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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagactgatatacttgcatttctcacatcagaatgcttcttatgaattctattacaagaagaaagtaactctttaccttcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATCCTCTATCTGAGAGAGATTGATGATGCCGACAAATTGGTTGAAGCAATTA

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 5
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|86038366|gb|DR334121.1|DR334121
EST:     TGGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCT
genomic: TGGGG-ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCT
EST: gi|86038353|gb|DR334108.1|DR334108
EST:     TGGNGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: TGG-GGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038384|gb|DR334139.1|DR334139
EST:     TGGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: TGGGG-ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038379|gb|DR334134.1|DR334134
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACT
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACT
EST: gi|86038373|gb|DR334128.1|DR334128
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038364|gb|DR334119.1|DR334119
EST:     TGGNGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAA-GGTGCAGGACTCTAAGAATAT
genomic: TGG-GGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAG-ACTCTAAGAATAT
EST: gi|86038359|gb|DR334114.1|DR334114
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAG-TGCAGACTCTAAGA-TATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038370|gb|DR334125.1|DR334125
EST:     TGGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: TGGGG-ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038368|gb|DR334123.1|DR334123
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGAT
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGAT
EST: gi|86038365|gb|DR334120.1|DR334120
EST:     CTGGGTATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038377|gb|DR334132.1|DR334132
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAARGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038374|gb|DR334129.1|DR334129
EST:     TGGGGGATGTCTTCAAGTATCAGACGCTCATAATKGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGG
genomic: TGGGG-ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGG
EST: gi|86038380|gb|DR334135.1|DR334135
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGWTTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038356|gb|DR334111.1|DR334111
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038381|gb|DR334136.1|DR334136
EST:     TGGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: TGGGG-ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038383|gb|DR334138.1|DR334138
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGT
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGT
EST: gi|86038357|gb|DR334112.1|DR334112
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038361|gb|DR334116.1|DR334116
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|86038362|gb|DR334117.1|DR334117
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
EST: gi|125073392|gb|EL137742.1|EL137742
EST:     ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATAT
genomic: ATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATAT
EST: gi|301501396|gb|HO206936.1|HO206936
EST:     CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACT                         GTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC
genomic: CTGGGGATGTCTTCAAGTATCAGACGCTCATAATTGCAACTGGTTCTACTgtaaagactg ... tcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcttatgaattctattacaagaagaaagtaactctttaccttcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATCCTCTATCTGAGAGAGATTGATGATGCCGACAAATTGGTTGAAGCAATTA
                             aagtaac  putative branch site (score: 2)
                                   ctctttaccttccttt  CT-rich tract
      ttatgaattctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagactgatatacttgcatttctcacatcagaatgcttcttatgaattctattacaagaagaaagtaactctttaccttcctttgcagGTTCTCAGATTGACTGATTTTGGAGTAAAAGGTGCAGACTCTAAGAATATCCTCTATCTGAGAGAGATTGATGATGCCGACAAATTGGTTGAAGCAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA