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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caccgaaaacgctgctttggttggattggttttgagtatatctgtagtttttttcatctgtgtagtttaatatttcctttgctttgttttgggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGACGAAGAAATAGATGAAGATGATGAGGATGACCACGGGGAAACCCTTTGTG

Basic information

species Arabidopsis thaliana
transcript AT3G42790.1
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|86069053|gb|DR364810.1|DR364810
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTNTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCNGCCAAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|125171321|gb|EL194271.1|EL194271
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGG
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGG
EST: gi|86069050|gb|DR364807.1|DR364807
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAAAGGGAAAAAGCTCAAAGACCAAGCAGCNNAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|86069049|gb|DR364806.1|DR364806
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|86069051|gb|DR364808.1|DR364808
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCA
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCA
EST: gi|86069052|gb|DR364809.1|DR364809
EST:     CATCTGCTGCAAATCAAAACGGAAANAAATCCAAGTCTAACTCTAAAGNT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCCAAGCAGCCAAAAGAGGAGGA
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACC-AAGCAGCCAAAAGAGGAGGA
EST: gi|125232062|gb|EL246147.1|EL246147
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|164179205|gb|ES068003.1|ES068003
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACC
EST: gi|86069046|gb|DR364803.1|DR364803
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCT
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCT
EST: gi|86059812|gb|DR355569.1|DR355569
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|124988406|gb|EL060794.1|EL060794
EST:     ATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTACTAAAGTT                         AGAACTTCAGAGG
genomic: ATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACT-CTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGG
EST: gi|164200803|gb|ES090266.1|ES090266
EST:     TCTGTCTGCAAATCAAAACGGAAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACC
genomic: TCTG-CTGCAAATCAAAACGG-AAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACC
EST: gi|125117374|gb|EL166541.1|EL166541
EST:     AAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: AAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|116471935|gb|EG514527.1|EG514527
EST:     CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTCCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: CATCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|124861112|gb|EH945549.1|EH945549
EST:     AATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGA
genomic: AATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGA
EST: gi|125035356|gb|EL107625.1|EL107625
EST:     AACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGG-AAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: AACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
EST: gi|125014601|gb|EL086870.1|EL086870
EST:     TCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTT                         AGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC
genomic: TCTGCTGCAAATCAAAACGGAAACAAATCCAAGTCTAACTCTAAAGTTgtaagactct ... gggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttttcatctgtgtagtttaatatttcctttgctttgttttgggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGACGAAGAAATAGATGAAGATGATGAGGATGACCACGGGGAAACCCTTTGTG
                   gtttaat  putative branch site (score: 4)
               tgtagtttaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caccgaaaacgctgctttggttggattggttttgagtatatctgtagtttttttcatctgtgtagtttaatatttcctttgctttgttttgggaatgcagAGAACTTCAGAGGGAAAAAGCTCAAAGACCAAGCAGCCAAAAGAGGAGGACGAAGAAATAGATGAAGATGATGAGGATGACCACGGGGAAACCCTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- -cgaaaac
- - - - - - -gctttgg
- - - - - - - - - - - - - -ggttttg