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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctagtgtagtgggtgaagaactaacgatttaaaattttgtctgatacacattggatttaagagtgattctttctttgcaaatgctctctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG

Basic information

species Arabidopsis thaliana
transcript AT5G66600.1
intron # 1
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|116429901|gb|EG472493.1|EG472493
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCATAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAG
EST: gi|116429925|gb|EG472517.1|EG472517
EST:     GGTAGAATG-TCGATTTGAGGA-TGTCCAAAATCACAAGCG-TCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAGGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
EST: gi|116429918|gb|EG472510.1|EG472510
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
EST: gi|116429926|gb|EG472518.1|EG472518
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAGGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
EST: gi|116429914|gb|EG472506.1|EG472506
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
EST: gi|116429919|gb|EG472511.1|EG472511
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
EST: gi|116429916|gb|EG472508.1|EG472508
EST:     GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAG                         TGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG
genomic: GGTAGAATGTTGGATTTGAGGATTGTCCAAAATCACAAGCGTTCAAAGAGgtaaaatgtc ... ctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacacattggatttaagagtgattctttctttgcaaatgctctctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG
 gtctgat  putative branch site (score: 4)
                                       tgctctctct  putative PPT
            atttaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctagtgtagtgggtgaagaactaacgatttaaaattttgtctgatacacattggatttaagagtgattctttctttgcaaatgctctctctgaacagTGCCAGCTTTCCAGAAAAGAAAAGAGTTGAAGGAGATAAAACCTCAAATAGTTCTCATGAAGCCTCTCAACGAATGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - -aactaac
- - - - - - - - - - - - - - - - - - - - - - - atacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctct