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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcatttagttccatgacatattataacaacttcattacgaaagcttttcttttatatcatagctaaaaagtatgaaagcactctcttgatgttttcttgtggtgaatgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGCGGAGGAAGAAGAGTGAGTGATCTATGTTTCTAATAAACAAGCCATGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G36230.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G36230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 8
gtgtgcatttagttccatgacatattataaca-acttcattacgaaagcttttcttttatatcatagctaaaaagtatgaaagcactctcttgatgttttcttgtggtgaatgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGCGGAGGAAGAAGAGTGAGTGATCTATGTTTCTAATAAACAAGCCATGAAG
              ||| ||  | | ||| ||  ||| |||    ||  |||||||  ||     | ||   ||  |  ||   |   |   | ||||   || ||   ||||    ||||||||| || || ||     | ||||| |||||||||||||| || ||||| ||||||||||| ||||||    ||| | | |   | |  ||       
-----------aaacca-gagctttgataccatgcttgatttttcaa--ttttcttaaatgcttaaactgtgaacaa--aacttatgattacggtgttggtttttg---aatgca-acagGCAAACTTTCGTCAAGGCACTGGAGCCCTTTGTGAATTGGCTGGAGGAGGCCGAGGAAGAAGAATGAGTGCAGCATGCTGCAATCTACCTCGCTTCTCTC
















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|125049526|gb|EL121795.1|EL121795
EST:     GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAG                         GCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTG
genomic: GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAGgtgtgcattt ... atgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTG
EST: gi|164094723|gb|ES115910.1|ES115910
EST:     CACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAG                         GCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGC
genomic: CACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAGgtgtgcattt ... atgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGC
EST: gi|125051831|gb|EL123898.1|EL123898
EST:     GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAG                         GCAAACCTTTGTGAA
genomic: GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAGgtgtgcattt ... atgtttgcagGCAAACCTTTGTGAA
EST: gi|125090932|gb|EL148755.1|EL148755
EST:     GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAG                         GCAAACCTTTGTGAAAAGTTTAG
genomic: GAAGACACCATTCTCCACTGGTTCCGTAAAGGAACCAACTCAAAGGGCAGgtgtgcattt ... atgtttgcagGCAAACCTTTGTGAAAAGTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaaaaagtatgaaagcactctcttgatgttttcttgtggtgaatgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGCGGAGGAAGAAGAGTGAGTGATCTATGTTTCTAATAAACAAGCCATGAAG
     aaaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcatttagttccatgacatattataacaacttcattacgaaagcttttcttttatatcatagctaaaaagtatgaaagcactctcttgatgttttcttgtggtgaatgtttgcagGCAAACCTTTGTGAAAAGTTTAGAGCCATTTGTGAATTGGCTTGAAGAGGCGGAGGAAGAAGAGTGAGTGATCTATGTTTCTAATAAACAAGCCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG