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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttaaacaaaattgtgtgacttctttctggatgtaatgtttgttaaagtttctgagttccattgtttggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAGCGTGGGAAGAAAGCGAAAAGAGCAAAGCAGAGAACAA

Basic information

species Arabidopsis thaliana
transcript AT3G61260.1
intron # 2
splice site 3'
intron type U2

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|124742906|gb|EH834068.1|EH834068
EST:     TCGCTCGATAGAG                         ATGTTGAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: TCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|124720471|gb|EH811873.1|EH811873
EST:     CCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: CCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|124973990|gb|EL047580.1|EL047580
EST:     CACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAAGGAAAAGAGATTGTCTTTCGTCAGA
genomic: CACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAA-GGAAAAGAGATTGTCTTTCGTCAGA
EST: gi|163966973|gb|ES008688.1|ES008688
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGNGATTGTC
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTC
EST: gi|116446100|gb|EG488692.1|EG488692
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|125299302|gb|EL313387.1|EL313387
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTC
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTC
EST: gi|125256134|gb|EL270219.1|EL270219
EST:     CACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: CACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|124781998|gb|EH871941.1|EH871941
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAG
EST: gi|124713993|gb|EH805395.1|EH805395
EST:     CTGCACCGGCGAAACCTGTGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: CTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|124826103|gb|EH910969.1|EH910969
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAAGGAAAA
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAA-GGAAAA
EST: gi|86080975|gb|DR376732.1|DR376732
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTWGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|116446101|gb|EG488693.1|EG488693
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
EST: gi|124941508|gb|EL017853.1|EL017853
EST:     TAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAG
genomic: TAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAG
EST: gi|125042092|gb|EL114361.1|EL114361
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTG
EST: gi|116446103|gb|EG488695.1|EG488695
EST:     TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAG                         ATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG
genomic: TGTAGAAGAGCCTGCACCGGCGAAACCTGCGTCTGCATCGCTCGATAGAGgtgagcttaa ... tggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctggatgtaatgtttgttaaagtttctgagttccattgtttggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAGCGTGGGAAGAAAGCGAAAAGAGCAAAGCAGAGAACAA
            taatgtttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttaaacaaaattgtgtgacttctttctggatgtaatgtttgttaaagtttctgagttccattgtttggtttgtagATGTTAAGCTAGCTGATTTGTCAAAGGAAAAGAGATTGTCTTTCGTCAGAGCGTGGGAAGAAAGCGAAAAGAGCAAAGCAGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG