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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaaagctttctccttttgattaacccacacgagaaaaagctctcttcttttgtaggaattcaaaaagctcgtctcttcttgttcgattcaatcagattagaaaaagtttctggatttgagctggattgatctaggtttaacttggattactttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAGGATCTCCAGAAAGACCCTCCAACCTCCTGCAGTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G41700.1
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|86027901|gb|DR323654.1|DR323654
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027892|gb|DR323645.1|DR323645
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGTAGCTGAAG
genomic: CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027888|gb|DR323641.1|DR323641
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027897|gb|DR323650.1|DR323650
EST:     ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027908|gb|DR323661.1|DR323661
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|125126497|gb|EL171657.1|EL171657
EST:     ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGA
genomic: ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGA
EST: gi|86027890|gb|DR323643.1|DR323643
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|125225640|gb|EL239725.1|EL239725
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAA
genomic: CATCTGCAGGAGTGAATCGCAAAACC-AAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAA
EST: gi|125258902|gb|EL272987.1|EL272987
EST:     AGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
genomic: AGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
EST: gi|124723978|gb|EH815380.1|EH815380
EST:     TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTG
EST: gi|124815662|gb|EH900528.1|EH900528
EST:     GGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
genomic: GGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
EST: gi|124829504|gb|EH914095.1|EH914095
EST:     GCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGA
genomic: GCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGA
EST: gi|86027904|gb|DR323657.1|DR323657
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027906|gb|DR323659.1|DR323659
EST:     ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|125184096|gb|EL199050.1|EL199050
EST:     TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGG
EST: gi|86027896|gb|DR323649.1|DR323649
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGWTCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|125264534|gb|EL278619.1|EL278619
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAA
genomic: CATCTGCAGGAGTGAATCGCAAAACCAAA-TTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAA
EST: gi|164153133|gb|EL994079.1|EL994079
EST:     GAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGC
genomic: GAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGC
EST: gi|125288799|gb|EL302884.1|EL302884
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAA
genomic: CATCTGCAGGAGTGAATCGCAAAACC-AAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAA
EST: gi|86027910|gb|DR323663.1|DR323663
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: CATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|124772553|gb|EH862682.1|EH862682
EST:     AAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAG
genomic: AAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAG
EST: gi|86027894|gb|DR323647.1|DR323647
EST:     ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|86027907|gb|DR323660.1|DR323660
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|125209339|gb|EL224293.1|EL224293
EST:     CATCTGCAGGAGTGAATCGCAAAACCAAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGG
genomic: CATCTGCAGGAGTGAATCGCAAAACC-AAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGG
EST: gi|86027902|gb|DR323655.1|DR323655
EST:     ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: ATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
EST: gi|124823645|gb|EH908511.1|EH908511
EST:     GCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
genomic: GCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGAT
EST: gi|86027893|gb|DR323646.1|DR323646
EST:     GCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAG                         GGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG
genomic: TCATCTGCAGGAGTGAATCGCAAAACCAAATTTGGAGGATTCTTTCTGAGgtatcaaagc ... ctttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctggatttgagctggattgatctaggtttaacttggattactttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAGGATCTCCAGAAAGACCCTCCAACCTCCTGCAGTGCAG
                              gtttaac  putative branch site (score: 3)
                                          ttacttttt  putative PPT
                                         attacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcaaagctttctccttttgattaacccacacgagaaaaagctctcttcttttgtaggaattcaaaaagctcgtctcttcttgttcgattcaatcagattagaaaaagtttctggatttgagctggattgatctaggtttaacttggattactttttgtagGGGTTTCTCAGTGAGAAAATGGCTTCGAAACGGATCTTGAAGGAGCTGAAGGATCTCCAGAAAGACCCTCCAACCTCCTGCAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG