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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttctgtctaatttcaaatctttatgagtgcgtcacacaaaacatagaaacaatataacactgatgtctcgtgagattgctcattaaagtctgt...

Basic information

species Arabidopsis thaliana
transcript AT1G54100.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os09g26880.4 (Oryza sativa), 5'ss of exon 5
ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttctgtctaatttcaaatctttatgagtgcgtc--acacaaaacatagaaacaatataacactgatgtct-cgtgagattgctcattaaagtctgt--
 ||||||||||||||||  ||||||||||||||||||| || |||||||| ||||| || || |||||||     ||||  | | | |   | || ||||      ||  |   ||| | ||     |   | | |   || | |    ||| ||  | || |      
GTGTGGAATCCTCTTGGAGTTGTTGGTGTTATCACAGCATTCAATTTTCCTTGTGCTGTGCTGGgtaagt-----gtcttctcttagaatatcattagtgaaatcaacttagtgcattgcaattccctgttatttacccctacatactcttgatctatcaaatgcaaaa

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G130440_T01 (Zea mays), 5'ss of exon 6
ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttctgtctaatttcaaatctttatgagtgcgtcacacaaaacatagaaacaatataacactg-atgtctcgtgagattgctcattaaagtctgt
 |||||||||| |||||  |||| |||||||| || || |||||||| || ||||| || |||||||||||| ||| |   |   |  | |     | | | |  |   ||         | ||| ||  ||  ||    | | || |  ||| |||   |   |
GTGTGGAATCCCCTTGGAGTTGTGGGTGTTATAACGGCATTTAATTTCCCTTGTGCTGTGCTTGgtaagtct-ctgacagctcatatgtttggtgcattacatttctagaatttgtattgccataaaagtctacataatgcatcagctctctctttactttgcat

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ38712 (Selaginella moellendorffii), 5'ss of exon 6
ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtc-------ttctgtctaatttcaaatctttatgagtgcgtcacacaaaacatagaaacaatataacactgatgtctcgtgagattgctcattaaagtctgt
 | |||||||||||||| |||||||| || ||||| || |||||||||||||| || || ||||||| |         || | |    | | |||  |||||  ||  ||  |      |  ||                                               
GTTTGGAATCCTCTTGGTATTGTTGGAGTCATCACTGCTTTTAATTTTCCCTGCGCTGTACTTGgtacgatgaatgagttttcttctttgttaaacttttatttgt-tgtgcctttgttctcag-----------------------------------------------

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: EFJ31432 (Selaginella moellendorffii), 5'ss of exon 6
ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtc-------ttctgtctaatttcaaatctttatgagtgcgtcacacaaaacatagaaacaatataacactgatgtctcgtgagattgctcattaaagtctgt
 | |||||||||||||| |||||||| || ||||| || |||||||||||||| || |||||||||| |         || | |    | | |||  |||||  ||  ||  |      |  ||                                               
GTTTGGAATCCTCTTGGTATTGTTGGAGTCATCACTGCTTTTAATTTTCCCTGCGCTGTTCTTGgtacgatgaatgagttttcttctttgttaaacttttatttgt-tgtgcctttgttctcag-----------------------------------------------

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|116486592|gb|EG529184.1|EG529184
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116420799|gb|EG463391.1|EG463391
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116420807|gb|EG463399.1|EG463399
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301502094|gb|HO207634.1|HO207634
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGGAAAG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGGAAAG
EST: gi|301501173|gb|HO206713.1|HO206713
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301502366|gb|HO207906.1|HO207906
EST:     GGCATTGTTGGTGTTATCACAGCCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: GGCATTGTTGGTGTTATCACAGC-GTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGGAATCCTCTTGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttctgtctaatttcaaatctttatgagtgcgtcacacaaaacatagaaacaatataacactgatgtctcgtgagattgctcattaaagtctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacaat