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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatctttactttactctctctcacggcacacaataatgtgattctgaactaaatcttgtgatgatgctgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATACCTGCCACCAGCTAGATCAGGTTTTCTCGTGACTTACTGTAGTCATCAT

Basic information

species Arabidopsis thaliana
transcript AT5G05780.2
intron # 9
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|124743164|gb|EH834326.1|EH834326
EST:     TTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG                         TTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATA
genomic: TTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAGgttagatctt ... tgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATA
EST: gi|86079670|gb|DR375427.1|DR375427
EST:     CATCCCTCATCCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG                         TTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATA
genomic: CATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAGgttagatctt ... tgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATA
EST: gi|164103065|gb|EL985801.1|EL985801
EST:     CATCCCTCATCCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG                         TTACTGAACAAGGAACATGAAAAAGCAGA
genomic: CATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAGgttagatctt ... tgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGA
EST: gi|164177158|gb|ES023472.1|ES023472
EST:     CATCCCTCATCCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG                         TTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTG
genomic: CATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAGgttagatctt ... tgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcacacaataatgtgattctgaactaaatcttgtgatgatgctgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATACCTGCCACCAGCTAGATCAGGTTTTCTCGTGACTTACTGTAGTCATCAT
                        aactaaa  putative branch site (score: 2)
 acaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatctttactttactctctctcacggcacacaataatgtgattctgaactaaatcttgtgatgatgctgtgtttcagTTACTGAACAAGGAACATGAAAAAGCAGAGGACTCAAAGCCTGTGGCCATACCTGCCACCAGCTAGATCAGGTTTTCTCGTGACTTACTGTAGTCATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA