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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttgaggatttaccgtttcaattccacggtttgtctttcattgatgacctctttcctcatttgttttatgatatttactttgtgatgtgttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCGGGGTAGTCCGATTTGCTCAGGTCAGTATGGAACTTGCAAGAATCGAAGC

Basic information

species Arabidopsis thaliana
transcript AT1G12520.3
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|125321251|gb|EL335336.1|EL335336
EST:     TTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTAC
genomic: TTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTT-C
EST: gi|124820730|gb|EH905596.1|EH905596
EST:     CGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
genomic: CGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
EST: gi|125223499|gb|EL237584.1|EL237584
EST:     GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCA
genomic: GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCA
EST: gi|125042108|gb|EL114377.1|EL114377
EST:     GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCAGAAT
genomic: GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAAT
EST: gi|124825645|gb|EH910511.1|EH910511
EST:     GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
genomic: GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
EST: gi|125238445|gb|EL252530.1|EL252530
EST:     GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
genomic: GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCG
EST: gi|124893088|gb|EH971990.1|EH971990
EST:     GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAG                         ATTTCTTAGTCTCA
genomic: GGAGCAAACTGGTCGAAAAGCTCGCTTAATTGGACAAGGTGTTCCTCAAGgttagatatc ... gttttggcagATTTCTTAGTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacctctttcctcatttgttttatgatatttactttgtgatgtgttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCGGGGTAGTCCGATTTGCTCAGGTCAGTATGGAACTTGCAAGAATCGAAGC
 cattgat  putative branch site (score: 4)
               atttgttttatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttgaggatttaccgtttcaattccacggtttgtctttcattgatgacctctttcctcatttgttttatgatatttactttgtgatgtgttttggcagATTTCTTAGTCTCAGCTGCAGTAGCAGAATTCAAAGGCCCTGACATTTTCGGGGTAGTCCGATTTGCTCAGGTCAGTATGGAACTTGCAAGAATCGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - -aattcca
- - - - - - - - - - - - - - -ggtttgt