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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttatcaatcgttgctctttgcttggtttatcgtggttaatgagtcatagctaatgatccagtctggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 8
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|86064682|gb|DR360439.1|DR360439
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
EST: gi|164064708|gb|ES002678.1|ES002678
EST:     AGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCTACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGACTGAGAAGAAGAGAGAGGAAGAGG
genomic: AGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGC-ACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAG-CTGAGAAGAAGAGAGAGGAAGAGG
EST: gi|164117634|gb|ES001029.1|ES001029
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAG
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGATAAGAAGAGAGAGGAAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
EST: gi|164012945|gb|ES136216.1|ES136216
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACG
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGTACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
EST: gi|164041709|gb|ES128121.1|ES128121
EST:     CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGC
genomic: CAGAGTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGC
EST: gi|164065432|gb|EL985271.1|EL985271
EST:     GTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGAT                         GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAAGAAGAGAGAGGAAGAG
genomic: GTACGCTAAGAAGTTGGCCGAGGAAACCTGGGGAAAGCACAAGGATgtaagtttat ... ggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAA-GAAGAGAGAGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttggtttatcgtggttaatgagtcatagctaatgatccagtctggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG
                            agctaat  putative branch site (score: 3)
                ttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttatcaatcgttgctctttgcttggtttatcgtggttaatgagtcatagctaatgatccagtctggttttacagGCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA