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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttaatagctttttctttgttcacttaatgatgtacttagttctcctttgatggtgtatgattacatttgttttcttgtttggtcttcattgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCAATGGGATGTGCTCCCGCGGAGCTGGCTCAGCATAGCCGCAATGGCGAGT

Basic information

species Arabidopsis thaliana
transcript AT3G04290.1
intron # 3
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|125307702|gb|EL321787.1|EL321787
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACT
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACT
EST: gi|86020702|gb|DR316448.1|DR316448
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTT
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTT
EST: gi|124753534|gb|EH843664.1|EH843664
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAAC
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAAC
EST: gi|47831098|gb|CK120782.1|CK120782
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
EST: gi|124837866|gb|EH922305.1|EH922305
EST:     CATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
genomic: CATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
EST: gi|124902138|gb|EH976218.1|EH976218
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAA
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAA
EST: gi|163989646|gb|ES174584.1|ES174584
EST:     TGTATCTCATTTCCGAATACGGAAAGATTCTCAGT                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
genomic: TGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
EST: gi|86020684|gb|DR316430.1|DR316430
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
EST: gi|86020690|gb|DR316436.1|DR316436
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAA
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAA
EST: gi|125139341|gb|EL178164.1|EL178164
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTG
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTG
EST: gi|47832310|gb|CK121994.1|CK121994
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCA
EST: gi|86020693|gb|DR316439.1|DR316439
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTG
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTG
EST: gi|124835799|gb|EH920238.1|EH920238
EST:     TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGA                         AAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACT
genomic: TACCAGACTACGTTGTGTATCTCATTTCCGAATACGGAAAGATTCTCAGAgtaagtttaa ... attgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttgatggtgtatgattacatttgttttcttgtttggtcttcattgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCAATGGGATGTGCTCCCGCGGAGCTGGCTCAGCATAGCCGCAATGGCGAGT
  ctttgat  putative branch site (score: 5)
                                        tcttcatt  putative PPT
                 attacatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttaatagctttttctttgttcacttaatgatgtacttagttctcctttgatggtgtatgattacatttgttttcttgtttggtcttcattgaaatagAAACTCTACGAACTGGGTGCAAGACGAGTTTTGGTAACTGGAACTGGTGCAATGGGATGTGCTCCCGCGGAGCTGGCTCAGCATAGCCGCAATGGCGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - -cacttaa
- - - - - - - - - - - - - - - - - - - - - ttctcct