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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttatatctgcttctcatactcttcctaatttcgtatatggctcctgtttaaatgtgtttgcaactatttggatatttcag

Basic information

species Arabidopsis thaliana
transcript AT5G40850.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40850.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0064g01470.t01 (Vitis vinifera), 5'ss of exon 2
GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttatatc------------------------------------tgcttctcatactcttcctaa-----tttcgtatatggctcctgtttaaatgtgtttgcaactattt---ggatatttcag
|| ||||| |||||| |||| || | ||||||||||||||| || || ||||| || |||||||| || ||||| ||||| || || |||                                     || ||| |  | || ||  |      ||  || ||  | |  |  || ||  | ||| ||| |||||   || | | | ||
GAGGAGATACATGAATTACTTCTGAGTTTTGCTGAAGCTGGAGCTACAGTTGTGAGACTTAAAGGAGGGGATCCACTGgtgagtttctattgcaaaacgtgaaaaagatgagtatggcattgcaagttgtttcacggaatcatctcagaaatgttgtgtttagtgttttttattgaactttttttcaaatattttctgggtgtattag

upper sequence: AT5G40850.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ22702 (Selaginella moellendorffii), 5'ss of exon 2
GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttatatctgcttctcatactcttcctaatttcgtatatggctcctgtttaaatgtgtttgcaactatttggatatttcag
|| ||||||||||| || ||||| |||||||| || ||||| ||||| ||| | ||||| || || || |||||||||||| |   ||     |||    |  | || ||  |   |   ||   | | |                                  
GACGAGATTCATGAGCTGCTCCTCAATTTTGCAGAGGCTGGCGCCACCGTTTTAAGGCTCAAGGGAGGTGATCCTCTGgtatgaacattctctcttagtgttatatttctcctcaaggccattcttgcag----------------------------------

upper sequence: AT5G40850.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ19235 (Selaginella moellendorffii), 5'ss of exon 2
GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttatatctgcttctcatactcttcctaatttcgtatatggctcctgtttaaatgtgtttgcaactatttggatatttcag
|| ||||||||||| || ||||| |||||||| || ||||| ||||| ||| | ||||| || || || |||||||||||| |     | ||   |||| || | ||     | || |  | |||   | ||  |                             
GACGAGATTCATGAGCTGCTCCTCAATTTTGCAGAGGCTGGCGCCACCGTTTTAAGGCTCAAGGGAGGTGATCCTCTGgtatg-----aactttctctcttagtgttatatttctcctcaaaggccattcttgcag----------------------------

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|124793533|gb|EH883212.1|EH883212
EST:     CTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: CTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|125307007|gb|EL321092.1|EL321092
EST:     TCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: TCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|125010014|gb|EL082283.1|EL082283
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGA
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGA
EST: gi|116459489|gb|EG502081.1|EG502081
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|164074990|gb|ES108058.1|ES108058
EST:     CCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: CCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|116459485|gb|EG502077.1|EG502077
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|125298776|gb|EL312861.1|EL312861
EST:     TGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: TGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|86080219|gb|DR375976.1|DR375976
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
EST: gi|124828851|gb|EH913687.1|EH913687
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTT
EST: gi|124731674|gb|EH823076.1|EH823076
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAAATGGACTTTCTGCAACAGCAAGGGAT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAA-TGGACTTTCTGCAACAGCAAGGGAT
EST: gi|124886815|gb|EH965717.1|EH965717
EST:     TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTT
genomic: TTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTT
EST: gi|124908510|gb|EH982590.1|EH982590
EST:     CTTAAAGGTGGAGATCCTCTG                         GTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT
genomic: CTTAAAGGTGGAGATCCTCTGgtaagcttat ... gatatttcagGTCTTTGGACGGGGCGGCGAAGAAATGGACTTTCTGCAACAGCAAGGGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTGgtaagcttatatctgcttctcatactcttcctaatttcgtatatggctcctgtttaaatgtgtttgcaactatttggatatttcag

- - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC