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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATCGAGAGAGTGAAGGCTATTGGTAAGCATTCTCTTCTTGGTGCCAGCGGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatccgtttggttcaatttttttatattttaatctttccttgtcaattatcaagcctcacaagcccttggttttacacag

Basic information

species Arabidopsis thaliana
transcript AT1G56450.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56450.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G43120.1 (Glycine max), 5'ss of exon 3
ACATCGAGAGAGTGAAGGCTATTGGTAAGCATTCTCTTCTTGGTGCCAGCGGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatccgtttggttcaattttt-ttatattttaatctttccttgtcaatt--atcaagcct----cacaagcccttggtt--ttacacag------
   | ||| |  | ||| ||||||| |||||||||||||||||||| ||||| || || || ||||||||||||||||| ||||| ||||||||||| | || || |    ||   || ||| ||  || |   | | | |   || || |  |  |  |||  |    || ||     || |   ||| |         
GTGTTGAGCGTATCAAGCCTATTGGAAAGCATTCTCTTCTTGGTGCTAGCGGGGAGATAAGTGACTTTCAGGAGATTCTGCGTTACCTTGATGAGCTTATgtgagtactttttccttttaatattaattgttactcagtatgcactggtgatcttaaataagtttaaggcagaaagatgtgatgagttaaatgatggtct

upper sequence: AT1G56450.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G40470.1 (Glycine max), 5'ss of exon 3
ACATCGAGAGAGTGAAGGCTATTGGTAAGCATTCTCTTCTTGGTGCCAGCGGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatccgtttggttc--aatttttttatattttaatctttccttgtcaattatcaa-----gcctcacaagccct--tggttttacacag------
   | ||| |  | ||| ||||||| |||||||||||||||||||| ||||| || || || ||||||||||| ||| | || || ||||| ||||| | || || | |  |||  ||   || |||     |      | |       | |||  ||       || |    | || |  | |  ||    ||      
GTGTTGAGCGTATCAAGCCTATTGGAAAGCATTCTCTTCTTGGTGCTAGCGGGGAGATAAGTGACTTTCAGGAAATTTTGCGCTACCTTGACGAGCTTATgtgagtacctttttcttttataagtttagggcagaacggtgtgatgagttaaatggtctgtgtctgctttgttatccttgcttggcttgtttagttattt

upper sequence: AT1G56450.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv06s0004g03190.t01 (Vitis vinifera), 5'ss of exon 4
ACATCGAGAGAGTGAAGGCTATTGGTAAGCATTCTCTTCTTGGTGCCAGCGGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatccgtttggttcaatttttttatattt-----taatctttccttgtcaattatcaagcctcacaagcccttggttttacacag------------------------------------------------
   | ||| || ||||| ||||||| ||||| ||||||||||| || || |||||||| || || || ||||||||| | | |||||||||||| || | ||||| |   | ||  || | ||   | | |        ||      |||| |   || | |   ||    ||||  || |  || |||                                                 
GTGTGGAGCGAATGAAGCCTATTGGAAAGCACTCTCTTCTTGGAGCAAGTGGAGAAATAAGTGATTTCCAGGAGATTTTACATTATCTTGATGAACTTATgtaagcagtagcttcttttacttgcatgaaagcaacaaatagctaaaccttattccttcttattactt-ttagcctatgctaatatacaagcttcaagttagttatgatttctggttttggatgttttactattgcag

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|86055052|gb|DR350809.1|DR350809
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
EST: gi|116438502|gb|EG481094.1|EG481094
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
EST: gi|125162895|gb|EL189665.1|EL189665
EST:     TCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAA
genomic: TCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAA
EST: gi|86055051|gb|DR350808.1|DR350808
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCAC                         CCTGAATGNTAACATGTGGGGATGATGGT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGG-ATGATGGT
EST: gi|86055050|gb|DR350807.1|DR350807
EST:     GGAGAAATCAGCGACTTTCAGGAGATTCTCCATTATCTTGATGAGCTCAC                         CCTGAATGATAACATNTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT
genomic: GGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatcc ... ttttacacagCCTGAATGATAACATGTGGGATGATGGTAACTCTTTGGGACCAAAAGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATCGAGAGAGTGAAGGCTATTGGTAAGCATTCTCTTCTTGGTGCCAGCGGAGAAATCAGCGACTTTCAGGAGATTCTCCGTTATCTTGATGAGCTCACgtaagaatccgtttggttcaatttttttatattttaatctttccttgtcaattatcaagcctcacaagcccttggttttacacag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA