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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggatctaaagtaagacttcttaatttaaccattaatgtctttcttgaatatgttatacttttatccaacaattttattttttggttcatgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAGAAGTTTGATATTTTT

Basic information

species Arabidopsis thaliana
transcript AT3G18035.1
intron # 2
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|164088226|gb|ES129361.1|ES129361
EST:     TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATC
genomic: TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATC
EST: gi|124935482|gb|EL012463.1|EL012463
EST:     CCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATCCTGGAGAACTCAAGAAG
genomic: CCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
EST: gi|163990222|gb|ES002636.1|ES002636
EST:     TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGAC
genomic: TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGAC
EST: gi|164123500|gb|ES014839.1|ES014839
EST:     TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
genomic: TTATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
EST: gi|164109588|gb|ES117478.1|ES117478
EST:     TATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAA
genomic: TATGAAGCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAG-AAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAA
EST: gi|164101552|gb|ES030199.1|ES030199
EST:     TATGAAGTCCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATC
genomic: TATGAAG-CCTAAGAGAGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATC
EST: gi|125205965|gb|EL220919.1|EL220919
EST:     GAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTGG
genomic: GAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGG
EST: gi|124742371|gb|EH833533.1|EH833533
EST:     AGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
genomic: AGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
EST: gi|125321611|gb|EL335696.1|EL335696
EST:     AGGACGAGGACGTCCTGTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAGG
genomic: AGGACGAGGACGTCCTGTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAG
EST: gi|163997062|gb|EL975211.1|EL975211
EST:     GTAGGTAGACCCAGAAAG                         ATTGGAACATCAGTCACGACTGGGACACAAGATTCTG
genomic: GTAGGTAGACCCAGAAAGgtaaattttc ... atgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgaatatgttatacttttatccaacaattttattttttggttcatgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAGAAGTTTGATATTTTT
     atatgttatactttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggatctaaagtaagacttcttaatttaaccattaatgtctttcttgaatatgttatacttttatccaacaattttattttttggttcatgaacctagATTGGAACATCAGTCACGACTGGGACACAAGATTCTGGAGAACTCAAGAAGAAGTTTGATATTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - -atctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacaa