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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttatcaattatacggtatattcgtgtttttccgagattgttaatacaaagtcgcatgtagatataatcgtcaggtctcactgaaacagtttcattggctcttgtgtacagCTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTTTTTGCCTGCGGTTTTTGAAGCATTTGGGAGCCAAAGCGCGGATGTCCGCA

Basic information

species Arabidopsis thaliana
transcript AT2G20190.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 16
gtaagatttatcaattatacggtatattcgtgtttttccgagattgttaatacaaagtcgcatgtagatataatcgtcaggtctcactgaaacagtttcattggctcttgtgtacagCTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTTTTTGCCTGCGGTTTTTGAAGCATTTGGGAGCCAAAGCGCGGATGTCCGCA
   |||   ||  ||||    | | |||| | ||      ||| |      |||    |   ||| | | | || |   | | | | ||    ||  || |  | | || | | |||||||| ||| ||||||| ||||||||| | ||||  |||||| | || |||||||||||  ||||||| ||||||||||  || || || ||||| || |
---agacaaatatattacctcgcagattcatttt-----aagact------acagtagcatgtgttgtttttatggat-gattttattgtt-tagcctc-tctgtttttattttcagCTTGTTGGTCGGCTCTCACAAGAGGAAGTCATGGCACAATTGCCTTCCTTTTTGCCTGCTCTTTTTGATGCATTTGGGAATCAGAGTGCAGATGTTCGTA
















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|164062974|gb|ES130641.1|ES130641
EST:     TGACGGAAGATGAGAAAACTCTTGTCGCTCGCATAAATTGTTTAACGAAG                         CTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTT
genomic: TGACGGAAGATGAGAAAACTCTTGTCGCTTGCATAAATTGTTTAACGAAGgtaagattta ... ttgtgtacagCTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTT
EST: gi|125216232|gb|EL230315.1|EL230315
EST:     TGACGGAAGATGAGAAAACTCTTGTCGCTTGCATAAATTGTTTAACGAAG                         CTTGTGGGTAGGCT
genomic: TGACGGAAGATGAGAAAACTCTTGTCGCTTGCATAAATTGTTTAACGAAGgtaagattta ... ttgtgtacagCTTGTGGGTAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagatataatcgtcaggtctcactgaaacagtttcattggctcttgtgtacagCTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTTTTTGCCTGCGGTTTTTGAAGCATTTGGGAGCCAAAGCGCGGATGTCCGCA
                  gtctcac  putative branch site (score: 3)
                                          ctcttgt  putative PPT
     atataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttatcaattatacggtatattcgtgtttttccgagattgttaatacaaagtcgcatgtagatataatcgtcaggtctcactgaaacagtttcattggctcttgtgtacagCTTGTGGGTAGGCTCTCGCAAGAGGAATTAATGGATCAATTGTCGTCTTTTTTGCCTGCGGTTTTTGAAGCATTTGGGAGCCAAAGCGCGGATGTCCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC