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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatcgttaaggaaacaagtactaatccatagattgtttcag

Basic information

species Arabidopsis thaliana
transcript AT1G79990.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatc--gttaaggaaacaagtactaatccatagattgtttcag-----------------------------------------------------------------------------------------------------
|| ||| |||| ||||||||||| ||||| |||| ||| ||||| ||||||||||||||||||||||     | |      | ||  || |||| |  ||    ||   ||    |     |   ||||  | |    |                                                                                                      
CGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTACATCCAACAGAGCCATGgtaatgcctcctctgctgctgttgttttctttctgaattcgattcctgatgtgaagctaacatcataattgggaatatctgtagtttgtgaggatttagtcactaatagtgatgtttgttatacgagtttactgttggcatcatttaattaattgcttcatgcaaccttgttaattcag

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatc--gttaaggaaacaagtactaatccatagattgtttcag-----------------------------------------------------------------------------------------------------
|| ||| |||| ||||||||||| ||||| |||| ||| ||||| ||||||||||||||||||||||     | |      | ||  ||  ||| |  ||    || | ||    |     |   ||||  | |    |                                                                                                      
CGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATGgtaatgcctcctctgctgctgttgttttgtttctgaattcaatttatgatgtgaagctaacatcataattgggaatatctgtagtttgtgaggatttagtcactaataccgatgtttgttgtacaactttactgttggcatcatttaattaattgcttgatgcaaacttgttaattcag

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaat---ttgagcgcattcattcttcattgctttatatatcg------ttaaggaaacaagtactaatccatagattgtttcag---------------
|| ||| |||| ||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||   ||   |    |  | |||  |   |||||   | |      || | || |  |     |||  |||    | || |                
CGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATGgtaatgccttatccttggttgtgctttgtgattttatcactggaattattttaagatatgaaactaaatttataaccagctttataatttgctgctcatt

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaat---ttgagcgcattcattcttcattgctttatatatcg------ttaaggaaacaagtactaatccatagattgtttcag---------------
|| ||| |||| ||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||   ||   |    |  |  ||  |   |||||   | |      || |  | |  |     |||  |||      || |                
CGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATGgtaatgccttatccttggttgtgttttgtgattttatcactagaattattttaatatatgaagctaaatttataaccacctttataatttgttgctcatt

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatcgttaagga--------------aacaagtactaatccatagattgtttcag----------
 | ||  | || ||||||||||| ||||| |||||||| ||||| |||||| | ||||||||||||||  |     ||    | | |||  | ||  | | |||    |              || | | | | |  | |||||  || | |          
AGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATGgtaattataatatgtttggccataatttatgtactttttgtttcaaattttctctgacttgaataggaaatgagacttagatgtttgctggccattgtgg

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 3
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatat-----cgttaaggaaacaagtactaatccatagattg----tttcag---------------------------------------------
 | ||  |||| |||||||| |||||||| ||||| || ||||| |||||||| || ||||||||||||   | |||     |||| ||  |||   | |     | ||| |  || || ||  |  |   |  ||     ||| ||                                             
AGAAAACTTGCACAAAGATCTGAAAGAGTAAAATCAGTGGATCTACATCCAACTGAACCATGgtaattttc-ctcatcttcacttcgttaatttgagtttgtctcccttaggtcaaaaaatataacgctgcatttttaagcttttagacaatgtttatagaaaattttgcaattacaagatgctgcatgcag

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ09529 (Selaginella moellendorffii), 5'ss of exon 1
------CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatcgttaaggaaacaagtactaatccatagattgtttcag
      || ||| |||| ||| |||||||  | || |||| ||||||||||||||| ||||||||||||||        | |  ||||   | |       |  ||  ||    |  |     | |                  
CTCCAGCGCAAGCTTGCGCAACGATCAGAGCGCGTGAAATGTGTAGATCTCCATCCCACAGAGCCATGgta-------tgtagccattagac-taagagcgtgaatgattttctatgcgttcgccag-----------------

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 1
------CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatcgttaaggaaacaagtactaatccatagattgtttcag
      || ||| |||| ||| |||||||  | || |||| ||||||||||||||| ||||||||||||||        | |  |||||  | |       |  ||  ||    |  ||    | |                  
CTCCAGCGCAAGCTTGCGCAACGATCAGAGCGCGTGAAATGTGTAGATCTCCATCCCACAGAGCCATGgta-------tgtagccattcgac-taagagcgtgaatgattttctatgcattcgccag-----------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATGgtaatttgagcgcattcattcttcattgctttatatatcgttaaggaaacaagtactaatccatagattgtttcag

- - - - - - -  AGATCA