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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttttgaaagatctatttgagttgatcataatcaggctgcttgtgtgatctctctgttgttggtttttcttatgatttggttttgtatcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTCTTGAAATGCTAAATACTTCGGGGAATGAACGATCTTCGAAGATTCATGA

Basic information

species Oryza sativa
transcript LOC_Os11g36070.5
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|88721762|gb|CI745061.1|CI745061
EST:     CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAG                         GCAATATGGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
genomic: CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
EST: gi|88692480|gb|CI736055.1|CI736055
EST:     CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAG                         GCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
genomic: CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
EST: gi|88352092|gb|CI626092.1|CI626092
EST:     CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAG                         GCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
genomic: CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
EST: gi|88730714|gb|CI754327.1|CI754327
EST:     CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGNAACGATGAAG                         GCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
genomic: CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
EST: gi|88731451|gb|CI755064.1|CI755064
EST:     CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAG                         GCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC
genomic: CGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTC

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: 75 (upstream exon), 35 (downstream exon)
Score: 6

CGGACGCTGGCGCTGCCCGACCTCGCCGACGAGGAGTTGCTGAGATCTCTCGTGAAGAGGCAGATTCTTGCGTCGTCGCTGTCCGCCGGCAACGATGAAGgtttgggggc ... tcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTCTTGAAATGCTAAATACTTCGGGGAATGAACGATCTTCGAAGATTCATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgatctctctgttgttggtttttcttatgatttggttttgtatcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTCTTGAAATGCTAAATACTTCGGGGAATGAACGATCTTCGAAGATTCATGA
                                             tcattttt  CT-rich tract
                                      ttttgtatcattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttttgaaagatctatttgagttgatcataatcaggctgcttgtgtgatctctctgttgttggtttttcttatgatttggttttgtatcatttttagGCAATATTGACCTGATTGCTGAAGCAAGGTCTAAAGAGATCTCGAATTTTCTTGAAATGCTAAATACTTCGGGGAATGAACGATCTTCGAAGATTCATGA

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