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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAGTAAACGCTGCTAAGGATGCAACCGAATTGGTAGCTAAACTAAGAGCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATTCAAGgtgataagcaatctgtttgtgtcttttccctttgaggttctgtttgaaaatgttatatgctcattggcttcatgttgagaaaacgtaaatgcag

Basic information

species Arabidopsis thaliana
transcript AT3G20050.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20050.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 5'ss of exon 15
TTGCAGTAAACGCTGCTAAGGATGCAACCGAATTGGTAGCTAAACTAAGAGCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATTCAAGgtg----ataagcaatctgt-ttgtgtcttttccctttgaggt--tctgtttgaaaatgttatatgctcattggcttcatgttgagaaaacgtaaatgcag---------------------------------------------------
|||| || || ||||| || || || || ||||| || || |||||| | || |||||||||||||| ||||| ||||| |||||||||||    |||||||      |  ||| |   | ||   | | ||   | |||      |      ||||   ||  |    |        |   |  |||| | ||   |||                                                    
TTGCTGTGAATGCTGCAAAAGACGCGACTGAATTAGTTGCAAAACTACGGGCTTACCACCACACTGCCCAAACGAAGGCAGATAAGAAGCATCTCTCAAGgtattctgtttgcagttcttattacatatatttagtctgaaacaaccaagaaaaaaaaactagtttaaaacaaaagaaacactatgaaaccctaggagcaatttttcagttgcttataatgtgaatcttttttgacttcaaaatttttgcag
















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|164163338|gb|ES125920.1|ES125920
EST:     CACTATTCAAG                         CATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG
genomic: CACTATTCAAGgtgataagca ... gtaaatgcagCATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG
EST: gi|125084726|gb|EL144833.1|EL144833
EST:     GCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATTCAAG                         CATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATT
genomic: GCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATTCAAGgtgataagca ... gtaaatgcagCATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATT
EST: gi|164157411|gb|ES048323.1|ES048323
EST:     ACAAACCAAGGCTGATAAGAAGCACTATTCAAG                         CATGGGACTTGACCTCGTAAACGGAAC
genomic: ACAAACCAAGGCTGATAAGAAGCACTATTCAAGgtgataagca ... gtaaatgcagCATGGGACTTGACCTCGTAAACGGAAC
EST: gi|124829518|gb|EH914109.1|EH914109
EST:     TACCACCACACTGCACAAACCAAGGCTGTATAAGAAGCACTATTCAAG                         CATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG
genomic: TACCACCACACTGCACAAACCAAGGCTG-ATAAGAAGCACTATTCAAGgtgataagca ... gtaaatgcagCATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG
EST: gi|125136607|gb|EL176637.1|EL176637
EST:     AGAAGCACTATTCAAG                         CATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG
genomic: AGAAGCACTATTCAAGgtgataagca ... gtaaatgcagCATGGGACTTGACCTCGTAAACGGAACCATCCGCAACAATTTGGAAGCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAGTAAACGCTGCTAAGGATGCAACCGAATTGGTAGCTAAACTAAGAGCGTACCACCACACTGCACAAACCAAGGCTGATAAGAAGCACTATTCAAGgtgataagcaatctgtttgtgtcttttccctttgaggttctgtttgaaaatgttatatgctcattggcttcatgttgagaaaacgtaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC