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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggttttagttctagcttcttgtttcattgttttattacggtgttgatttgaaattgacttcatagtgaatacttaaaaccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAAAGAACAAGAAACTAGTCGTGAACATCGAAGAGATTATGATCGCAGGAGT

Basic information

species Arabidopsis thaliana
transcript AT3G03340.1
intron # 11
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|19741401|gb|AU226754.1|AU226754
EST:     GGATGAGAAGGCCAATATACGCAAGGAAAG                         ATCAAAGGAAC-GAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAA
genomic: GGATGAGAAGGCCAATATACGCAAGGAAAGgttaggtttt ... ccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAA
EST: gi|86074325|gb|DR370082.1|DR370082
EST:     GATGAGAAGGCCAATATACGCAAGGAAAG                         ATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAA
genomic: GATGAGAAGGCCAATATACGCAAGGAAAGgttaggtttt ... ccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAA
EST: gi|125012597|gb|EL084866.1|EL084866
EST:     GATGAGAAGGCCAATATACGCAAGGAAAG                         ATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGA
genomic: GATGAGAAGGCCAATATACGCAAGGAAAGgttaggtttt ... ccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacggtgttgatttgaaattgacttcatagtgaatacttaaaaccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAAAGAACAAGAAACTAGTCGTGAACATCGAAGAGATTATGATCGCAGGAGT
                  aattgac  putative branch site (score: 3)
                                  aatacttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggttttagttctagcttcttgtttcattgttttattacggtgttgatttgaaattgacttcatagtgaatacttaaaaccatacttagATCAAAGGAACGGAACAGTAAGGAGAGAGAATCAAGTAAAGACCGAGAGAAAGAACAAGAAACTAGTCGTGAACATCGAAGAGATTATGATCGCAGGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA