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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagcatttacaaacaagtaagaaccatcttctgatcatctctggaatcacctgctaaagaaaactagataatttttgaacattttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTCTCACATAAGTAAGGTAGAAGAAGTATATGATCATCAGATGTGGAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT1G27110.3
intron # 6
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|116378181|gb|EG420773.1|EG420773
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428736|gb|EG471328.1|EG471328
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAGTTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428741|gb|EG471333.1|EG471333
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428746|gb|EG471338.1|EG471338
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428724|gb|EG471316.1|EG471316
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116378186|gb|EG420778.1|EG420778
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428726|gb|EG471318.1|EG471318
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAGGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428743|gb|EG471335.1|EG471335
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428737|gb|EG471329.1|EG471329
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428729|gb|EG471321.1|EG471321
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAGGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428721|gb|EG471313.1|EG471313
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428745|gb|EG471337.1|EG471337
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAG                         GTTTTCGCATAGTTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
EST: gi|116428731|gb|EG471323.1|EG471323
EST:     AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCCCATCCTTAAG                         GTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC
genomic: AAGTTCATGGAAGAACACTCAGATTCATGGGATTCTTGCTCATCCTTAAGgtaatagcat ... ttttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctggaatcacctgctaaagaaaactagataatttttgaacattttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTCTCACATAAGTAAGGTAGAAGAAGTATATGATCATCAGATGTGGAAAGAG
               tgctaaa  putative branch site (score: 2)
                  taaagaaaactagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatagcatttacaaacaagtaagaaccatcttctgatcatctctggaatcacctgctaaagaaaactagataatttttgaacattttaattagGTTTTCGCATAATTGGTGGCACGTAGCTGTTTGTTACTTGGAAGGAGGGTCTCACATAAGTAAGGTAGAAGAAGTATATGATCATCAGATGTGGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG