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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaaattagggttttatactctgtttcacttgatgagtatttcaaaattttggatttgttgttaatttgtgtcgatttttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGAATTGAGGAGAGACAGATACGGCACTCCTGTAAATCCTGAGAAATTGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G05060.1
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|86046597|gb|DR342352.1|DR342352
EST:     CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAG                         ATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
genomic: CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
EST: gi|116475903|gb|EG518495.1|EG518495
EST:     CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTATAAG                         ATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
genomic: CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
EST: gi|124907635|gb|EH981715.1|EH981715
EST:     CCACAAGTCACTTTCGGCCGTAGAAG                         ATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
genomic: CCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
EST: gi|86080231|gb|DR375988.1|DR375988
EST:     CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAG                         ATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
genomic: CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
EST: gi|86046598|gb|DR342353.1|DR342353
EST:     CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTSACTTTCGGCCGTAGAAG                         ATGGGATTTACCGGAATCTGAGGAATTCGGTTTTGGGCGTCAACAGCTA
genomic: CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAG-AATTCGGTTTTGG-CGTCAACAGCTA
EST: gi|86046596|gb|DR342351.1|DR342351
EST:     CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAG                         ATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA
genomic: CCTCTCAGAGGTTATGTGTCTCTGCCACAAGTCACTTTCGGCCGTAGAAGgttcaaatta ... tttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgagtatttcaaaattttggatttgttgttaatttgtgtcgatttttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGAATTGAGGAGAGACAGATACGGCACTCCTGTAAATCCTGAGAAATTGAAA
                           tgttaat  putative branch site (score: 3)
 tttttatt  putative PPT
 tatttcaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaaattagggttttatactctgtttcacttgatgagtatttcaaaattttggatttgttgttaatttgtgtcgatttttattgcagATGGGATTTACCGGAATCTGAGAATTCGGTTTTGGCGTCAACAGCTAATGAATTGAGGAGAGACAGATACGGCACTCCTGTAAATCCTGAGAAATTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA