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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttaatctctacccttcacatttattctatgtttagattctcccatatcttctcatagacttgatattgtttgttgttgttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTAATCACCGCGACTCTCACAGGCTCTCTCTACTTTCTTGCTGCGTCTCCAA

Basic information

species Arabidopsis thaliana
transcript AT2G35260.1
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|164077652|gb|ES139204.1|ES139204
EST:     TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGC
genomic: TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGC
EST: gi|116414687|gb|EG457279.1|EG457279
EST:     TCTTGAAAGGAACACAGTTGATGACAGATTCTAAAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
genomic: TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
EST: gi|124706254|gb|EH797656.1|EH797656
EST:     GATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCTCATTTGCTGAAGTCTTTG
genomic: GATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTG
EST: gi|125200138|gb|EL215092.1|EL215092
EST:     GAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAG
genomic: GAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAG
EST: gi|125298244|gb|EL312329.1|EL312329
EST:     ACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
genomic: ACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
EST: gi|116414696|gb|EG457288.1|EG457288
EST:     TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
genomic: TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
EST: gi|116414695|gb|EG457287.1|EG457287
EST:     TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
genomic: TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTA
EST: gi|164082369|gb|ES072024.1|ES072024
EST:     TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTG                         ACCGGAGTGTTTCCTCCATTTGTCCCATTTGC
genomic: TCTTGAAAGGAACACAGTTGATGACAGATTCTAGAGGCATGGCATCTCTGgtaaatttaa ... ttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattctcccatatcttctcatagacttgatattgtttgttgttgttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTAATCACCGCGACTCTCACAGGCTCTCTCTACTTTCTTGCTGCGTCTCCAA
                        acttgat  putative branch site (score: 5)
                                             ttacctct  putative PPT
                             atattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttaatctctacccttcacatttattctatgtttagattctcccatatcttctcatagacttgatattgtttgttgttgttacctctagACCGGAGTGTTTCCTCCATTTGTCCCATTTGCTGAAGTCTTTGCAGCTGTAATCACCGCGACTCTCACAGGCTCTCTCTACTTTCTTGCTGCGTCTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC