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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttttgctttatagatatcttgtttctgaatgttttcttctgcttgattgtgctggatttgtgaatgtcttcttttgtttgtttctacttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGGCAAATGTCATCCCGATTGCTTAAAAGCAAACAATGAGCAAGAAGATTAC

Basic information

species Arabidopsis thaliana
transcript AT4G29770.2
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|86057008|gb|DR352765.1|DR352765
EST:     AGGCGACATTTCACTGATTTTTCTCTACGCGACGTAGATCTGTGTCTCCG                         GAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
genomic: AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCGgtaactttct ... ttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
EST: gi|86057009|gb|DR352766.1|DR352766
EST:     AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCG                         GAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
genomic: AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCGgtaactttct ... ttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
EST: gi|86057006|gb|DR352763.1|DR352763
EST:     AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCG                         GAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
genomic: AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCGgtaactttct ... ttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGG
EST: gi|86057007|gb|DR352764.1|DR352764
EST:     AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCG                         GAGTTCATCGCAGATGGANAGTCATTGTTAGAATGTTTTGCAATCACGGAT
genomic: AGGCGACATTTCACTGAGTTTTCTCTACGCGACGTAGATCTGTGTCTCCGgtaactttct ... ttaaaaccagGAGTTCATCGCAGATGG--AGTCATTGTTAGAATGTTTTGCAATCACGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattgtgctggatttgtgaatgtcttcttttgtttgtttctacttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGGCAAATGTCATCCCGATTGCTTAAAAGCAAACAATGAGCAAGAAGATTAC
 gcttgat  putative branch site (score: 5)
                        tcttcttttgtttgtt  putative PPT
                                          tacttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttttgctttatagatatcttgtttctgaatgttttcttctgcttgattgtgctggatttgtgaatgtcttcttttgtttgtttctacttaaaaccagGAGTTCATCGCAGATGGAGTCATTGTTAGAATGTTTTGCAATCACGGATGGCAAATGTCATCCCGATTGCTTAAAAGCAAACAATGAGCAAGAAGATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG