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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatgttacacttttataacattctagtagtaatcttcaggatgtttaatcttttatgttgaaacttttgcttttggtattggctatgattgacacatttatctgatgcag

Basic information

species Arabidopsis thaliana
transcript AT1G17370.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17370.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 3
CGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg--ttacact---tttataacattctagtagtaatcttcaggatgtttaatcttttatgttgaaacttttgcttttggtattggctatgattgacacatttatctgatgcag-------------------------------------------------
 ||||| ||||| ||||  |||||  ||||||| || |||||||||||||||||  | ||||||||||| ||| |||| || ||  |||| || |||||||| | || |   |||  ||   ||  |||  ||    | |||    | | | ||   |    | ||||   ||  | ||    ||   |   | || | ||  ||  | ||||   | |                                                   
TGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAAAAGgtatattcttctttatgctatcttgttaatttttggattgtacctgttaagctg--aagatctgtatggaaaagttattagacttctcacatgtta-gtttagcat-tctatcccttactttgctggtttatcatcatattgacatctccattgattctcctcggtgcag
















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|124748243|gb|EH838373.1|EH838373
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116486725|gb|EG529317.1|EG529317
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116386087|gb|EG428679.1|EG428679
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|124866650|gb|EH951087.1|EH951087
EST:     CTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: CTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116486731|gb|EG529323.1|EG529323
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116486728|gb|EG529320.1|EG529320
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116386137|gb|EG428729.1|EG428729
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|124784788|gb|EH874495.1|EH874495
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
EST: gi|116477129|gb|EG519721.1|EG519721
EST:     TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAG                         TCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA
genomic: TTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatg ... tctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAAAAGgtgtgttatgttacacttttataacattctagtagtaatcttcaggatgtttaatcttttatgttgaaacttttgcttttggtattggctatgattgacacatttatctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA