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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttgttgttgttgttgttgttgttgtaatgttggcgatgtaatggatggttgttgattattgtgtgtgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGAACAAAGATTACGGAG

Basic information

species Arabidopsis thaliana
transcript AT1G32580.1
intron # 2
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|86065047|gb|DR360804.1|DR360804
EST:     TTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAAACTTGAAG                         GACTTCCTGGTG
genomic: TTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAA-CTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTG
EST: gi|125089980|gb|EL148145.1|EL148145
EST:     TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGAC
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGAC
EST: gi|164173152|gb|ES165799.1|ES165799
EST:     TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTAT
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTAT
EST: gi|163985430|gb|ES141411.1|ES141411
EST:     TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCT
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCT
EST: gi|164015103|gb|ES097756.1|ES097756
EST:     CAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
genomic: CAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
EST: gi|125161044|gb|EL188344.1|EL188344
EST:     TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTT
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTT
EST: gi|116482448|gb|EG525040.1|EG525040
EST:     TTTTGGATTTGGTAGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
EST: gi|164201125|gb|ES031018.1|ES031018
EST:     AGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
genomic: AGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGA
EST: gi|86065043|gb|DR360800.1|DR360800
EST:     TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAG                         GACTTCCTGGTGTTCTCTTCAT
genomic: TTTTGGATTTGGTTGTGAGATTGATGAAGAGACATCAAACAAACTTGAAGgtatgtcttg ... tgtgtttcagGACTTCCTGGTGTTCTCTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtaatgttggcgatgtaatggatggttgttgattattgtgtgtgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGAACAAAGATTACGGAG
                             tgttgat  putative branch site (score: 4)
                               ttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttgttgttgttgttgttgttgttgtaatgttggcgatgtaatggatggttgttgattattgtgtgtgtgtttcagGACTTCCTGGTGTTCTCTTCATTTTACCAGACTCTTATGTTGATCAAGAGAACAAAGATTACGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA