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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaatacacaaacaaagcttgtcacaaaactctgattttactagaatacttcaaatatctgtgtcttgccacaatgggatttaagctaaaactctaatatgttatgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCAAATCTGCTAACTTCCCATTGTGGAGAAAACCAAAAGTTACATAAGAAGT

Basic information

species Arabidopsis thaliana
transcript AT5G27720.1
intron # 7
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|164219369|gb|ES133811.1|ES133811
EST:     GGCAGAGGCAGAGGAACTTCAATGGGG-AGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: GGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|124973680|gb|EL047289.1|EL047289
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTT
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTT
EST: gi|164043943|gb|ES089912.1|ES089912
EST:     GGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: GGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|47831834|gb|CK121518.1|CK121518
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|116444724|gb|EG487316.1|EG487316
EST:     GATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: GATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|47832106|gb|CK121790.1|CK121790
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|116449433|gb|EG492025.1|EG492025
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
EST: gi|164040263|gb|ES122100.1|ES122100
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAAC
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAAC
EST: gi|86080718|gb|DR376475.1|DR376475
EST:     CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAG                         GAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA
genomic: CAGAGGCAGAGGCAGAGGAACTTCAATGGGGAAGATGGGTGGCAACAGAGgtaaaaaata ... tgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcttgccacaatgggatttaagctaaaactctaatatgttatgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCAAATCTGCTAACTTCCCATTGTGGAGAAAACCAAAAGTTACATAAGAAGT
                                ctctaat  putative branch site (score: 3)
                                   taatatgttatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaatacacaaacaaagcttgtcacaaaactctgattttactagaatacttcaaatatctgtgtcttgccacaatgggatttaagctaaaactctaatatgttatgaaaaacagGAGCAGGTCGCGGCCGTGGTTGATGCAACAAGTTTTAAAGACTCGCTGCCAAATCTGCTAACTTCCCATTGTGGAGAAAACCAAAAGTTACATAAGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT