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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccttgaaaagtttaaatctttcgattccaaaggtgcaatgtcttgattgtgtttaaaacctgcaactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTAAAGAACATGTCAATCTCATTGACGAGAGACTAGCTAAACTAATATACAG

Basic information

species Arabidopsis thaliana
transcript AT2G21960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21960.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 6
------------gtacccttgaaaagtttaaat-ctttcgattccaaaggtgcaa---tgtcttga------ttgtgtttaaaacc-tgcaactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTAAAGAACATGTCAATCTCATTGACGAGAGACTAGCTAAACTAATATACAG
                  |||    ||||  || |         || |  ||  |   ||   | |      || |||||       ||   | ||| ||| |||||  |  | || || || ||  | |  || ||  | || || || ||||||||||||||||||||||| ||||| || |  ||||| || || ||
gtactgcccttttcttttttggctggttttcatgcacaatgcatcagatatgtgactttgctctaacccattttctgtttggtcttgtgtttcattctagTTGCTTATCTGCTGGGCCTACCCATTTTTGATTATTCCCTGGATATTGGGAAAGAACATGTCAATCTCATTGATGAGAGGCTTGAAAAACTTATCTATAG
















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|125238981|gb|EL253066.1|EL253066
EST:     CGAATTGCTGCACATGAAGCAGCCCACTTCTTAG                         TGGCTTACTTAATACGGGC
genomic: CGAATTGCTGCACATGAAGCAGCCCACTTCTTAGgtacccttga ... aactttccagTGGCTTACTTAAT-CGGGC
EST: gi|124799155|gb|EH888834.1|EH888834
EST:     CCCTGATTATCAAGAACGAATTGCTGCACATGAAGCAGCCCACTTCTTAG                         TGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA
genomic: CCCTGATTATCAAGAACGAATTGCTGCACATGAAGCAGCCCACTTCTTAGgtacccttga ... aactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA
EST: gi|124966811|gb|EL040890.1|EL040890
EST:     CCTGATTATCAAGAACGAATTGCTGCACATGAAGCAAGCCCACTTCTTAG                         TGGCTTACTTAATCGGGCTTC
genomic: CCTGATTATCAAGAACGAATTGCTGCACATGAAGCA-GCCCACTTCTTAGgtacccttga ... aactttccagTGGCTTACTTAATCGGGCTTC
EST: gi|125319627|gb|EL333712.1|EL333712
EST:     ATGAAGCAGCCCACTTCTTAG                         TGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA
genomic: ATGAAGCAGCCCACTTCTTAGgtacccttga ... aactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA
EST: gi|125191231|gb|EL206185.1|EL206185
EST:     TGAAGCAGCCCACTTCTTAG                         TGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA
genomic: TGAAGCAGCCCACTTCTTAGgtacccttga ... aactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgattccaaaggtgcaatgtcttgattgtgtttaaaacctgcaactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTAAAGAACATGTCAATCTCATTGACGAGAGACTAGCTAAACTAATATACAG
                      tcttgat  putative branch site (score: 4)
                                               ctttcc  putative PPT
                               tgtttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccttgaaaagtttaaatctttcgattccaaaggtgcaatgtcttgattgtgtttaaaacctgcaactttccagTGGCTTACTTAATCGGGCTTCCAATCCTCGGGTACTCGTTAGACATCGGTAAAGAACATGTCAATCTCATTGACGAGAGACTAGCTAAACTAATATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC