|gb|EH928574.1|EH928574
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGG
EST: gi|152035175|gb|BP846886.2|BP846886
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|47831983|gb|CK121667.1|CK121667
EST:     GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGTAAAGCAGCTCGAAG
genomic: GAGCAGCGACACCATCGACAATGTCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
EST: gi|125260000|gb|EL274085.1|EL274085
EST:     TCAAGGCCAAGATCCAAGACAAAGAAG                         GAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG
genomic: TCAAGGCCAAGATCCAAGACAAAGAAGgtatcattct ... ctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttagctttttgaaattcagatctcttatcatttacttgtttctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAGATGGCCGTACTTTGGCTGACTACAACATCCAGAAAG
                        tctcttatcatttact  CT-rich tract
         tttttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcattcttcctcactcaatctggattcttctctttagctttttgaaattcagatctcttatcatttacttgtttctcctttaagGAATCCCTCCGGATCAGCAGAGATTGATCTTCGCCGGAAAGCAGCTCGAAGATGGCCGTACTTTGGCTGACTACAACATCCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG