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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtcaatggttttagtaggattttttgttttaaattcgaagatggtgtaggtccgtttactaacatgaaagtatatgttctcattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTTCAAGAAGCAGCGAAATCATTCAAAGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G60640.1
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|86064529|gb|DR360286.1|DR360286
EST:     TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTC
genomic: TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTC
EST: gi|86064531|gb|DR360288.1|DR360288
EST:     TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
genomic: TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
EST: gi|164039912|gb|ES199617.1|ES199617
EST:     GAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAAATGAATCTGAAAAGGTTCTTACGGAATT
genomic: GAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACC-AAAAATGAATCTGAAAAGGTTCTTACGGAATT
EST: gi|125041641|gb|EL113910.1|EL113910
EST:     TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGTAAAAGGTTCTTACGG
genomic: TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTG-AAAAGGTTCTTACGG
EST: gi|164110532|gb|ES038247.1|ES038247
EST:     CTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
genomic: CTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
EST: gi|86064530|gb|DR360287.1|DR360287
EST:     TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
genomic: TCACCAGAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
EST: gi|164001818|gb|ES205866.1|ES205866
EST:     GAGAGACTGCNCCGGAAATTTTTGAGAGTGCAATCAAGAAACAG                         TTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT
genomic: GAGAGACTGCTCCGGAAATTTTTGAGAGTGCAATCAAGAAACAGgtctgtcaat ... cattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaagatggtgtaggtccgtttactaacatgaaagtatatgttctcattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTTCAAGAAGCAGCGAAATCATTCAAAGGAAAG
                     tactaac  putative branch site (score: 0)
                                         ttctcatttt  putative PPT
                               aaagtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtcaatggttttagtaggattttttgttttaaattcgaagatggtgtaggtccgtttactaacatgaaagtatatgttctcattttgcagTTGTTGTTGTTTGTAACCAAAAATGAATCTGAAAAGGTTCTTACGGAATTTCAAGAAGCAGCGAAATCATTCAAAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA