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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag

Basic information

species Arabidopsis thaliana
transcript AT3G15980.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 5
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag
||||| |||||||| || ||||||||||||||  | ||||| ||||| || ||||||||||| |||||||||||||| ||  | | | ||   |     | || |   ||   |    |  ||  | | ||   |    | ||    ||  |  |      |          
AATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAATgtaagtttttctgca-ttttgttggctctgtagttcaatgatgtaacatctacttgatgtaactataacacaacaattataccttccag--------

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagc-tattattttcattc-ccactttcgtggattgtt---caaaag--cttactctggtgttcctcgctattacag---------------------
|| |||||||||||||| || |||||  |||| || || || |||||||| |||||||||||  |||||||||| || ||    |||   | || |||||||||   | ||||||   ||| || |||   ||  || ||     ||||  |||  | |    |  |  |   |||                        
AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAACgtaagttattgtattatct-aaatgttcattatgttatttcttttctcctcttgaatgtgttattgcgtgaaagttctttttttaccatggcatgaagttatgtttgtaatttgtgttcctacag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaat-----ctgt-tcaacctcaaatgttcagctattattt---tcattcccact-ttcgtggattgttcaaaagcttactctggtgttcctcgctattacag---------------------------------------------
|||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || ||||||||        |||| | ||   |  |||||||| |    |||   | |   ||||| ||  | |    ||  || |   | |   |      |   | ||   |                                             
AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAATgtgagttctgtcactgtcttaattgcctatgttcagttgacctttcagttacatccactattttttgtcctttttaatgtcaaattaagaagaaattatttttctggtcaaattgaaatgtattaatacaaaagtttccttttatcttgtag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgaga---------atctgttcaacctcaaatgttcagctattattttcatt---cccact--ttcgtggattgt---tcaaaagcttactctggtgttcctcgctattacag---------------------------------------
|||||||| |||||||| ||||||||||||||| | ||||| |||||||||||||||||||| ||||| || ||||||||          | ||  | ||   |  ||||||||      |||   ||    |||||  || |||  || |   |||||     |  |     ||  |     | | |                                        
AATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAATgtgagttctgtcattaccttattaattgcctatgttcagtcgacctttctgttacatccactgatttgtgtcttttatgtcaaattaagaagcaatcattttttctggtcaaatggacatgtactaacacaaaagtttccttttatcttgtag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 15
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgag--aatctgttca-acctcaaatgtt-cagctatta--ttttcattc--ccactttcgtggat----tgttcaaaagcttactctggtgttcctcg-ctattacag-------------------------------
||| | ||||||||||| ||||||||||| ||  | || || || ||| ||||||||||||| |||||||||||||||||  ||| |   || |    | ||  |  || |   |  |||| |||   |   ||  |   ||    | |||   | || ||  |||| | ||| | ||||||                                  
AATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAATgtgagttaattttcacatattgtagatactgtagatcacagttttttattgtgctggttaagcacatattgtattctgcaactgacaatggtatgccttgtctattatttactaacgcaactctaacttgataacatctag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagc-tattattttcattcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag-----------
||  |||| |||||||| ||||||||  |||| || || || |||||||| |||||||||||| | ||||||||||| |||   |||  | | ||||||| | |   | || |||   || ||  || |     ||||     |      | |        |  |||| | |            
AACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAATgtaagatattgt--atcgtcaaatgattattatcttgtttctttttccttttacccaccttgtgatgcatggcgttataaacaaaatgactatgatatgtgctttttag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcatt------------cccactttcgtggattgttcaaaagcttactctg----gtgttcctcgctattacag
||| |||| |||||||| ||||||||  |||| || || || |||||||| |||||||||||| | ||||||||||| |||   |||  | ||||||||| | |     || |||| ||            ||||| | | ||   || |    |   ||         | | |    ||| || |||
AATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAATgtaagatattgt--atcctcaaatgattattatctagtttctttttccttcttttacccacctccttgtgatgatggggattataacacaaaacgagatttgtgct-ttgcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag-------------------------------------------------------------------
|| || || |||||||| ||||||||| ||||| | |||||||||||||| |||||||||||  |||||||||||||||| || |     | ||  |   ||    |||  || |    |   ||||   | |     ||    ||  | |       |  | | ||| | |                                                                   
AACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAATgtgaggattttcgtgaacttcatcttttccttatagttgttgg-cttgctttgaagaacatcccaccccctccccccaacacaca-cacaatttctgctgaatgtatattttgtagatctttactggtagtgcccttgaaacatattgacttccattattgcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaa-tctgttcaacctcaaatgttc-----agctatta-----ttttca-------ttcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag--------------------------------
|| || || |||||||| ||||||||| ||||| | |||||||| ||||| |||||||||||  |||||||||||||||| | |||  | ||| |||  | |||     || | ||       |||||       ||  | | ||  |   |    | || |  || |     | || |  ||  ||  |                                
AACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAATgtgaggactctcatgaacttcatcttttccttatagatgttggcttgctttcaagaatattttgccccttactatttctgccgaatgtatatttgacagatctttactggtagtgccctttaaacattttgacttccactattgcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 3
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatc------tgttcaacctcaaatgttcagctattatt--ttcattcccactttcgtgg-attgttcaaaagcttactctggtgttcctcgctattacag------
|| || || |||||||| ||||||||| ||||  | |||||||||||||| |||||||| ||| |||||||||||||||| ||       ||| |  || |      ||   | || ||  || | |     | |  ||| | |    |       ||| |     |  |  ||   || |      
AACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAATgtgaggattctaaattgtcccccccccccctctcttatgtttttggttaaatgaatatctgatggcacttactagtgaagcactgtaaacattttaacttccactgttgcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatc-----tgttcaacct----------caaatgttcagctattat-------tttcattcccactttcgtggatt-gttcaaaagcttactctggtgttcctcgctattacag--------------------------------
|| || || |||||||| || |||||||||||  | |||||||||||||| |||||||| ||| | |||||||||||||| ||      |  |  |||           ||  |||| |  | ||||         || ||  | |     ||  || | | ||| |  || |||| ||   ||  ||| |  ||                                
AACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAATgtgaggattctaaatacttgacccttttattttacacttgttgactttttatgaaaaagcatcgttttcccccctatgtttttggttaaatgaata-tctgatggcacttactagtgaagcacagtaaacattttaacttccattgttgcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactt-tcgtggattgttca-aaagcttactc----tggtgttcctcgctattacag-----------------------------------
||||||||||||||||| |||||||||||||| || ||||| |||||| | ||||| |||||||| ||||||||||| ||    |  ||    |    |  ||   |   | ||| ||    | |  || | ||||  ||| |||   || ||    |    |   | |  ||||                                      
AATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAATgtaag--ctttctccctttttggttctcttatcccacttttatgagaaatcatcatagatttgtcataaaatctattcgttttacaatcatttgagattaagtacctcacttaacaaccaaatatgtttatttggcag

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 14
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 14
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactttcgt-----ggattgttcaaaagcttactctggtgttcctcgct----attacag----------------------
|| || ||||||||||| ||||| ||||| || |||||||| |||||||| ||||| |||||| |||||||||||||  | |||     |   | ||   |     ||   | |  | | |  ||||| |     | ||||  |||| || |  | ||| |  |  |  |    |||  |                       
AACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAATgtatggatcctcaaattattaatcctctttttaacttgtgtaattctcctttcctctatagaattggccaaatgcatgatttggagcactgcattccaaattgaactttttttaatttaattttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAATgtgagaatctgttcaacctcaaatgttcagctattattttcattcccactttcgtggattgttcaaaagcttactctggtgttcctcgctattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG