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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggaacttgtaactctagttaatctcgtatggctcttttcatgtagttaatttcattacttgtcgtttctagGCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G31990.2
intron # 4
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|152038432|gb|AV822767.2|AV822767
EST:     CTTATCGTACTGAGGAACTCCAGCCTTATGTGCTTAATGTTGTTAAAAAG                         GCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG
genomic: CTTATCGTACTGAGGAACTCCAGCCTTATGTGCTTAATGTTGTTAAAAAGgttggaactt ... tcgtttctagGCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG
EST: gi|125010217|gb|EL082486.1|EL082486
EST:     AACTCCAGCCTTATGTGCTTAATGTTGTTAAAAAG                         GCGGAGAATTTGATGTTGGAGAGGGGAGATAACAAAGAG
genomic: AACTCCAGCCTTATGTGCTTAATGTTGTTAAAAAGgttggaactt ... tcgtttctagGCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatctcgtatggctcttttcatgtagttaatttcattacttgtcgtttctagGCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG
                           agttaat  putative branch site (score: 4)
                                             tcgtttct  putative PPT
                          tagttaatttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggaacttgtaactctagttaatctcgtatggctcttttcatgtagttaatttcattacttgtcgtttctagGCGGAGAATTTGATGTTGGAGAGAGGAGATAACAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT