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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttctatcaatcccttttgatttaactctcttcatctctttattatctctgaatccgtctcttgtaaaatttgattttgtattgaatagaaagttttgtttgtttgttgtctatgaaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAGGGACATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCA

Basic information

species Arabidopsis thaliana
transcript AT3G53740.1
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|125221609|gb|EL235694.1|EL235694
EST:     CTTTTGTTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: CTTTTG-TCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|125262375|gb|EL276460.1|EL276460
EST:     GTCCGTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: GTCC-TTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|164076696|gb|ES165393.1|ES165393
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGTCCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|124848449|gb|EH932886.1|EH932886
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGNTGACAACTCCA
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCA
EST: gi|86037334|gb|DR333089.1|DR333089
EST:     CTTTTGTCTGAACCACCGGA-GAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: CTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|125026590|gb|EL098859.1|EL098859
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGGCAACTCCACAAGTGAAGACCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|164156891|gb|ES189483.1|ES189483
EST:     TCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: TCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|164059923|gb|ES173921.1|ES173921
EST:     GTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: GTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|124836635|gb|EH921074.1|EH921074
EST:     CGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGTACCGG
genomic: CGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAG-ACCGG
EST: gi|124881117|gb|EH960019.1|EH960019
EST:     TCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: TCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|124979576|gb|EL052605.1|EL052605
EST:     TTCTTTTGTTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: TTCTTTTG-TCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|125089288|gb|EL147714.1|EL147714
EST:     TCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: TCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|164166801|gb|ES035147.1|ES035147
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|124842439|gb|EH926876.1|EH926876
EST:     GTCCTTCTTTTGTTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTG
genomic: GTCCTTCTTTTG-TCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTG
EST: gi|125021395|gb|EL093664.1|EL093664
EST:     TCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTG
genomic: TCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTG
EST: gi|86053782|gb|DR349539.1|DR349539
EST:     GGCGTCCTTCTTTTGTCTGAACCACCGGA-GAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|164182627|gb|ES052486.1|ES052486
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCANAAGTGAAGACCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|124773324|gb|EH863453.1|EH863453
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAATGAAGACCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|86086302|gb|DR382061.1|DR382061
EST:     GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|164224515|gb|EL987433.1|EL987433
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|125158597|gb|EL187117.1|EL187117
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACT
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACT
EST: gi|86037373|gb|DR333128.1|DR333128
EST:     CCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGAWGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
genomic: CCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|125306217|gb|EL320302.1|EL320302
EST:     TGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: TGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|164085207|gb|ES205655.1|ES205655
EST:     GGGGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|124778126|gb|EH868069.1|EH868069
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|164229541|gb|ES127348.1|ES127348
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGTACCGG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAG-ACCGG
EST: gi|164221574|gb|ES125702.1|ES125702
EST:     GGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGCTCGTTGGGTTGAACAAG
genomic: GGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAG
EST: gi|164103532|gb|ES050768.1|ES050768
EST:     TTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAAGTGAAGACCGGTTTG
genomic: TTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAA-GTGAAGACCGGTTTG
EST: gi|125130009|gb|EL173459.1|EL173459
EST:     GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAG
genomic: GGCGTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAG
EST: gi|124979166|gb|EL052249.1|EL052249
EST:     GTCCTTCTTTTGTCTGAACCACCAGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAG
EST: gi|124864646|gb|EH949083.1|EH949083
EST:     GTCCTTCCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
genomic: GTCCTT-CTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGG
EST: gi|125134490|gb|EL175381.1|EL175381
EST:     CTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGG
genomic: CTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGG
EST: gi|124820814|gb|EH905680.1|EH905680
EST:     GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAG                         AAGATGACAACTCCACAAGTGAAGACCGGTTTG
genomic: GTCCTTCTTTTGTCTGAACCACCGGAGGAGCTCGATCCATTGATTAGgtatcttcta ... aaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattttgtattgaatagaaagttttgtttgtttgttgtctatgaaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAGGGACATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCA
 atttgat  putative branch site (score: 5)
                                         tatgaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttctatcaatcccttttgatttaactctcttcatctctttattatctctgaatccgtctcttgtaaaatttgattttgtattgaatagaaagttttgtttgtttgttgtctatgaaatttacagAAGATGACAACTCCACAAGTGAAGACCGGTTTGTTCGTTGGGTTGAACAAGGGACATGTTGTTACCAGACGTGAATTAGCTCCTCGTCCTCGTTCTCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC