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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGATGCAAAGAAATTGTGTCCTGGAATTTCAGCTGAAATTATTACGGAATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcacatagactcgtatctatctttgaatatgcatttgaatgttagaaggcaagacctgacgacttgctacgtttatgtattttttcttgtttgta...

Basic information

species Arabidopsis thaliana
transcript AT2G33340.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33340.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA20G21330.1 (Glycine max), 5'ss of exon 7
TCCTGATGCAAAGAAATTGTGTCCTGGAATTTCAGCTGAAATTATTACGGAATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcacatagactcgtatctatctttgaatatgcatttgaatgttagaagg---caagacctgacgacttgctacgtttatgtattttttcttgtttgta--
||||| |||||||||| |   ||||||||| ||  ||   || ||| | ||  | |||||||| |||||||||||||||||| || |||| ||||||||||||||   | | |     ||| ||  | | |||||  |||   || ||  |  |   |   |  || |  | |  |  | | | || ||  ||   | || |   
TCCTGGTGCAAAGAAAATTCATCCTGGAATATCTTCTAGCATAATTTCTGAGCTAACTGATTGCAATGCTGCTCTTTCCCAGCAGAGAAAGAAGCGACAGgtact---cttggtgatatatataa-tataaatatatattgacattttcaagtgtttctttagttgtcttcattttgagctca-gttttgctttgagcttttgac

upper sequence: AT2G33340.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G26870.1 (Glycine max), 5'ss of exon 7
TCCTGATGCAAAGAAATTGTGTCCTGGAATTTCAGCTGAAATTATTACGGAATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgc---acatagactcgtatctatctttgaatatgcatttgaatgttagaaggcaagacctgacgacttgctacgtttatgtattttttcttgtttgta
||||| |||||||||| |   ||||||||| ||  ||   || ||| | ||  | |||||||| |||||| ||||||||||| || |||| ||||||||||||||     | ||| | |  ||| |    |||  |   ||  | ||| |       |   |  |   |    | |  | ||| |   |||   |   |||  
TCCTGGTGCAAAGAAAATTCATCCTGGAATATCTTCTAGCATAATTTCCGAGCTAACTGATTGCAATGCTTCTCTTTCCCAGCAGAGAAAGAAGCGACAGgtactctctgatatatatttatattttcaattgtttcctcaggttaatatcttttttcttcattttgagctcggttttgctta-gagctttggataagttg--
















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|116465161|gb|EG507753.1|EG507753
EST:     AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAG                         ATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
genomic: AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcaca ... ttttctgtagATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
EST: gi|116444558|gb|EG487150.1|EG487150
EST:     AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAG                         ATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
genomic: AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcaca ... ttttctgtagATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
EST: gi|125261523|gb|EL275608.1|EL275608
EST:     ATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGACGAAAAAAGCGACAG                         ATTCCTCAAACATTGGC
genomic: ATTGACTGATTGTAATGCTGCTCTTTCCCAGAAG-CGAAAAAAGCGACAGgtactgcaca ... ttttctgtagATTCCTCAAACATTGGC
EST: gi|116472806|gb|EG515398.1|EG515398
EST:     AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAG                         ATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
genomic: AATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcaca ... ttttctgtagATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
EST: gi|125036843|gb|EL109112.1|EL109112
EST:     TTTCCCAGAAGCGAAAAAAGCGACAG                         ATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA
genomic: TTTCCCAGAAGCGAAAAAAGCGACAGgtactgcaca ... ttttctgtagATTCCTCAAACATTGGCGTCAATAGATACTTTGGAGAGGTTCACTCAGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGATGCAAAGAAATTGTGTCCTGGAATTTCAGCTGAAATTATTACGGAATTGACTGATTGTAATGCTGCTCTTTCCCAGAAGCGAAAAAAGCGACAGgtactgcacatagactcgtatctatctttgaatatgcatttgaatgttagaaggcaagacctgacgacttgctacgtttatgtattttttcttgtttgta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC