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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATCAATAGCCGTACACGCGTGAAGACTGACAATATTATCTTTTTCGAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattcttcgatcctctttgattttcctggaaatattttttcggtgatcgtgaaactactggaatcgctcgataggtggtacgaaattaggcgagat...

Basic information

species Arabidopsis thaliana
transcript AT4G40040.1
intron # 1
splice site 5'
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|124705757|gb|EH797159.1|EH797159
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTA
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTA
EST: gi|116468465|gb|EG511057.1|EG511057
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGCACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|301503181|gb|HO208721.1|HO208721
EST:     GTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTACGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|116431394|gb|EG473986.1|EG473986
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAGCAGCTCGT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGT
EST: gi|125201534|gb|EL216488.1|EL216488
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTC
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTC
EST: gi|124916729|gb|EH990603.1|EH990603
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAG
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAG
EST: gi|301501157|gb|HO206697.1|HO206697
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|164015436|gb|ES013795.1|ES013795
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAG
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAG
EST: gi|164220082|gb|ES095540.1|ES095540
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCNGAG                         ATGGCTCGTAC
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTAC
EST: gi|116447859|gb|EG490451.1|EG490451
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|124822226|gb|EH907092.1|EH907092
EST:     GGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCNGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAG
genomic: GGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAG
EST: gi|124838471|gb|EH922910.1|EH922910
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCNGAG                         ATGGCTCGTACTAAGCAAAC
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAAC
EST: gi|152035605|gb|BP859103.2|BP859103
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|124727858|gb|EH819260.1|EH819260
EST:     GAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAA
genomic: GAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAA
EST: gi|164104439|gb|EL975105.1|EL975105
EST:     GAGAG-TTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|124886290|gb|EH965192.1|EH965192
EST:     AGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: AGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|116427491|gb|EG470083.1|EG470083
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|125217465|gb|EL231548.1|EL231548
EST:     AAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: AAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|47829096|gb|CK118780.1|CK118780
EST:     TGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: TGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|164113180|gb|ES024834.1|ES024834
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
EST: gi|163998620|gb|ES055994.1|ES055994
EST:     AATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTTAGAGAGTTTTCTGAG                         ATGGCTCGTAC
genomic: AATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCT-AGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTAC
EST: gi|116468466|gb|EG511058.1|EG511058
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGCACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|164101417|gb|ES210944.1|ES210944
EST:     CTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAA-GGCTCCT
genomic: CTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|301501881|gb|HO207421.1|HO207421
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|116390647|gb|EG433239.1|EG433239
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|124720213|gb|EH811615.1|EH811615
EST:     TTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: TTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|47830179|gb|CK119863.1|CK119863
EST:     TGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: TGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|116427493|gb|EG470085.1|EG470085
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|163998481|gb|ES135991.1|ES135991
EST:     AATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
genomic: AATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTC-TGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
EST: gi|164167824|gb|ES148540.1|ES148540
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCCT
EST: gi|124943227|gb|EL019425.1|EL019425
EST:     GGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
genomic: GGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTACTAAGCAAACAGCTCGTAAGTCTACTGGAGGAAAGGCTCC
EST: gi|164222491|gb|ES111378.1|ES111378
EST:     GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAG                         ATGGCTCGTAC
genomic: GAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattct ... tgttgaacagATGGCTCGTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATCAATAGCCGTACACGCGTGAAGACTGACAATATTATCTTTTTCGAATTCGGAGCTCAAGTTTGAAATTCGGAGAAGCTAGAGAGTTTTCTGAGgtacgattcttcgatcctctttgattttcctggaaatattttttcggtgatcgtgaaactactggaatcgctcgataggtggtacgaaattaggcgagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcgctcga