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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttggtcagtgtttttcattgttcttggcaactagaaccagtgtttgtgtttctaccaaggaaacaagtatctcgttgtgtttatttgtctgttgatgtgatgttttactgttttgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAGGAACTGAACTTTACTCTGAAAGATCCTGCAGCAGTTCTCGCATTG

Basic information

species Arabidopsis thaliana
transcript AT5G47710.1
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|125259893|gb|EL273978.1|EL273978
EST:     TCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAG                         TCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGGTGGAATGA
genomic: TCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAGgtatgtttgg ... tgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTG-TGGAATGA
EST: gi|164049319|gb|ES201732.1|ES201732
EST:     GATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAG                         TCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAAT
genomic: GATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAGgtatgtttgg ... tgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAAT
EST: gi|19875004|gb|AU235835.1|AU235835
EST:     GAGATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAG                         TCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAG
genomic: GAGATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAGgtatgtttgg ... tgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAG
EST: gi|86074770|gb|DR370527.1|DR370527
EST:     GAGATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAG                         TCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAG
genomic: GAGATTTCAAGTCAAGTGATCCTTATGTGATTGTCAAATTAGGAAATGAGgtatgtttgg ... tgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctcgttgtgtttatttgtctgttgatgtgatgttttactgttttgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAGGAACTGAACTTTACTCTGAAAGATCCTGCAGCAGTTCTCGCATTG
                     tgttgat  putative branch site (score: 4)
                                       ctgtttt  putative PPT
         tgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttggtcagtgtttttcattgttcttggcaactagaaccagtgtttgtgtttctaccaaggaaacaagtatctcgttgtgtttatttgtctgttgatgtgatgttttactgttttgaaaaccagTCAGCGAAGACCAAAGTGATCAACAATTGCCTGAATCCAGTGTGGAATGAGGAACTGAACTTTACTCTGAAAGATCCTGCAGCAGTTCTCGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG