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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttcagattctatcactagtcttagaattgaaactacagtttgtattttggggataagatttttcttatagagttggctttgttgttaaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGT

Basic information

species Arabidopsis thaliana
transcript AT1G09340.1
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|124878057|gb|EH957494.1|EH957494
EST:     TGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: TGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|125053559|gb|EL124601.1|EL124601
EST:     CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAA
genomic: CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAA
EST: gi|116412032|gb|EG454624.1|EG454624
EST:     CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|124977512|gb|EL050825.1|EL050825
EST:     TTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: TTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|125042609|gb|EL114878.1|EL114878
EST:     ACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: ACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|116412031|gb|EG454623.1|EG454623
EST:     CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: CTTCTTCTCTGTCTGACTTCAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|125264802|gb|EL278887.1|EL278887
EST:     CAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: CAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
EST: gi|125064364|gb|EL132013.1|EL132013
EST:     TTCAATGGCGCTAAGCTCCATTTACAAGTCCAG                         TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG
genomic: TTCAATGGCGCTAAGCTCCATTTACAAGTCCAGgtctttttca ... aaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttggggataagatttttcttatagagttggctttgttgttaaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGT
           ataagatttttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccttcagattctatcactagtcttagaattgaaactacagtttgtattttggggataagatttttcttatagagttggctttgttgttaaaattgcagTACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGATTCTGATAATGGGTGGTACTCGATTCATTGGTCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - gaaacta
- - - - - - - - - - - - - - - - - - - - agtttgt
- - - - - - - - - - - - - - - - - - - - - - - -attttgg