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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttagtgccagtcagtcattagcttgaattagtttagatagaatttagcaagttttataaagagcactaacatccaatttattattgcgtttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCTGAAACCATATATAGATACGGTAAACATTGTGTGTGATATAGCAGTTTGT

Basic information

species Arabidopsis thaliana
transcript AT1G06460.1
intron # 6
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|86077661|gb|DR373418.1|DR373418
EST:     TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTAT                         GGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
genomic: TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
EST: gi|86084351|gb|DR380110.1|DR380110
EST:     TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTAT                         GGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
genomic: TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
EST: gi|125288794|gb|EL302879.1|EL302879
EST:     AGGATAATGTTTCCGCTGAATTTAT                         GGANGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
genomic: AGGATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
EST: gi|124765656|gb|EH855786.1|EH855786
EST:     ATAATGTTTCCGCTGAATTTAT                         GGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
genomic: ATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
EST: gi|86086217|gb|DR381976.1|DR381976
EST:     TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTAT                         GGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
genomic: TGGCCACTCCCCAGCAATGTGAACAAGGATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCT
EST: gi|124728737|gb|EH820139.1|EH820139
EST:     GCAATGTGAACAAGGATAATGTTTCCGCTGAATTTAT                         GGATGGGATTCTGAGAATAGTAATTCCAAAG
genomic: GCAATGTGAACAAGGATAATGTTTCCGCTGAATTTATgtaagtagaa ... tttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcaagttttataaagagcactaacatccaatttattattgcgtttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCTGAAACCATATATAGATACGGTAAACATTGTGTGTGATATAGCAGTTTGT
                    cactaac  putative branch site (score: 1)
                           atccaatttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttagtgccagtcagtcattagcttgaattagtttagatagaatttagcaagttttataaagagcactaacatccaatttattattgcgtttgaaacagGGATGGGATTCTGAGAATAGTAATTCCAAAGCTTTGAGGGTTCATCGTTCTGAAACCATATATAGATACGGTAAACATTGTGTGTGATATAGCAGTTTGT

- - - - - - - - - - - - - - - - - - agatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaac