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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttatttgtgatcatattaaaacttgttattgatgttgttccttaatctttggatttgtgaagttgtactgatggtcaattacttcaatggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT

Basic information

species Arabidopsis thaliana
transcript AT1G20693.2
intron # 4
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|164234508|gb|ES101559.1|ES101559
EST:     GAAGGAAAACCCCAAGAACAAGTCTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT
genomic: GAAGGAAAACCCCAAGAACAAGTCTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
EST: gi|164010533|gb|ES061091.1|ES061091
EST:     TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT
genomic: TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
EST: gi|164158781|gb|ES187958.1|ES187958
EST:     TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTC
genomic: TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTC
EST: gi|163969828|gb|ES148976.1|ES148976
EST:     AAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT
genomic: AAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
EST: gi|164237972|gb|ES129256.1|ES129256
EST:     CTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTATCTGATTCT
genomic: CTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
EST: gi|116400368|gb|EG442960.1|EG442960
EST:     TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACT                         GTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
genomic: TCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGTAGCTACTgtgagtgtta ... tggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatctttggatttgtgaagttgtactgatggtcaattacttcaatggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT
                       tactgat  putative branch site (score: 2)
                                  aattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttatttgtgatcatattaaaacttgttattgatgttgttccttaatctttggatttgtgaagttgtactgatggtcaattacttcaatggattacagGTTGGAAAAGCTGCTGGAGACAAGTGGAAGTCCTTGTCTGATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG