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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAAAGGATGGCTTTTGGATGGATATCCAAGGAGTGCATCACAGGCAACAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactgttcttaatttcaatgttccttatctctcatctaaaggctttctctagaacttgctagattttacctatacttgtgagttcaatgcaatgg...

Basic information

species Arabidopsis thaliana
transcript AT5G47840.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G47840.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0041g01280.t01 (Vitis vinifera), 5'ss of exon 5
GCAAAAAGGATGGCTTTTGGATGGATATCCAAGGAGTGCATCACAGGCAACAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactgttcttaatttcaatgttccttatctctcatctaaaggctttctctagaact----tgctagattttacctatacttgtgagttcaatgcaatgg
  |||| ||||||||||| |||||||| || |||||   ||| || || || |||||||||| |||||| ||  ||||||| || |||||| |||| |||||||| | |  |  |  | |   ||||  ||||   |  | || ||   |||  |   | |      | |||||      |        |||| ||    ||| 
AGAAAAGGGATGGCTTTTAGATGGATACCCTAGGAGCCAATCTCAAGCTACTGCTCTCAAGGAATTTGGGTTTGAGCCTGACCTTTTCATTCTCCTAGAAgtaaggatttcttcttttgttgctgtttgttattggtattttatagctattcaattacattgaggcaccagattgggaagagg---acaagttgaactacatg-
















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|125039954|gb|EL112223.1|EL112223
EST:     ATTCCAGCCTGATCTATTCATTGTCCTCGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: ATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|125001535|gb|EL073804.1|EL073804
EST:     ATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: ATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|125281979|gb|EL296064.1|EL296064
EST:     TTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: TTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|124736103|gb|EH827505.1|EH827505
EST:     TTCATTGTCCTCGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: TTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|125240241|gb|EL254326.1|EL254326
EST:     CCTGATCTATTCATTGTCCTCGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: CCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|47832013|gb|CK121697.1|CK121697
EST:     CAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTGGAA                         GTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
genomic: CAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCTAATTGAAAGAGTTGTTGGGCGTCGATTGGATCCT
EST: gi|164192404|gb|ES027864.1|ES027864
EST:     CAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTGGAA                         GTTCCTGAAGAAATTCT
genomic: CAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactg ... tttgggacagGTTCCTGAAGAAATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAAAGGATGGCTTTTGGATGGATATCCAAGGAGTGCATCACAGGCAACAGCTCTCAAGGGATTTGGATTCCAGCCTGATCTATTCATTGTCCTCGAAgtaagcactgttcttaatttcaatgttccttatctctcatctaaaggctttctctagaacttgctagattttacctatacttgtgagttcaatgcaatgg

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctct