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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactaacttgcaagctttgaatactagtcatgatagatctttgccatgttcttgagtattcatcttttacttaataactttgcaagaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG

Basic information

species Arabidopsis thaliana
transcript AT4G17615.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 6
gtaatactaacttgcaagctttgaatactagtcatgatagatctttgccatgttcttgagtattcatcttttacttaataactttgca-agaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG
                ||     | ||| || | |      |  |||   ||||  |    | | || ||||| || | | || |    ||  ||| | | |  || |||| |  | ||||||||| |||||||| || || ||||| |||||||||||||||||  |||||||||||||||| ||||||||||| ||||||
----------------agagaaaattacaagacttttctcttgattgttgtgttgat--tcaattatgtttta-ttgaaacctctatgtaggcatcttcattctatttgattt--tggcagGTCAAACAAATGTTAATTGCACTTCTGTGCGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG

upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 6
gtaatactaacttgcaagctttgaatactagtcatgatagatctttgccatgttcttgagtattcatcttttacttaataactttgca-agaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG
                ||     | |||  | | |      |  |||   ||||  |    | | || ||||| || | | ||      ||  ||| | | |  || |||| |  | ||||||||| |||||||| || || ||||| || ||||||||||||||  |||||||||||||||| ||||||||||| ||||||
----------------agagaaaattacaggacttttctcttgattgttgtgttgat--tcaattatgtttta-ttgaaacctccatgtaggcatcttcattctatttgattt--tggcagGTCAAACAAATGTTAATTGCACTTCTGTGTGAATCTGAAATGAAGTTGGCTGATGAAACCATCGAGATAATACTTGATAAG
















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|86058729|gb|DR354486.1|DR354486
EST:     CGTTTAGGCTTTACGACATGGACTGCACGGGTTACATTGAACGACAAGAG                         GTCAAAGCAA-TGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAAC
genomic: CGTTTAGGCTTTACGACATGGACTGCACGGGTTACATTGAACGACAAGAGgtaatactaa ... atatttgcagGTCAA-GCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAAC
EST: gi|86077867|gb|DR373624.1|DR373624
EST:     CGTTTAGGCTTTACGACATGGACTGCACGGGTTACATTGAACGACAAGAG                         GTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCT
genomic: CGTTTAGGCTTTACGACATGGACTGCACGGGTTACATTGAACGACAAGAGgtaatactaa ... atatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttacttaataactttgcaagaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG
     ttacttaataacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatactaacttgcaagctttgaatactagtcatgatagatctttgccatgttcttgagtattcatcttttacttaataactttgcaagaaatcgttaatgaatgtgatatatttgcagGTCAAGCAAATGTTGATCGCGCTTCTCTGCGAATCTGAAATGAAACTGGCTGATGAAACCATAGAGATAATACTCGATAAG

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