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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttagtagtaactcttaatcgatacatggagtgtgagtgttgaaagttgcctctttaattattgggctttcatgatgtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTCAGACTATGCTAGCAAAGAAACGGAGAGGCTTGGACGGGTGCTTGGGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G47470.2
intron # 9
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|301502106|gb|HO207646.1|HO207646
EST:     TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|86076404|gb|DR372161.1|DR372161
EST:     TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|86080467|gb|DR376224.1|DR376224
EST:     TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|116441307|gb|EG483899.1|EG483899
EST:     TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|164022339|gb|ES013862.1|ES013862
EST:     GTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: GTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|164091404|gb|ES208880.1|ES208880
EST:     TCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|124812111|gb|EH896977.1|EH896977
EST:     AGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATA
genomic: AGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATA
EST: gi|125098504|gb|EL154630.1|EL154630
EST:     TAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
genomic: TAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTC
EST: gi|125189662|gb|EL204616.1|EL204616
EST:     TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAG                         GTATGGAAAGCTTTACTCGAAACTCGCAAAGAGC
genomic: TTGTCTCGCATAGAAGAGGAAGCAAGTACCCTTAAGGGCTCCACCACGAGgtatgttagt ... gtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgagtgttgaaagttgcctctttaattattgggctttcatgatgtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTCAGACTATGCTAGCAAAGAAACGGAGAGGCTTGGACGGGTGCTTGGGAAG
                     ctttaat  putative branch site (score: 4)
                                            tgtctct  putative PPT
                    tctttaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttagtagtaactcttaatcgatacatggagtgtgagtgttgaaagttgcctctttaattattgggctttcatgatgtctctatagGTATGGAAAGCTTTACTTGAAACTCGCAAAGAGCTACATAGAAAAAGGTTCAGACTATGCTAGCAAAGAAACGGAGAGGCTTGGACGGGTGCTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG