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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaaaactagctttggaactattgcttctctcttggtctaaaaatgtcatctttgttaaaaagaatttggatgattctttagGTAGTGAGAGGTTGGCTTTTAAACCAGAAGGCTATAACTTTTGGGAATGGAGAGGTCACAAGATTCATTATGTTGTTCAAGGAGAAGGCTCGCCTCTAGT

Basic information

species Arabidopsis thaliana
transcript AT4G36530.1
intron # 3
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|125120330|gb|EL168099.1|EL168099
EST:     TACTTCTTCTGCTTCTTCTCAGTCTGTTCGAG                         GTAGTGAGAGGTTGGCTTTTAAACCAGAAGGCTATAACTTT-GGGAATGGA
genomic: TACTTCTTCTGCTTCTTCTCAGTCTGTTCAAGgtaaaaaaaa ... gattctttagGTAGTGAGAGGTTGGCTTTTAAACCAGAAGGCTATAACTTTTGGGAATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcttggtctaaaaatgtcatctttgttaaaaagaatttggatgattctttagGTAGTGAGAGGTTGGCTTTTAAACCAGAAGGCTATAACTTTTGGGAATGGAGAGGTCACAAGATTCATTATGTTGTTCAAGGAGAAGGCTCGCCTCTAGT
        gtctaaa  putative branch site (score: 3)
                                               ttcttt  putative PPT
                        tttgttaaaaagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaaaaactagctttggaactattgcttctctcttggtctaaaaatgtcatctttgttaaaaagaatttggatgattctttagGTAGTGAGAGGTTGGCTTTTAAACCAGAAGGCTATAACTTTTGGGAATGGAGAGGTCACAAGATTCATTATGTTGTTCAAGGAGAAGGCTCGCCTCTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA