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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatatcattccttaccatacacactaatcatctatgtttgcaatttgcatgaccattaccaattcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACAAGAGTAACTTAATGGCACAAGTGGAGCTACCAGTGTATAGTTTTTCATG

Basic information

species Arabidopsis thaliana
transcript AT5G58260.2
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|124811556|gb|EH896422.1|EH896422
EST:     CTAACGTCAGGGTTATTGCTGAATGTGGCAACTG                         GAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACA
genomic: CTAACGTCAGGGTTATTGCTGAATGTGGCAACTGgtgagtatat ... tcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACA
EST: gi|125256816|gb|EL270901.1|EL270901
EST:     CTTCCCTCTCTTCGTCCTAACGTCAGGGTTATTGCTGAATGTGGCAACTG                         GAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAAT
genomic: CTTCCCTCTCTTCGTCCTAACGTCAGGGTTATTGCTGAATGTGGCAACTGgtgagtatat ... tcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAAT
EST: gi|124769569|gb|EH859699.1|EH859699
EST:     AACGTCAGGGTTATTGCTGAATGTGGCAACTG                         GAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACA
genomic: AACGTCAGGGTTATTGCTGAATGTGGCAACTGgtgagtatat ... tcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACA
EST: gi|125159742|gb|EL187679.1|EL187679
EST:     CTTCCCTCTCTTCGTCCTAACGTCAGGGTTATTGCTGAATGTGGCAACTG                         GAGAAAGTTCGTGTGGAAG
genomic: CTTCCCTCTCTTCGTCCTAACGTCAGGGTTATTGCTGAATGTGGCAACTGgtgagtatat ... tcccctgcagGAGAAAGTTCGTGTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacactaatcatctatgtttgcaatttgcatgaccattaccaattcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACAAGAGTAACTTAATGGCACAAGTGGAGCTACCAGTGTATAGTTTTTCATG
   cactaat  putative branch site (score: 2)
                                            ttcccctgc  putative PPT
      taatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatatcattccttaccatacacactaatcatctatgtttgcaatttgcatgaccattaccaattcccctgcagGAGAAAGTTCGTGTGGAAGCCTCTAGCAGAAATTGCAAATCTAGCTGCACAAGAGTAACTTAATGGCACAAGTGGAGCTACCAGTGTATAGTTTTTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT