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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgttgagggacttgtagccctgctaatttttatgtttttgtttcattgttctgtttcttgtttagatttttagtctgcctgcctttgagaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
gatgttgagggacttgtagccc-tgctaatttttatgtttttgtttcattgttctgtttcttgtttagatttttagtctgcctgcctttgagaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAA
  | ||  |||| |   ||    |  |  |||||         |||| ||||||| ||  ||  |   |||| |||| |   |  ||||||| || |||||||| ||||| ||||| ||||  |||||  ||||||| || |||||||||||||||||  | ||||||||||| ||| |||| || ||  |||| || |||
-ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
















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|116486725|gb|EG529317.1|EG529317
EST:     CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|125137507|gb|EL177362.1|EL177362
EST:     CTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
genomic: CTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|124828874|gb|EH913710.1|EH913710
EST:     CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGG
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGG
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     GGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGATGT
genomic: GGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|116477129|gb|EG519721.1|EG519721
EST:     CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGT
EST: gi|125221163|gb|EL235248.1|EL235248
EST:     CCAAGTGGAAATCTCCCCC-TGGTTTTGATCCAAGTACTTGCCGCAGTGT                         GTACGTTGGAAACATCCAT
genomic: CCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtta ... gaaattgcagGTACGTTGGAAACATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgttctgtttcttgtttagatttttagtctgcctgcctttgagaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAA
              ttgtttagattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgttgagggacttgtagccctgctaatttttatgtttttgtttcattgttctgtttcttgtttagatttttagtctgcctgcctttgagaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
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