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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGTGACGACTCCTATGAATCATACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatttaatagacaactaggaatattcaagattagaactttctgttcttaaagtgtttgaactctaaccttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G17290.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17290.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 13
CCTGGTGACGACTCCTATGAATCATACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatttaatagacaactaggaatattcaagattaga--actttctgttcttaaagtgt--ttgaactctaacc--ttgcag-------------------------------------------------------------------------------------------------------
  ||| || || ||||||||||| ||  |    |||||||| ||||| ||||||||  ||||||| ||||||||||||||  |   |||  |  | |   | |    || ||||||  | |   |  |  | || ||     | |||   |||  |||                                                                                                          
GTTGGAGATGAATCCTATGAATCTTATTTCATGGAGAAGGACGGAATACTCTCATCCCTGGCAAGGCGTGCAAAGgttagtta---aatgaattaatctcattccataaaattagacaagtgaatactgattaaatggagcaggactgagaccaattgtcacactgatttgcctcttttagtatacaatcgctagtttcaggctgacccaggatgataccttagttttatcatttttcctttcctgtttccttcatgactgcag
















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|125313549|gb|EL327634.1|EL327634
EST:     CATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGACAAGACGTGCAAAG                         ACTCTTGAAGAG
genomic: CATAGCAGAGAAGGATGGAATTCTCTCATCTTTGG-CAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAG
EST: gi|124978412|gb|EL051595.1|EL051595
EST:     ATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAG                         ACTCTTGAAGAGGCTCTGAACAAGCTAG
genomic: ATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAGGCTCTGAACAAGCTAG
EST: gi|301502353|gb|HO207893.1|HO207893
EST:     GGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAG                         ACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
genomic: GGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
EST: gi|164156340|gb|ES034096.1|ES034096
EST:     GGCAAGACGTGCAAAG                         ACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
genomic: GGCAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
EST: gi|301501574|gb|HO207114.1|HO207114
EST:     ACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAG                         ACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
genomic: ACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
EST: gi|116471643|gb|EG514235.1|EG514235
EST:     ACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAG                         ACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA
genomic: ACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatt ... aaccttgcagACTCTTGAAGAGGCTCTGAACAAGCTAGAGGGAGTTACATGCAATAGAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGTGACGACTCCTATGAATCATACATAGCAGAGAAGGATGGAATTCTCTCATCTTTGGCAAGACGTGCAAAGgttagccatttaatagacaactaggaatattcaagattagaactttctgttcttaaagtgtttgaactctaaccttgcag

- - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG