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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag

Basic information

species Arabidopsis thaliana
transcript AT5G14040.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G14040.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 5
GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag
  || |||||  | ||||| || ||  | || |||||||| || ||  | |||||||||||||||||| | ||||| ||||||||||| || ||||| ||||||||| ||| ||||| || |||        | || || | |   ||| |                                     
CTCTCTTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACACTCACTGGAGCACAGTGGGGAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttctcgctctcatctcttgtggggaaatctcaaatctctattccag------------------------------------

upper sequence: AT5G14040.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ34707 (Selaginella moellendorffii), 5'ss of exon 5
GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag
  || |||||  | ||||| || ||  | || |||||||| || ||  | |||||||||||||||||| | ||||| ||||||||||| || ||||| ||||||||| ||| ||||||   |||        | || || | |   ||| |                                     
CTCTCTTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACACTCACTGGAGCACAGTGGGGAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttctcgctctct---cttgtggggaaatctcaaatctctattccag------------------------------------

upper sequence: AT5G14040.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ34706 (Selaginella moellendorffii), 5'ss of exon 5
GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag
  ||  ||||  | ||||| || ||  | || |||||||| || ||  | |||||||| ||||||| | | ||||| ||||||||||| || ||||| ||||||||| ||  || | ||| ||   | | | |  ||  |   | || |    | |       || || |                  
CTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACGACGCCTTCAAAGTCTTCGTTGGACTgtaagtttcttgctat-ttctctccttgtgggaagttc-tcaaatctcctctct-cgtgctcttccatcccag---------------

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|164042419|gb|ES081285.1|ES081285
EST:     GGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCA
genomic: GGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCA
EST: gi|125266817|gb|EL280902.1|EL280902
EST:     TGCCTTC-AAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAGCTACTGAAGC
genomic: TGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAGCTACTGAAGC
EST: gi|125117125|gb|EL166392.1|EL166392
EST:     TGCCTTCAAAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAG
genomic: TGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAG
EST: gi|125226367|gb|EL240452.1|EL240452
EST:     TGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATC
genomic: TGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATC
EST: gi|164084730|gb|ES148122.1|ES148122
EST:     GGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCA
genomic: GGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCA
EST: gi|164210001|gb|ES159885.1|ES159885
EST:     ACAGTGGGGATTATACGATGCCTTCAAAGTTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAGCTACTGAAGC
genomic: ACAGTGGGGATTATACGATGCCTTCAAAG-TGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCGCAGCTACTGAAGC
EST: gi|125251806|gb|EL265891.1|EL265891
EST:     ACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCT                         GCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCG
genomic: ACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcct ... tggtattcagGCCAACCACTGGTGGTGTTGCTCCAGCTCCTGCCATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGTTCACAAGAGGGCTTCCTCTTAGAATTGTGATGATCGGGACGTTGACTGGAGCACAGTGGGGATTATACGATGCCTTCAAAGTGTTTGTTGGCCTgtaagttcctctctctcttcacttactttcgtaccttaattgtaccttcaaaatgcaaaactctcaattcttttgatttggtattcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA