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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaagtgatttcatgtttacttcaaatgtttctcatctgtttttttggtttcatgaatcaaaagttcaactttcataaacaactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGAAGCTGTAGGAGAAGGATCCATGATAA

Basic information

species Arabidopsis thaliana
transcript AT2G17420.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G17420.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g22140.1 (Oryza sativa), 3'ss of exon 1
---ctaaagtgatttcatgtttacttcaaatgtttctcatctgtttttttggt-ttcatgaatcaaaagttcaactttcataaacaactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGA-AGCTGTAGGAGAAGGATCCATGATAA
    |  | || ||  |  |  |  ||    |  | |    | |    ||| | |   | | |     |  |||  || || |  |||   | |  || |||||| ||||||||||| |||||||| ||||| ||| |||| ||||||||| | ||||| |  |||| |||||||  | | |||    |    | ||   | |  
gtgatctattgcttgaaaatccatctccggagaat-tagcttatcccattgatatatgtaatttctgtgaacaaaatttatgataaac---acgtctgatgcagGTTGCATGGCGGCGTTGGATGCGGAGCACTACCTACAGGAGATTGGAGCACAGGAAGACAAGACTGATTGACTATATCTGGGACAAGCAGGTCGCAGTTC-

upper sequence: AT2G17420.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G21630.1 (Glycine max), 3'ss of exon 1
ctaaagtgatttcatgtttact-tcaaatgtttctcatc-tgtttttttggtttcatgaatcaaaagttcaactttcataaac---------aactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGAAGCTGTAGGAGAAGGATCCATGATAA
                |  ||  ||| |||  |  ||   |     |  | |   ||||| ||||||    | | ||  |||          ||   |||   || ||||||||| ||||| || ||||||||||| |||||||| |||| |||||| |  |||||||||||||||| |||| |  | ||||   | ||     | |||  
-----------aagcatcaacaatcatatgcataacacaatcaaaatcagataaaatgaagcaaaagccttattctcccaaaggataatggaaatcatattattgttgcagGGTGTATGGCAGCCTTGGATGCAGAACATTACTTGCAAGGGATTGGTTTGCAGGAGGGTAAGAGTGTTTGATGTTGTTGTACCCGGAGTTCAGAAGATGC

upper sequence: AT2G17420.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0044g01750.t01 (Vitis vinifera), 3'ss of exon 1
ctaaagtgatttcatgtttact-tcaaatgttt-ctcatctgtttttttggtttcatgaatcaaa-agttcaactttcataaacaactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGA--AGCTGTAGGAGAAGGATCCATGATAA
   || ||  ||  | ||  |  |    ||||| |||||     || ||| ||      || ||| |    ||| |   |   |   |||    ||| | ||||||||||||| ||||| ||||||||||||||| | |||||||||||||| ||||| ||||| |||||||||  |  |  | |  |  |  |||| |  ||| 
-ccaattg--ttggtattggccattgcctgtttgctcattacaattattgtttattctcatgaaacaacctaacataggttctcttgtttcatcatgatacagGGTGCATGGCAGCATTAGATGCAGAGCATTACCTGCAAGAGATTGGATCCCAGGAAGGTAAAAGTGATTGACTACCAAGTATCTGCCAGAGATC-AAAATA-

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|86080647|gb|DR376404.1|DR376404
EST:     AGATGTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: AGATGTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTGgtttgtactc ... gatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|116443151|gb|EG485743.1|EG485743
EST:     AGATGTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: AGATGTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTGgtttgtactc ... gatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|125228326|gb|EL242411.1|EL242411
EST:     CAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGA
genomic: CAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTGgtttgtactc ... gatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGA
EST: gi|125305639|gb|EL319724.1|EL319724
EST:     GTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCG
genomic: GTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTGgtttgtactc ... gatggtgcagGGTGCATGGCG
EST: gi|124971996|gb|EL045719.1|EL045719
EST:     GTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCGGCATTGGA
genomic: GTTCAAGACAAGAAGTATAGACAGGCCATCACTGCTGCAGGAACTGgtttgtactc ... gatggtgcagGGTGCATGGCGGCATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttcatgaatcaaaagttcaactttcataaacaactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGAAGCTGTAGGAGAAGGATCCATGATAA
                              ataaacaactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaagtgatttcatgtttacttcaaatgtttctcatctgtttttttggtttcatgaatcaaaagttcaactttcataaacaactttatggatggtgcagGGTGCATGGCGGCATTGGATGCAGAGCATTACTTACAAGAGATTGGATCTCAGGAGGGTAAGAGTGATTGAAGAAGCTGTAGGAGAAGGATCCATGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
ctaaagt
- - - - - - - - - - cttcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaac