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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacactacaacattttatttagaaaattatggtgacttagtttcaacattattagataagcaacacaattctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g33420.1
intron # 12
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|88906563|gb|CI375635.1|CI375635
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGGATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCACTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|88508920|gb|CI436426.1|CI436426
EST:     GATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: GATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|86833000|gb|CI333599.1|CI333599
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGG-ATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|88245218|gb|CI245067.1|CI245067
EST:     TAGCATTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|86535277|gb|CI175483.1|CI175483
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|88829511|gb|CI074381.1|CI074381
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|89174390|gb|CI110588.1|CI110588
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|29675804|gb|CB672079.1|CB672079
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|86869834|gb|CI316562.1|CI316562
EST:     AGCACGTTACTCAAGATTATGTGCCACGGTTGAATCCAACAATAAAGGAG                         -TGGAAGTACAGGAGCAGTAGCACGTGCATTGATAGCAACTGGGAGTAAAG
genomic: AGCA-GTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|29675806|gb|CB672081.1|CB672081
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAATTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
EST: gi|88227256|gb|CI228369.1|CI228369
EST:     TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAG                         TTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
genomic: TAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 75 (downstream exon)
Score: 28

ATGTGGGAGCTGAATGAGAAAGGAAACCTCATTAGCAGTTACTCAAGATTATGTGCCACGGTGGAATCCAACAATAAAGGAGgtacacacta ... ctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatggtgacttagtttcaacattattagataagcaacacaattctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG
                   aacattattagataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacactacaacattttatttagaaaattatggtgacttagtttcaacattattagataagcaacacaattctgtatgcagTTGTAACTACAGGAGCAGTAGCACGTGCATGGATAGCAACTGGGAGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA