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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttcttctatgtacagtacaatacaatggtgaaaagtctttgtttttatttcctgtatgctcatcctgttatgttcatttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G33150.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM5G848768_T01 (Zea mays), 5'ss of exon 4
CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgta---------tgtttctt----ctatgtacagtac--aatacaatggtgaaaagtctttgtttttatttcctgta-------------tgct-catcctgttatgttcat----ttgcag
|||  |||  | |||||||| || || || || ||  | |  ||||| || ||| | || |  || ||||||||||||||||| | |||||| ||||||||||         ||||  ||      ||| |   |||  ||||  | |  ||  |  || | || |  |   |   |             || | |||||  | ||| |  |    ||||||
CCAGCTGACATCGGTGACATCGTCGTTGGGACGGTGCTTGGCCCTGGTTCCCAGCGTGCAAACGAGTGCAGGATGGCTGCGTTGTTTGCTGGATTCCCTGgtaactgataactgttgtttacgatcatgcatgctacctaatatgaagaagacgatcctatcttctggtggacaaaaaaagaagagataatgatgcatcccatgatgatgttgttgttgcag

upper sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G24590.3 (Glycine max), 5'ss of exon 4
CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttcttctatgtacagtaca-----atacaatggtgaaaagtctttgtttttatttcctgtatgctcatcctgttatgttcatttgcag
||||||||||| || || |||||||| |||| ||| ||||| |||||| |||| ||||| ||||||||| | |||||||| || ||||||||||| || ||||||| |    | |  | |||         || |   || | | |  |  | |||  | |    ||| |   |  |||||| |||||      
CCAAGTGAAGTTGGGGATATTGTTGTAGGTAGTGTATTGGCTCCTGGAGCTCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCCGgtatgtctagaatttagatagtttgtgcttgtaaacctgttatatgattcgggtttggtatt---tatacatgtgatgttattttcatccag--

upper sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G18980.1 (Glycine max), 5'ss of exon 4
CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgttt----cttctatgtacagtacaatacaa--tggtgaaaagtctttgtttttatttcctgtatgctcatcctgttatgttcatttgcag
|| || ||||| || || ||||| || || | ||| ||||| |||||| |||| ||||| ||||||||| | |||||||| || ||||||||||| ||||||||||||     ||  ||  |  || |     ||  || |  |   |||  |||| |  ||    ||| ||  |  |||||| |||||      
CCCAGCGAAGTTGGGGATATTGTCGTAGGGAGTGTATTGGCTCCTGGAGCTCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatt----tatacttgtgatgttattttcatccag--

upper sequence: AT2G33150.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 5'ss of exon 4
CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttcttctatgtacagtacaatacaatggtgaaaagtctttgtttttatttc-ctgtatgctcatcctgttatgttcatttgcag
|||| |||||| || ||||||||||| ||||| || ||||| || || || || ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||| |   || ||  | |  || | |  ||       |||||    |||||  |||   |  ||  | | || |    || |||
CCAAATGAAGTTGGGGACATTGTTGTTGGTACAGTATTGGCGCCAGGCTCCCAAAGAGCAAGTGAATGCAGGATGGCTGCATTCTATGCTGGTTTCCCTGgtatatttcct---tgaactatcctttatatttttgg-----ttttgtacccatttcattgttcacaaatattat-atctgtgatttcag

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|301502268|gb|HO207808.1|HO207808
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|125015925|gb|EL088194.1|EL088194
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGA
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGA
EST: gi|125298740|gb|EL312825.1|EL312825
EST:     AGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGG
genomic: AGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGG
EST: gi|125118197|gb|EL167016.1|EL167016
EST:     CTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAATGCTCATCTGGGCTTCAGG
genomic: CTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|301501479|gb|HO207019.1|HO207019
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTTGAATAGACAGTGCTCATCTGGGCTTCAG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGT-GAATAGACAGTGCTCATCTGGGCTTCAG
EST: gi|86046971|gb|DR342726.1|DR342726
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGT
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGT
EST: gi|86046960|gb|DR342715.1|DR342715
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|301501943|gb|HO207483.1|HO207483
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|152035756|gb|BP855676.2|BP855676
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|86046966|gb|DR342721.1|DR342721
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAA
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAA
EST: gi|86046967|gb|DR342722.1|DR342722
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATA
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATA
EST: gi|301501553|gb|HO207093.1|HO207093
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|116412117|gb|EG454709.1|EG454709
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|301501331|gb|HO206871.1|HO206871
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|86046955|gb|DR342710.1|DR342710
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCT
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCT
EST: gi|301501980|gb|HO207520.1|HO207520
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|86046964|gb|DR342719.1|DR342719
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGG
EST: gi|124772455|gb|EH862584.1|EH862584
EST:     CAGAGTAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAA
genomic: CAGAG-AGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAA
EST: gi|86046951|gb|DR342706.1|DR342706
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCT
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCT
EST: gi|86046962|gb|DR342717.1|DR342717
EST:     TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTG                         AAACCGTGGCTGTCAGAACTGTGGAATAGACA
genomic: TCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttct ... tcatttgcagAAACCGTGGCTGTCAGAACTGTG-AATAGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGTGAAGTAGGTGACATTGTTGTGGGTACTGTTTTGGCACCTGGATCTCAGAGAGCCAGTGAATGCAGGATGGCTGCGTTCTATGCTGGTTTCCCTGgtatgtttcttctatgtacagtacaatacaatggtgaaaagtctttgtttttatttcctgtatgctcatcctgttatgttcatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG