Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcag

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 9
TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttaca-atatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaac---gcaaactcttgag-----gcctaaa---tcttatagattaacatacagttgtatatatctgatgaagcgtt-tatatatgtgatacattgtggcag-----------------------------
||||||||| ||||||||||||||||||||| | ||||| ||  ||||||| || || |||||||| ||||| ||||||||||| || || ||||| ||||||| ||  ||||||  | ||   |||  ||  | ||| |||  | |||| |||  | ||     |    |      || || |  |        || ||||   |  | |   |   | | ||  |  |  | ||   | ||| |   |   |      | || ||  |                                
TGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAACATGTTGATCATTCTCGCAAATCAGCTGAACAGGCTGTGAAGgtaagta--gcttacctaaatttgtgagctca-tgcacaaaatacatatttatcattgccccggcatgccctctctagctaattagtagatatctgcttaaacgtttctttttctggtcctccaaatcaaagtttccagtaaagagccatgcttgcagactgcagtgctgtttctcattctgtgataacttgttttatgtag

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 9
TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttacaatatggctgatatcgc-tacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgag---------gcctaaatcttatagatt----aacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcag------------------------
||||||||| ||||||||||||||||||||| | ||||| ||  ||||||| || || |||||||| ||||| |||||||| || || || ||||| ||||||| ||  ||||||  ||    ||  | | | | ||| | |  | |||| |||  | ||     |    |  | | | || || ||         || ||||  || |   ||      | | ||  |  |  | ||   | ||| |   ||   ||   | |  | |  ||                         
TGTTGGTGATGTTGCTACTTTCCCTTTGAAATTATACGGTGAATTGAGAAGAGTTGAACATGTTGATCATTCTCGCAAATCGGCTGAACAGGCTGTGAAGgtaagta--gcttacc-taaatttgtcagctcatgcacaatatacatatttatcattgccccggcatgctct-ctctagctattcagtagatatctgcttaaacgttttttttttctggtcctccaaatcgaagtttcaagtaaagagccaatgcttgcagtgctgtttctcattctgtgattacttgttttatgtag

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 9
TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttacaatatggctgat-atcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcag
||| || || ||||||||||||||  ||||| |||||   ||  | ||||| || || ||||| |||||| |||| |||||||| ||||||||||| ||||||    |   || |  ||||  |  | |    ||      | |    || ||   |   ||     |        ||  |    |      | | || |                                                             
TGTGGGAGATGTTGCTACTTTCCCACTGAAATTGTACAATGAAATTAGAAGAGTTGAACATGTCGACCATGCCCGGAAATCAGCTGAGCAAGCTGTCAAGgtatgcgactttt-ctttatgcttagttacttttatgaaccatcttagttgatttgtttaatctgctaattgggtgaagttaccaaaaatacattgttctg------------------------------------------------------------

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|86078827|gb|DR374584.1|DR374584
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47828341|gb|CK118025.1|CK118025
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125217538|gb|EL231621.1|EL231621
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAG
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAG
EST: gi|47828077|gb|CK117761.1|CK117761
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125272888|gb|EL286973.1|EL286973
EST:     TGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGTAGCGGTGGAGGAATACGACTATCTT
genomic: TGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47829815|gb|CK119499.1|CK119499
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125020210|gb|EL092479.1|EL092479
EST:     GTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47830852|gb|CK120536.1|CK120536
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGTGACGTTGCTACTTTCCCTTTGAAAATGTACGGAGACGTGAGAAGGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT