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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag

Basic information

species Arabidopsis thaliana
transcript AT3G44340.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os11g29200.1 (Oryza sativa), 5'ss of exon 15
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag-
 || |||| ||| || ||  | ||| ||| |||||| ||||||||||||||||  || || || ||||| |||||||| ||||| ||||||||||| |||||   | ||  |||||||    | |     |||    |||  | |  || ||  |    | |||   ||||   |   | |  |   
TTCCGCTCGTTCGGATCCGGCCAAGCTATTCAACGACCTTAGATGGAATATCAGTAGACCTCAGGGTTTCGAGGCTGTTATGCGTGTCAGATGCAGCCAGgtgg-gattaatggcagaccttttttcttcagt--gctttacgttacagtttggtcataacataattctttctccacatgtgatcag

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os12g24250.1 (Oryza sativa), 5'ss of exon 17
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag
 || || ||||| || ||  | ||| | | ||| ||||| |||||||||||||  || ||||| || ||||||||||||||||| || || |||||||| ||||   | | |   |     | |  | ||  ||| | |  ||    |  ||   |  |   | |   |||  |     |||    
TTCTGCCCTTTCTGATCCAGCCAAGCTGTTCAATGATCTCAGATGGAATATCAGTAGACCCCAGGGATTTGAGGCTGTCATGCGTGTGAGGTGCAGTCAAgtaagtatatttctgatccttcccccttcatatcatactcaagtggtaacttgaattttcgtt-ctgttttaatgtgccattag--

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G019236_T06 (Zea mays), 5'ss of exon 15
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag-
 || ||||||||||| ||  | ||| | | ||| ||||| |||||||||||||  || ||||| |||||||||||||| ||||| || || |||||||||||   ||||  |  |||     |      |   ||   | |    ||||  |   ||  |  |      |||     |  |  |   
TTCTGCTCTTTCAGATCCAGCCAAGCTCTTCAATGATCTCAGATGGAATATCAGTAGACCCCAGGGTTTTGAGGCTGTTATGCGTGTAAGGTGCAGTCAGgtgg-gtttaatctcaggtcatttctattag--cactctacgttatgagtctgaatgtgacttgttttcttttcacctcttcatcag

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GRMZM2G142697_T02 (Zea mays), 5'ss of exon 1
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag----
 || ||||||||||| ||  | ||| | | ||| ||||| |||||||||||||  || ||||| |||||||||||||| ||||| || || |||||||||||   ||||| |         |||  | | | |   | ||||| || ||  |  | |||       | || | ||   | |  |      
TTCTGCTCTTTCAGATCCAGCCAAGCTCTTCAATGATCTCAGATGGAATATCAGTAGACCCCAGGGTTTTGAGGCTGTTATGCGTGTAAGGTGCAGTCAGgtgg-gttttat---------ctcatttctattagcacttcagtttaagagt-ctggatgtgacttatttctttctcatctcctcatcag

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA20G24330.1 (Glycine max), 5'ss of exon 17
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag
|||||||||||| ||  |  ||||  | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| || || |||||||||||| | | ||           || || | |  |       || | |   |    |    || |  || ||||||   || |   ||
CTCAGCTCTTTCTGATACTGCAAAACTTTACAATGATCTTAGATGGAACATCACTAGGCCACAAGGTTTTGAGGCTGTAATGCGTGTGAGGTGCAGTCAGgtagtctgtttcacttt----ctttg-ctaccttgtcacacaacatatag--gctctgcaattttcatttttgttcttt-tgccag

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA10G42720.1 (Glycine max), 5'ss of exon 17
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag-
|||||||||||| ||  |  ||||  | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| || || |||||||||||| ||| || ||    |      |  | |   |   |  ||            |   ||| |  |  ||||||    | ||||   
CTCAGCTCTTTCTGATACTGCAAAACTTTACAATGATCTTAGATGGAACATCACTAGGCCACAAGGTTTTGAGGCTGTAATGCGTGTGAGGTGCAGTCAGgtagtgtgtt-tgtttcactttctttgctaccccctgtcacacaacatataggctctgtaattttcgtttttgtt--cttttgtcag

upper sequence: AT3G44340.1 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv19s0014g05310.t01 (Vitis vinifera), 5'ss of exon 16
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcaga-gagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag-----------------------------------
|||||| ||||| || ||  | ||| | ||||| || ||||||||||| ||||| | |||||||||||||||||| || ||||| ||||||||||| |||||||| | || ||    | || || |      |    ||| |   ||    || | |||||| || |  ||||     ||| | |                                     
CTCAGCCCTTTCTGATCCTGCTAAGCTTTACAATGACCTTAGATGGAACATCACAAAGCCCCAAGGTTTTGAGGCAGTGATGCGTGTCAGATGCAGCCAGgtaatttcttttgttgtatgaactttagtt--gcttgattcc---tttcttttgtatgataattagctttttttatctttaatctgtgctatacaaattaatttcttttccatcttttacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGCTCTTTCAGACCCCCCAAAGTTATACAACGATCTTAGATGGAATATCACGAGGCCCCAAGGTTTTGAGGCTGTCATGCGAGTCAGATGCAGTCAGgtaatgttttgtggcagagagctctgtccaagtcaaatttcagcttgaggttatttgataaataccacttttgtcgattattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG