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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC

Basic information

species Arabidopsis thaliana
transcript AT3G12080.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 3
tagcattgacaactatgttcaataggcatcactttacaaaccaaat--attaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAAC-ATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC------
         |||      ||| ||   | | | | || ||| || |  |||| |||||      |||  | || ||    ||  ||| | |   | | ||| |  || || | | | | |    |  ||||||||  | ||  |||| || ||| ||||| ||||| | |||||||||||||||||||||||||| |||||||      
--------tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattt-tataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G06150.1 (Glycine max), 3'ss of exon 6
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC---------
          |    |||||| |   ||  | ||     | |   | ||||  ||| || | | | |  |         |    | | | |||||     | | |  || |   | |  |    |  |||||| | ||  |||| || ||| ||||| ||||| | || ||||||||||||||||||||||| |||||||         
-------attattcttgttcactgtaca--atttggatcaacttgttttaattcatcttttgagacccttcatttttcaatttataatttactttctgctaacctatagGAATCTAATAATCTTGTTGAAGAAGATTATGTTCCAGCAATTTCAATTGTTGGTAGACCTAATGTTGGCAAAAGTAGCATTTTGAATGCACTGGTTGGTG

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 3'ss of exon 7
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttt-tctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC------
   | || |   | ||  || ||| ||||  |  ||    ||     | |      ||   ||| |  |||      | |   ||  |||    | | |||      |||||  |||| |       ||||||||| ||  ||||||| ||||||||| |||| || ||||||||||| |||||||||||||| ||||||       
-ttctttcatttcaatcatccataagcatgcccatattttcccctattcatctggattatatacttaggttcttgataaattttttcatgctaatatatagGATCCTGAGAATCTTGATG------GAGAAGAAAATTATGTTCCTGCAATTGCAATTGTTGGACGACCAAATGTTGGTAAAAGTAGCATTTTGAATGCATTAGTTG

upper sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ14023 (Selaginella moellendorffii), 3'ss of exon 4
tagcattgacaactatgttcaataggcatcactttacaaaccaaatattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC---------
                                                             || ||     | ||  | |      ||    |||||||  |    |      ||  ||| | |   ||||   ||     |    |  | |||||||||||  |||||||||||||||| || |||||||| ||||||          
----------------------------------------------------------gtatagatgatcagtactgaaagacaataactgtttttctatttaccagGATGAGTT--AGAAGCGAGCGAAGGCGACCGGCCTTTATCTGTGGCAATTATTGGGAGGCCAAATGTTGGCAAGAGCAGCATTTTGAATGCAATAGTCGGGA

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|164010236|gb|ES134196.1|ES134196
EST:     GAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAG                         ATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATT
genomic: GAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAGgtttgtaatg ... acttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATT
EST: gi|124739910|gb|EH831072.1|EH831072
EST:     GAACAGGAGAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAG                         ATCATGGAGAACATTGAAGAGGAG
genomic: GAACAGGAGAGCTGCTTGATCTTGTTTGTTCTGGCCTAATTAAACTCGAGgtttgtaatg ... acttttctagATCATGGAGAACATTGAAGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAACATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC
            ttcttac  putative branch site (score: 2)
                                              cttttct  putative PPT
     aaacatttt  TA-rich tract