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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggtctccaatatttgtgaaaggtgcatgtgatgtaatactataatattttaattaatattgtgtatatatatgtctatgtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCATATGATGACACTCTAGAGAGCAAACAAGCAACTTGGAGGGCCAAAGAAT

Basic information

species Arabidopsis thaliana
transcript AT5G25980.2
intron # 6
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|116477703|gb|EG520295.1|EG520295
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|125282043|gb|EL296128.1|EL296128
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGG
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGG
EST: gi|116410415|gb|EG453007.1|EG453007
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|116446304|gb|EG488896.1|EG488896
EST:     CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|116439048|gb|EG481640.1|EG481640
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|116446415|gb|EG489007.1|EG489007
EST:     CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|116439115|gb|EG481707.1|EG481707
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGGAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|124869660|gb|EH954097.1|EH954097
EST:     TTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: TTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|125291696|gb|EL305781.1|EL305781
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAAGGGAAAGATTGGACCTGTGATGATAACTAGA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGA-GGGAA-GATTGGACCTGTGATGATAACTAGA
EST: gi|125243623|gb|EL257708.1|EL257708
EST:     CGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAA
genomic: CGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAA
EST: gi|125039647|gb|EL111916.1|EL111916
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGT
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGT
EST: gi|116446282|gb|EG488874.1|EG488874
EST:     CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: CTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|125061071|gb|EL129710.1|EL129710
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATGACTAG
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAG
EST: gi|116410414|gb|EG453006.1|EG453006
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATA-CTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|116447714|gb|EG490306.1|EG490306
EST:     AGCCTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
EST: gi|125207803|gb|EL222757.1|EL222757
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGA
EST: gi|116410418|gb|EG453010.1|EG453010
EST:     AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAG                         TACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA
genomic: AGCTTCTTGCTCATGCCACGGTCGTTGATCTATACAGGACGAGATATAAGgtcaggtctc ... gtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatactataatattttaattaatattgtgtatatatatgtctatgtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCATATGATGACACTCTAGAGAGCAAACAAGCAACTTGGAGGGCCAAAGAAT
                 aattaat  putative branch site (score: 3)
      tataatattttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggtctccaatatttgtgaaaggtgcatgtgatgtaatactataatattttaattaatattgtgtatatatatgtctatgtgaccacagTACCAAGGAGGGAAGATTGGACCTGTGATGATAACTAGATGGTTTCTACCATATGATGACACTCTAGAGAGCAAACAAGCAACTTGGAGGGCCAAAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA