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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctcttgtttccagtcaattgttgaggcgtttgtaatgcacagtgttttgtaaaacgttggattgctttggctttcaataacttaatgacttattttgtcttggtttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCCTATGCAATGACAGAGGCAACACATTTGATGAGCTCAAACCCCTTACCAG

Basic information

species Arabidopsis thaliana
transcript AT3G48990.1
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|116453490|gb|EG496082.1|EG496082
EST:     AATATCCTAAACTCCGGTTCATCAGGAGTTGCAGTGCTTCTTTGGCTCCG                         GTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCC
genomic: AATATCCTAAACTCCGGTTCATCAGGAGTTGCAGTGCTTCTTTGGCTCCGgtaatgctct ... tttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCC
EST: gi|116483995|gb|EG526587.1|EG526587
EST:     AATATCCTAAACTCCGGTTCATCAGGAGTTGCAGTGCTTCTTTGACTCCG                         GTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCC
genomic: AATATCCTAAACTCCGGTTCATCAGGAGTTGCAGTGCTTCTTTGGCTCCGgtaatgctct ... tttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCC
EST: gi|124749567|gb|EH839697.1|EH839697
EST:     CATCAGGAGTTGCAGTGCTTCTTTGGCTCCG                         GTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCA
genomic: CATCAGGAGTTGCAGTGCTTCTTTGGCTCCGgtaatgctct ... tttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgctttggctttcaataacttaatgacttattttgtcttggtttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCCTATGCAATGACAGAGGCAACACATTTGATGAGCTCAAACCCCTTACCAG
                                             tttttgtt  CT-rich tract
                 aataacttaatgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgctcttgtttccagtcaattgttgaggcgtttgtaatgcacagtgttttgtaaaacgttggattgctttggctttcaataacttaatgacttattttgtcttggtttttgttagGTGATATTGTCCAGGCTTGAGGAAGCGTTTGGAGCACCGGTGCTCGAGGCCTATGCAATGACAGAGGCAACACATTTGATGAGCTCAAACCCCTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA