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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttgggttttgacttttgacggttcctctgtataagcagtttgattgaagtcttaaatttattattattttaagttgttctatgaaattttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGCTTTACCACTTACAACATGCTTGCAAAAGAATCGCTTCTCTTGTCGCCTC

Basic information

species Arabidopsis thaliana
transcript AT5G64380.1
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|86020274|gb|DR316020.1|DR316020
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020273|gb|DR316019.1|DR316019
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020275|gb|DR316021.1|DR316021
EST:     ATTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020280|gb|DR316026.1|DR316026
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020276|gb|DR316022.1|DR316022
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020279|gb|DR316025.1|DR316025
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020277|gb|DR316023.1|DR316023
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
EST: gi|86020278|gb|DR316024.1|DR316024
EST:     TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAG                         GTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC
genomic: TTTGACCGGAGATGATGATGATGGTTACTGTACTCTTATAGACTTTGCAGgtaacaaact ... tttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaagtcttaaatttattattattttaagttgttctatgaaattttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGCTTTACCACTTACAACATGCTTGCAAAAGAATCGCTTCTCTTGTCGCCTC
 gtttgat  putative branch site (score: 5)
                                            ttttct  putative PPT
         ttaaatttattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttgggttttgacttttgacggttcctctgtataagcagtttgattgaagtcttaaatttattattattttaagttgttctatgaaattttctgatagGTAGTGGAGGAGGAGAAGGGAAAAATGTAGGAGAGGATCTTGTGGTGTTGCTTTACCACTTACAACATGCTTGCAAAAGAATCGCTTCTCTTGTCGCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - ggttttg
- - - - - - - - - - - - - cctctgt
- - - - - - - - - - - - - - - - - - - -agtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaat