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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttgttattttctttgtggtttttggtgattgcaaatcctctggtgatgttgattaaaaaaagtctcattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCAATATGATGGACAAAGACGAGCCGTTTGTCTACAACGAGGTGGATTACAA

Basic information

species Arabidopsis thaliana
transcript AT5G64540.1
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|116432277|gb|EG474869.1|EG474869
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432280|gb|EG474872.1|EG474872
EST:     GCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432276|gb|EG474868.1|EG474868
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432286|gb|EG474878.1|EG474878
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432275|gb|EG474867.1|EG474867
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432283|gb|EG474875.1|EG474875
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432288|gb|EG474880.1|EG474880
EST:     GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: GGAAAGCTTTAGCGGCAGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
EST: gi|116432290|gb|EG474882.1|EG474882
EST:     AGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTG                         TCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA
genomic: AGAGAGAAAGAGTGAATAAGTCGAGACTTCTCTGgtgatttgtt ... cattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtgattgcaaatcctctggtgatgttgattaaaaaaagtctcattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCAATATGATGGACAAAGACGAGCCGTTTGTCTACAACGAGGTGGATTACAA
                          tgttgat  putative branch site (score: 4)
                                          tctcatttt  putative PPT
                         atgttgattaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttgttattttctttgtggtttttggtgattgcaaatcctctggtgatgttgattaaaaaaagtctcattttgaagTCTGGTGATACAAGGATCCACAAAGGAATCTCAGATTCTCCTACTGTAGCAATATGATGGACAAAGACGAGCCGTTTGTCTACAACGAGGTGGATTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA