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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaaatgtctctgtttcgaaagttcttatttttacaatgttaattgaatcaagagattaatgatgcttaggatgtgtgtgtgtgtgtgtgtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCTGTTGCAACGAGCTCTTCTTCCTCCAGCTGGCTAAGTGGAGGCTACTCTA

Basic information

species Arabidopsis thaliana
transcript AT3G16480.1
intron # 1
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|86060715|gb|DR356472.1|DR356472
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060722|gb|DR356479.1|DR356479
EST:     CAGTCATAATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060721|gb|DR356478.1|DR356478
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060717|gb|DR356474.1|DR356474
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCNAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060718|gb|DR356475.1|DR356475
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060714|gb|DR356471.1|DR356471
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060716|gb|DR356473.1|DR356473
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
EST: gi|86060720|gb|DR356477.1|DR356477
EST:     CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAG                         GGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT
genomic: CAGTCATCATCATGTACCGTACGGCAGCTTCTCGAGCCAAGGCCCTTAAGgtcaatgtcc ... gtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatcaagagattaatgatgcttaggatgtgtgtgtgtgtgtgtgtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCTGTTGCAACGAGCTCTTCTTCCTCCAGCTGGCTAAGTGGAGGCTACTCTA
          gattaat  putative branch site (score: 3)
           attaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaaatgtctctgtttcgaaagttcttatttttacaatgttaattgaatcaagagattaatgatgcttaggatgtgtgtgtgtgtgtgtgtgtttatagGGCATTCTAAACCACAATTTTCGAGCTTCTCGTTATGCAAGTTCTAGTGCTGTTGCAACGAGCTCTTCTTCCTCCAGCTGGCTAAGTGGAGGCTACTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
atgaaat
- - - - - -ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - gaatcaa