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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgcctttctatgcgtgctttatttgatctcaattactgcagttttgctttttttcccccaaaagattctatattttagtttttgtgtattttatgagctagatcattctctctaaagttggttttgaggagtggaattactaaattggttatcttatattgattgatcttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCATGAGCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G05720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G05720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 1
gttcgtgcctttctatgcgtgctttatttgatctcaattactgcagttttgctttttttcccccaaaagattctatattttagtttttgtgtatt-ttatgagctagatcattctctctaaagttggttttgaggagtggaattactaaattggttatcttatattgattgatcttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCATGAGCAAG
                                                                                 |||||    | ||  | || | |  |     |  ||  |    || || | || |   |  ||  || |||      || |    | ||  | |  | ||||||||| ||||||||||| ||||| |||||  | || |||||||| |||||||||||||||
-------------------------------------------------------------------------------ggagtttgctagcatggtcataaacatgtatgatgccttcattcatgattctcagtat--ggttttttagattatg---ctaactccgtttattttcatctgcagAGTTAGTATCTGATTGTTTGAAGTGTTGCACAGAGGATTCTGATGATTCCATGAGCAAG
















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|86078488|gb|DR374245.1|DR374245
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022918|gb|DR318671.1|DR318671
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022908|gb|DR318661.1|DR318661
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022912|gb|DR318665.1|DR318665
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|19878749|gb|AU239580.1|AU239580
EST:     TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022917|gb|DR318670.1|DR318670
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022913|gb|DR318666.1|DR318666
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022916|gb|DR318669.1|DR318669
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022914|gb|DR318667.1|DR318667
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022909|gb|DR318662.1|DR318662
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022911|gb|DR318664.1|DR318664
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022915|gb|DR318668.1|DR318668
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
EST: gi|86022907|gb|DR318660.1|DR318660
EST:     TGCTCTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAG                         AGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA
genomic: TGCACTCTGCTCCGATTGCCACTCACTCTCTGAATACGTTAAGGACCAAGgttcgtgcct ... ttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaggagtggaattactaaattggttatcttatattgattgatcttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCATGAGCAAG
                                           tcttgttt  CT-rich tract
                         ttatcttatattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtgcctttctatgcgtgctttatttgatctcaattactgcagttttgctttttttcccccaaaagattctatattttagtttttgtgtattttatgagctagatcattctctctaaagttggttttgaggagtggaattactaaattggttatcttatattgattgatcttgtttgcagAGTTGGTATCTGATTGCTTGAAATGTTGTGCTGATGATTCTGAGGATTCCATGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG