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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacttacttccactataaccacattatagatgtcccatccggtttccatgcggtgtcagaccatacaagctaacttaacccgtgcgtttcgtacctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGGCTGCAGCTTCGTGACCCATACATCACGACATTGAACGTGTGTCAAGCCT

Basic information

species Arabidopsis thaliana
transcript AT2G42600.1
intron # 10
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|164093019|gb|ES206566.1|ES206566
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|163976568|gb|ES177685.1|ES177685
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|125315918|gb|EL330003.1|EL330003
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAA
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAA
EST: gi|124776269|gb|EH866396.1|EH866396
EST:     CCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: CCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|116477132|gb|EG519724.1|EG519724
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|125231375|gb|EL245460.1|EL245460
EST:     TTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTC-AG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGA
genomic: -TGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGA
EST: gi|125125539|gb|EL170974.1|EL170974
EST:     CAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: CAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|86087843|gb|DR383602.1|DR383602
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGA
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|124865013|gb|EH949450.1|EH949450
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTT-AGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|124924894|gb|EL002946.1|EL002946
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|86065049|gb|DR360806.1|DR360806
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|86068615|gb|DR364372.1|DR364372
EST:     TGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCCTCCAG                         -TTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTAC
genomic: TGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCC-TCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTAC
EST: gi|125002290|gb|EL074559.1|EL074559
EST:     CCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
genomic: CCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGG
EST: gi|124950611|gb|EL026060.1|EL026060
EST:     GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAG                         GTTGCAGGTCACAAAGACATTTTAGAAGGTGA
genomic: GTGAACAACTTCGAGTTAACTACCAAGAGACCAGACGCCTCCTCCTCCAGgtattactta ... acctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcggtgtcagaccatacaagctaacttaacccgtgcgtttcgtacctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGGCTGCAGCTTCGTGACCCATACATCACGACATTGAACGTGTGTCAAGCCT
                                       tttcgtacctttcc  CT-rich tract
                       taacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattacttacttccactataaccacattatagatgtcccatccggtttccatgcggtgtcagaccatacaagctaacttaacccgtgcgtttcgtacctttccagGTTGCAGGTCACAAAGACATTTTAGAAGGTGACCCTTACTTGAGGCAAAGGCTGCAGCTTCGTGACCCATACATCACGACATTGAACGTGTGTCAAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT