Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGAGAAGAAGATTGCAGATGTTCATGCTTGGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaacttagcaatagagaggtgaaacggttttaatgtgattgagaagtgaagtgttaatttgtgagttttttctcaatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G61260.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G61260.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G07970.1 (Glycine max), 5'ss of exon 4
AGCTGAGAAGAAGATTGCAGATGTTCATGCTTGGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaacttagcaatagagaggtgaaacggt--tttaatgtgattgagaagtgaagtgttaatttgtgagttttttctcaatgcag-----------
|||  | ||| || |  | | ||||  |||||||||||||||||||||||||||| | ||||| || || |  ||||| ||||||| ||    |   || |     | ||| ||  |    || | |  |  |  | | | |  |  || | ||   |  |||| ||                
AGCCCAAAAGCAGCTCTCTGCTGTTGCTGCTTGGGAAAACAGCAAGAAAGCAGCTCTTGAAGCTCAGCTGAGAAAAATTGAGgtattatttgttgctcagttattggttgatacaatgacatagttttttctattattcatg-atgcatgtttggcctagttctgaacattataatcaagata

upper sequence: AT3G61260.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G07970.4 (Glycine max), 5'ss of exon 3
------------------AGCTGAGAAGAAGATTGCAGATGTTCATGCTTGGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaacttagcaatagagaggtgaaacggt--tttaatgtgattgagaagtgaagtgttaatttgtgagttttttctcaatgcag-----------
                  |||  | ||| || |  | | ||||  |||||||||||||||||||||||||||| | ||||| || || |  ||||| ||||||| ||    |   || |     | ||| ||  |    || | |  |  |  | | | |  |  || | ||   |  |||| ||                
ATTGTTTTCTGTTAACAGAGCCCAAAAGCAGCTCTCTGCTGTTGCTGCTTGGGAAAACAGCAAGAAAGCAGCTCTTGAAGCTCAGCTGAGAAAAATTGAGgtattatttgttgctcagttattggttgatacaatgacatagttttttctattattcatg-atgcatgtttggcctagttctgaacattataatcaagata

upper sequence: AT3G61260.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv15s0046g03180.t01 (Vitis vinifera), 5'ss of exon 4
AGCTGAGAAGAAGATTGCAGATGTTCATGCTTGGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgta------------taataaacttagcaatagagaggtgaaacggttttaatgtgattgagaagtgaagtgttaatttgtga-gttttttctcaatgcag
 ||  |||| ||| || | ||||||  ||| |||||||||||||||||||||||||| |||||  | || ||||| || |||||             |  |  | ||   |||  |    || |||   ||   | | |||  || ||  |   || ||   |      |  | |  ||||||
GGCCCAGAAAAAGCTTTCTGATGTTTGTGCATGGGAAAACAGCAAGAAAGCAGCTGTTGAAGCTAATCTGAAGAAGATTGAGgttactgccccctgttgttttagtttttaattcacctttgcaacttcttccctat-attttgatgttcatgattcatccatactaaatggtgttcatgcag

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|125258574|gb|EL272659.1|EL272659
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCACCTAGAGAAGAAGAAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAG
EST: gi|125216784|gb|EL230867.1|EL230867
EST:     AGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
genomic: AGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
EST: gi|124926518|gb|EL004346.1|EL004346
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGA
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGA
EST: gi|125300806|gb|EL314891.1|EL314891
EST:     AAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATG
genomic: AAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATG
EST: gi|125158264|gb|EL186941.1|EL186941
EST:     CGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAA-GCAGAGTATGCAGAGAG
genomic: CGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAG
EST: gi|116446100|gb|EG488692.1|EG488692
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
EST: gi|125270235|gb|EL284320.1|EL284320
EST:     GGAAAACAAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGA
genomic: GGAAAAC-AGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGA
EST: gi|125023005|gb|EL095274.1|EL095274
EST:     CTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGC
genomic: CTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGC
EST: gi|125091790|gb|EL149613.1|EL149613
EST:     AAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATG
genomic: AAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATG
EST: gi|86080975|gb|DR376732.1|DR376732
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
EST: gi|116446101|gb|EG488693.1|EG488693
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
EST: gi|124849809|gb|EH934246.1|EH934246
EST:     CTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAGGCAGAGTATGC
genomic: CTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGC
EST: gi|116446103|gb|EG488695.1|EG488695
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG
EST: gi|124924697|gb|EL002768.1|EL002768
EST:     GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAG
genomic: GGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAG
EST: gi|124795618|gb|EH885297.1|EH885297
EST:     CTGTCGAAGCGCAACTCAAGAAAATCGAG                         GAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGNGAGGATGAAGAATAAG
genomic: CTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaa ... ctcaatgcagGAGCAACTAGAGAAGAAGAAAGCAGAGTATGCAGAGAGGATGAAGAATAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGAGAAGAAGATTGCAGATGTTCATGCTTGGGAAAACAGCAAGAAAGCAGCTGTCGAAGCGCAACTCAAGAAAATCGAGgtataataaacttagcaatagagaggtgaaacggttttaatgtgattgagaagtgaagtgttaatttgtgagttttttctcaatgcag

- - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA