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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaattgtcccgagttaaagtcttaaccatcaaaagctcttttgtctaagcagtctctacttatcttgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATCATCCACAGCACAAGCCCAACCTAACCGAAGACTCCACCCGAAACAAGCG

Basic information

species Arabidopsis thaliana
transcript AT2G18280.1
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|116376565|gb|EG419157.1|EG419157
EST:     TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAG                         GTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
genomic: TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAGgtaagcaatt ... tgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
EST: gi|116376569|gb|EG419161.1|EG419161
EST:     TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAG                         GTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
genomic: TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAGgtaagcaatt ... tgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
EST: gi|124736926|gb|EH828328.1|EH828328
EST:     CGGAGCAGCAGTACTTATGTTGGCAAATTAAG                         GTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
genomic: CGGAGCAGCAGTACTTATGTTGGCAAATTAAGgtaagcaatt ... tgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATC
EST: gi|125170005|gb|EL193716.1|EL193716
EST:     TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAG                         GTCTGGTTTTACTGGGAACCGAGTTCACAATATATGACAA
genomic: TCTGCAAAGAACTTCTCACGGAGCAGCAGTACTTATGTTGGCAAATTAAGgtaagcaatt ... tgtgggatagGTCTGGTTTT-CTGGGAACCAAGTTCACAATATATGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaccatcaaaagctcttttgtctaagcagtctctacttatcttgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATCATCCACAGCACAAGCCCAACCTAACCGAAGACTCCACCCGAAACAAGCG
 tcttaac  putative branch site (score: 2)
                                tctctacttatctt  putative PPT
       atcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaattgtcccgagttaaagtcttaaccatcaaaagctcttttgtctaagcagtctctacttatcttgtgggatagGTCTGGTTTTCTGGGAACCAAGTTCACAATATATGACAACCAAACAGCATCATCCACAGCACAAGCCCAACCTAACCGAAGACTCCACCCGAAACAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA