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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaacggtcccggctaaaatctggccatcgttttatatggaatcatctatgtatgtaccgaaataccccctgactgatttttttccatttttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTCGAGGTAGATCTGCCGTACGTTGACTTTTTACTACGAGTCAAACGGTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G21482.1
intron # 2
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|125305019|gb|EL319104.1|EL319104
EST:     AGACTCCGATTCCAACTCAACCATTGACAAG                         AGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAAGATT
genomic: AGACTCCGATTCCAACTCAACCATTGACAAGgtaataataa ... ttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAA-GATT
EST: gi|86088034|gb|DR383793.1|DR383793
EST:     AACTCGGTCTTCACTACAGAGACTCCGATTCCAACTCAACCATTGACAAG                         AGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTC
genomic: AACTCGGTCTTCACTACAGAGACTCCGATTCCAACTCAACCATTGACAAGgtaataataa ... ttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTC
EST: gi|125307557|gb|EL321642.1|EL321642
EST:     CCAACTCAACCATTGACAAG                         AGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTC
genomic: CCAACTCAACCATTGACAAGgtaataataa ... ttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgtatgtaccgaaataccccctgactgatttttttccatttttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTCGAGGTAGATCTGCCGTACGTTGACTTTTTACTACGAGTCAAACGGTCAG
                          gactgat  putative branch site (score: 3)
                            ctgatttttttccatt  CT-rich tract
                               atttttttccattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaacggtcccggctaaaatctggccatcgttttatatggaatcatctatgtatgtaccgaaataccccctgactgatttttttccatttttttgtgtagAGGGTGGAGAGATTGATCGGACGGCTAAGATTTAATGAAGGATTAAGATTCGAGGTAGATCTGCCGTACGTTGACTTTTTACTACGAGTCAAACGGTCAG

- - - - - - gctaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac