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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcctcattagtctttcacaactgacctgattttgtgtaaaatcaaaccagctgtagatcaataggttgttagctttttgtacaaagaacatacgcatgtacatatatagaggtgactctaatcggcattcaccaattcttgttggcagATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGTTCCAATCAACAGTACAATCTGCCTTCACCCTTGTCTGAAGAGAAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G09330.1
intron # 5
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|125261820|gb|EL275905.1|EL275905
EST:     CTTGTCCCTCAATGTGGCTAATATCATCGGCTTCACAAAGTGCAAGAAAG                         ATGCAAAGAAACAATTTCAG
genomic: CTTGTCCCTCAATGTGGCTAATATCATCGGCTTCACAAAGTGCAAGAAAGgtaagatcct ... ttgttggcagATGCAAAGAAACAATTTCAG
EST: gi|86076586|gb|DR372343.1|DR372343
EST:     CTTGTCCCTCAATGTGGCTAATATCATCGGCTTCACAAAGTGCAAGAAAG                         ATGCAAAGAAACAATTTCAGCAGTTTS-TTCGCAGACAATCGCATCACGGT
genomic: CTTGTCCCTCAATGTGGCTAATATCATCGGCTTCACAAAGTGCAAGAAAGgtaagatcct ... ttgttggcagATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGT
EST: gi|124882208|gb|EH961110.1|EH961110
EST:     GCTTCACAAAGTGCAAGAAAG                         ATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGT
genomic: GCTTCACAAAGTGCAAGAAAGgtaagatcct ... ttgttggcagATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtacatatatagaggtgactctaatcggcattcaccaattcttgttggcagATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGTTCCAATCAACAGTACAATCTGCCTTCACCCTTGTCTGAAGAGAAGAAAG
                      ctctaat  putative branch site (score: 3)
                                          ttcttgtt  putative PPT
     tacatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcctcattagtctttcacaactgacctgattttgtgtaaaatcaaaccagctgtagatcaataggttgttagctttttgtacaaagaacatacgcatgtacatatatagaggtgactctaatcggcattcaccaattcttgttggcagATGCAAAGAAACAATTTCAGCAGTTTGCTTCGCAGACAATCGCATCACGGTTCCAATCAACAGTACAATCTGCCTTCACCCTTGTCTGAAGAGAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA