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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtagcttgatgaaattttagtatctctatgttgtaagttttgagttaatcgaatactgatgacaatttgtgggctttttttctttcgttttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGTAGTTACCACGGCTGTTGTTTGTGCTCTGGTGCTTGGAATTTTATATG

Basic information

species Arabidopsis thaliana
transcript AT3G08930.1
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|164147971|gb|ES120429.1|ES120429
EST:     TTCTTTGTTATCCCCTTCGCAATG-TTTTCTATGAAGGCGACCAGGACAA                         GACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGT
genomic: TTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAAgttcgtagct ... tttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGT
EST: gi|116451406|gb|EG493998.1|EG493998
EST:     TTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAA                         GACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGTAGTTACCACGGC
genomic: TTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAAgttcgtagct ... tttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGTAGTTACCACGGC
EST: gi|164098201|gb|ES185617.1|ES185617
EST:     TTCTTTGTTATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAA                         GACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGT
genomic: TTCTTTGTCATCCCCTTCGCAATGTTTTTCTATGAAGGCGACCAGGACAAgttcgtagct ... tttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaatcgaatactgatgacaatttgtgggctttttttctttcgttttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGTAGTTACCACGGCTGTTGTTTGTGCTCTGGTGCTTGGAATTTTATATG
          tactgat  putative branch site (score: 2)
                              ctttttttctttcgtt  putative PPT
                               tttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtagcttgatgaaattttagtatctctatgttgtaagttttgagttaatcgaatactgatgacaatttgtgggctttttttctttcgttttttcacagGACTCTTGGAAAGAGGATAAAAAGTGCCTTAATTTGGGTAGTTACCACGGCTGTTGTTTGTGCTCTGGTGCTTGGAATTTTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT