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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtcttgattgacgaagctgcatgacttgatacttatgctatcttatatatccggatgatttaataattcgttttcttatgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
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|125233186|gb|EL247271.1|EL247271
EST:     TTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: TTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
EST: gi|116424148|gb|EG466740.1|EG466740
EST:     GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
EST: gi|124749106|gb|EH839236.1|EH839236
EST:     TTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAAGGTTTCTGCCAACCTTATCA
genomic: TTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAA-GGTTTCTGCCAACCTTATCA
EST: gi|164123245|gb|ES088084.1|ES088084
EST:     GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATC
genomic: GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATC
EST: gi|116444628|gb|EG487220.1|EG487220
EST:     GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: GATTCTCAAGTTGTATCTGACTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
EST: gi|124993909|gb|EL066178.1|EL066178
EST:     CTATGTCCGCTACTTCCTTCACCAGCATAC                         AATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG
genomic: CTATGTCCGCTACTTCCTTCACCAGCATACgtgagtgtct ... tgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctatcttatatatccggatgatttaataattcgttttcttatgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG
                        atttaat  putative branch site (score: 4)
                                     ttttcttat  putative PPT
                        atttaataattcgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtcttgattgacgaagctgcatgacttgatacttatgctatcttatatatccggatgatttaataattcgttttcttatgatttgcagAATTCAGCATGGACAACCCGCAACTGTTAAGGTTTCTGCCAACCTTATCAGGATGCTCGCATATAATAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG