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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaactcctctatttgttatggtaacttaagctgccacaccaagtaaaaaagctcatgtctattcttctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGACTTGTTCCTCCCTAAAGAGAGAAAGGATGTCCTCACTTCTACTGCTTGTT

Basic information

species Arabidopsis thaliana
transcript AT3G11170.1
intron # 4
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|124737206|gb|EH828608.1|EH828608
EST:     TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
genomic: TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
EST: gi|125233958|gb|EL248043.1|EL248043
EST:     TCTTTAGACTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGA
genomic: TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGA
EST: gi|124839720|gb|EH924159.1|EH924159
EST:     ATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
genomic: ATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
EST: gi|125136142|gb|EL176172.1|EL176172
EST:     TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGA
genomic: TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGA
EST: gi|124958789|gb|EL033508.1|EL033508
EST:     CCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
genomic: CCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
EST: gi|124965690|gb|EL039857.1|EL039857
EST:     TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCT
genomic: TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCT
EST: gi|125043481|gb|EL115750.1|EL115750
EST:     CTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGAACAGTGA
genomic: CTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGA-CAGTGA
EST: gi|124942171|gb|EL018460.1|EL018460
EST:     CCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
genomic: CCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGAC
EST: gi|124888514|gb|EH967416.1|EH967416
EST:     TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTG                         TGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAG
genomic: TCTTTAGATTTACACTGCCTCTCGTGATGCTTGCATACCCTTTCTACTTGgtaagaactc ... tctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacttaagctgccacaccaagtaaaaaagctcatgtctattcttctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGACTTGTTCCTCCCTAAAGAGAGAAAGGATGTCCTCACTTCTACTGCTTGTT
 tggtaac  putative branch site (score: 2)
                                     tctattcttctgtttc  putative PPT
                    aagtaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaactcctctatttgttatggtaacttaagctgccacaccaagtaaaaaagctcatgtctattcttctgtttcagTGGGCTCGAAGTCCGGGGAAAAAGGGTTCTCATTACCATCCAGACAGTGACTTGTTCCTCCCTAAAGAGAGAAAGGATGTCCTCACTTCTACTGCTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG