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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGAATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaagagataatgtttagatttgggtcacggagatgctttcacatgtctcttactcccttgactacaatgattacttaagatataatccggtgaccacatttttaatcggttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G25840.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 5'ss of exon 13
GCTTGAATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaagagataatgtttagatttgggtcacggagatgctttcacatgtctcttactcccttgactacaatgattacttaag-atataatccggtgaccacatttttaatcggttgcag---------------------------------------------------------------
  | |||||||||||  | ||||| ||||||||||||||||| ||||| || || |||||| || |||| || |  ||||||||  ||  ||       |||  | | ||||     |  |    |     | ||   |    || | ||   |  ||| || |||  |  |  | ||| | | |    ||| |  | |                                                                      
CTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAGgt--ggccaatctttacatgcat-gctttgcaaacctaaccaaccagagcgtgaagcagggtcacctgcacatgatggtttctttcgtgtccagtccagcgtcatgttttcttgttgacgatgacaagataattttcctagttcactatccaagaagttgatcgtttcaataattttattttgacag

upper sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA04G09130.1 (Glycine max), 5'ss of exon 13
-----------------GCTTG-AATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaagagataatgtttagatttgggt----cacggagatgctttcacatgtctcttactcccttgactacaatgattacttaagatataatccggtgaccacatttttaatcggttgcag
                 | ||| ||||||||||  ||||||| |||||||| |||||||| || || ||||| ||| || ||||||| |||| |||||||||  | |     | || || | |   | || ||      |    ||| ||  || ||   |  | |    |   | ||                                                 
TTATGACAAATCTTACAGTTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTCTTTCCATATACCAGCTTATTTCAGGAAAGACAAAAGAGgtcagaaatgctatattatatgtgtgtgtgtgtgtattgcaattatgattctacttgatacccatttttata--tgcag------------------------------------------------

upper sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA04G09130.2 (Glycine max), 5'ss of exon 13
-----------------GCTTG-AATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaagagataat----gtttagatttgggtcacggagatgctttcacatgtctcttactcccttgactacaatgattacttaagatataatccggtgaccacatttttaatcggttgcag
                 | ||| ||||||||||  ||||||| |||||||| |||||||| || || ||||| ||| || ||||||| |||| |||||||||  | |     | || ||    || |   | ||  |  |    ||| ||  || ||   |  | |    |   | ||   | |  |  ||                                    
TTATGACAAATCTTACAGTTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTCTTTCCATATACCAGCTTATTTCAGGAAAGACAAAAGAGgtcagaaatgctatattatatgtgtgtgtgtgtgtattgcaattatgattctacttgatacccatttttata--tgcaggaagttgtgcag------------------------------------

upper sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 5'ss of exon 13
GCTTGAATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaag-agataatgtttagatttgggtcacggagatgctttcacatgtctcttactcccttgactacaatgattacttaagatataatccggtgaccacatttttaatcggttgcag
 || |||||||||||| ||||| |||||||||||||||| || ||  |||| |||||| |  | ||||||| || ||||||||||  | ||||  | |||  |  |   ||||| |       |||| |   | | | || || | |  | || ||| ||   |  || ||  | ||   ||  |   |||||             
CCTGGAATTTGACAATCCTGAGCGACCTGAATGCAACAACCTTCTTACAATTTATCAGCTAATGTCAGGCAGGACAAAAGAGgtaaagtgaaattacatatggcctc--tttggttttta---atgcctatccctatgtcatattgctgttaccaca-tg--catatatgactttat---gtttctttatttt-------------

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|125079211|gb|EL141300.1|EL141300
EST:     CCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAG                         GAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC
genomic: CCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaa ... tcggttgcagGAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC
EST: gi|124986271|gb|EL058803.1|EL058803
EST:     TCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAG                         GAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC
genomic: TCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaa ... tcggttgcagGAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC
EST: gi|163977425|gb|ES119783.1|ES119783
EST:     CAATATATCAGATTGTTTTCAGGCAAGAAAAAAGAG                         GAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC
genomic: CAATATATCAGATTG-TTTCAGGCAAGAAAAAAGAGgtatggagaa ... tcggttgcagGAAGTGATGGAGGAATGCAAAGATATGAGCTGGGGTACATTTAAGCCTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGAATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAGgtatggagaaagagataatgtttagatttgggtcacggagatgctttcacatgtctcttactcccttgactacaatgattacttaagatataatccggtgaccacatttttaatcggttgcag

- - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA