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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttgtgtacgtccaaagatgacgtcaaacatgtctgacatagttgaatatgggcctgtctaaaaacacaatgttccattttcttcatcgtggaaatagGTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTGATTTGGATGTTCTTCATTTTCTAATATCAAATTTGAACTG

Basic information

species Arabidopsis thaliana
transcript AT3G20440.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0090g00920.t01 (Vitis vinifera), 3'ss of exon 8
atcttgtgtacgtccaaagatgacgtcaaacatgtctgacatagttgaatatgggcc---tgtctaaaaacacaatgttc-cattt--tcttcatcgtggaaatagGTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTGATTTGGATGTTCTTCATTTTCTAATATCAAATTTGAACTG
         ||  |||||   |   | |        |    | ||| |   | |  |   |||  |||   ||    ||| |||      ||   |     |||||||||| | || ||||||||  ||||||| ||| | ||||||||||| ||||||   ||||| || ||||||||  | ||||||||||| ||
------atcactcccaaatgggttataatttgcaggttggttggtttacctttgctccattgttcaaatgtactgaattctcatccaacttttcccacttgaatagGTAAACGAGGACATCACAAGTACTGGGGTACCAGAATGTTCAAATATGGTGATCCTGATGTGCTGCATTTTCTTCTCTCAAATTTGAATTG
















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|116407561|gb|EG450153.1|EG450153
EST:     GGTTGGGCTTTCTCTCTTCGATGGTTCAAATGATTGCTATTTTCATTATG                         GTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTG
genomic: GGTTGGGCTTTCTCTCTTCGATGGTTCAAATGATTGCTATTTTCATTATGgtaatttcca ... gtggaaatagGTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTG
EST: gi|116407538|gb|EG450130.1|EG450130
EST:     GGTTGGGCTTTCTCTCTTCGATGGTTCAAATGATTGCTATTTTCATTATG                         GTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTG
genomic: GGTTGGGCTTTCTCTCTTCGATGGTTCAAATGATTGCTATTTTCATTATGgtaatttcca ... gtggaaatagGTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatatgggcctgtctaaaaacacaatgttccattttcttcatcgtggaaatagGTAAAAGGGGGCATCACAAACACTGGGGCACCCGGATGTTCAAATACGGTGATTTGGATGTTCTTCATTTTCTAATATCAAATTTGAACTG
             gtctaaa  putative branch site (score: 3)
              tctaaaaa  TA-rich tract