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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctgtctattgggtttcctgattacatatgtgcatatttcctgtttcaaacaacttgtaggtgtgtataattttttttttttatgtttactttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGGACCTGCATTTCTTTGTTACTGGAGGTGAAAATGAAAACGAGCTCGTCTT

Basic information

species Arabidopsis thaliana
transcript AT4G08520.1
intron # 3
splice site 3'
intron type U2

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|301502441|gb|HO207981.1|HO207981
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|125314242|gb|EL328327.1|EL328327
EST:     GAAAAATAATGTCTTCTCG-AAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: GAAAAAT-ATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|86024307|gb|DR320060.1|DR320060
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAAATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|86024308|gb|DR320061.1|DR320061
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAAATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|86024309|gb|DR320062.1|DR320062
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAAATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|19875026|gb|AU235857.1|AU235857
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
EST: gi|47828401|gb|CK118085.1|CK118085
EST:     TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAG                         CTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG
genomic: TGAAAAATATGTCTTCTCGAAAACCTCCAAGACCAATGCTCGCACAGAAGgtaagatcaa ... ctttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaacaacttgtaggtgtgtataattttttttttttatgtttactttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGGACCTGCATTTCTTTGTTACTGGAGGTGAAAATGAAAACGAGCTCGTCTT
                          ttttttttttttatgt  CT-rich tract
                 tgtgtataattttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctgtctattgggtttcctgattacatatgtgcatatttcctgtttcaaacaacttgtaggtgtgtataattttttttttttatgtttactttttgcagCTGAGATCACACTGTTGGAGAGTAATATTGTTGTCTATAAGTTTGCCCAGGACCTGCATTTCTTTGTTACTGGAGGTGAAAATGAAAACGAGCTCGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - tcaaaca