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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatatatataacatgtcactaatcttttggtttgatctcttaatcatttccagttcagaatttgacatgaggatgctgaattttgtttttctacaatccagACAGAGTTTAACATGGAGGAGATATTGCGGAAATACATTCGTTATGCGTTGAATGAGAAACCGTTTAATCCCGACCTTGTTGCTGATCTCATTCATCTAA

Basic information

species Arabidopsis thaliana
transcript AT5G08540.1
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|86052734|gb|DR348491.1|DR348491
EST:     GAAAAGATGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAG                         ACAGAGTTTAACATG
genomic: GGAAAGCTGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAGgtgagaatat ... tacaatccagACAGAGTTTAACATG
EST: gi|86052732|gb|DR348489.1|DR348489
EST:     GAAAAGATGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGGACAAANG                         ACAGAGTTTAACATGGAGGAGA
genomic: GGAAAGCTGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAGgtgagaatat ... tacaatccagACAGAGTTTAACATGGAGGAGA
EST: gi|86052733|gb|DR348490.1|DR348490
EST:     GAAAAGATGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAG                         ACAGAGTTTAACATGGAGGAGATATTGCGGAAATACATTCGTTATGCGTTG
genomic: GGAAAGCTGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAGgtgagaatat ... tacaatccagACAGAGTTTAACATGGAGGAGATATTGCGGAAATACATTCGTTATGCGTTG
EST: gi|86052744|gb|DR348501.1|DR348501
EST:     GAAAAGATGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGA-CAAAAG                         ACAGAGTTTAACATGG
genomic: GGAAAGCTGGAACAGTGCATAGCTCTGAGCTTAAGGCACTTGAACAAAAGgtgagaatat ... tacaatccagACAGAGTTTAACATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccagttcagaatttgacatgaggatgctgaattttgtttttctacaatccagACAGAGTTTAACATGGAGGAGATATTGCGGAAATACATTCGTTATGCGTTGAATGAGAAACCGTTTAATCCCGACCTTGTTGCTGATCTCATTCATCTAA
             atttgac  putative branch site (score: 4)
                                  ttttgtttttctac  putative PPT
                                aattttgtttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaatatatataacatgtcactaatcttttggtttgatctcttaatcatttccagttcagaatttgacatgaggatgctgaattttgtttttctacaatccagACAGAGTTTAACATGGAGGAGATATTGCGGAAATACATTCGTTATGCGTTGAATGAGAAACCGTTTAATCCCGACCTTGTTGCTGATCTCATTCATCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT