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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcatatctaatatacttatgtttatgatatattgtttctggtattttatggttgctgacaatgatagctatgattctaacagGTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAACATGCACTGTGCACTTACAG

Basic information

species Arabidopsis thaliana
transcript AT1G20110.1
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|164056826|gb|EL994955.1|EL994955
EST:     GAGGAAATGGAGAGAAACCGCAAGTCTTCGTCTG                         GTTTGAGGGAAGGATCTGGGA
genomic: GAGGAAATGGAGAGAAACCGCAAGTCTTCGTCTGgtaatttttc ... attctaacagGTTTGAGGGAAGGATCTGGGA
EST: gi|86087854|gb|DR383613.1|DR383613
EST:     GAGGAAATGGAGAGAAACCGCAAGTCTTCGTCTG                         GTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAAAAT
genomic: GAGGAAATGGAGAGAAACCGCAAGTCTTCGTCTGgtaatttttc ... attctaacagGTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAACAT
EST: gi|164155830|gb|ES074964.1|ES074964
EST:     ATGGAGAGAAACCGCAAGTCTTCGTCTG                         GTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAAC
genomic: ATGGAGAGAAACCGCAAGTCTTCGTCTGgtaatttttc ... attctaacagGTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattgtttctggtattttatggttgctgacaatgatagctatgattctaacagGTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAACATGCACTGTGCACTTACAG
                         tgctgac  putative branch site (score: 2)
              tattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttcatatctaatatacttatgtttatgatatattgtttctggtattttatggttgctgacaatgatagctatgattctaacagGTTTGAGGGAAGGATCTGGGAGGCGGATGAAAGAAGTAGCTTGTCCAACATGCACTGTGCACTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT