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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttattttctgataaattttgttatttcaataactgattcttttgtactcaaatgggttctcagtctttttttctttgtttgatatcacccgtttcagGATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCTGTGGAACAAATACAAGGATGAGTTCGAGAAAGAGAAAAGCATGATTGGA

Basic information

species Arabidopsis thaliana
transcript AT5G09900.2
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|125028298|gb|EL100567.1|EL100567
EST:     AATTTATCAGAAATCCCTGATTTCAA                         GATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCT
genomic: AATTTATCAGAAATCCCTGATTTCAAgtatatttta ... cccgtttcagGATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCT
EST: gi|125185565|gb|EL200519.1|EL200519
EST:     AGAATTTATCAGAAATCCCTGATTTCAA                         GATGCTTCT-AAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCT
genomic: AGAATTTATCAGAAATCCCTGATTTCAAgtatatttta ... cccgtttcagGATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactcaaatgggttctcagtctttttttctttgtttgatatcacccgtttcagGATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCTGTGGAACAAATACAAGGATGAGTTCGAGAAAGAGAAAAGCATGATTGGA
                                  gtttgat  putative branch site (score: 5)
                                             cccgtttc  putative PPT
                       tttttttctttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttattttctgataaattttgttatttcaataactgattcttttgtactcaaatgggttctcagtctttttttctttgtttgatatcacccgtttcagGATGCTTCTAAAACAGGTAGTGACAATGGAGGTTATTCAATGGACATCTCTGTGGAACAAATACAAGGATGAGTTCGAGAAAGAGAAAAGCATGATTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA