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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcaatcatttagtgacgacccagaattagatagaattttacaatattttcatcttacaactttaatttattacatacgctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATCCATGATGCTGGAAGTATGATCAGTTATCACAAGAACCTCACAGGCCAGG

Basic information

species Oryza sativa
transcript LOC_Os12g15470.1
intron # 10
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|33793780|gb|CF322774.1|CF322774
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTTGGATTTCAT
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTT-GGATTTCAT
EST: gi|58609188|gb|CK037221.1|CK037221
EST:     CAGCATGGCTGAAGAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTTATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29638179|gb|CB643188.1|CB643188
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|86501069|gb|CI143702.1|CI143702
EST:     CAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|33684071|gb|CF312310.1|CF312310
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29644492|gb|CB649499.1|CB649499
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29668082|gb|CB664357.1|CB664357
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29661783|gb|CB658058.1|CB658058
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29659837|gb|CB656112.1|CB656112
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
EST: gi|29661784|gb|CB658059.1|CB658059
EST:     CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCA                         GTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC
genomic: CAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATC

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: 67 (upstream exon), 70 (downstream exon)
Score: 26

AGTGATGAAGTTGCAACAGCATGGCTGAACAACGATGACGTCAGAGCAGCAATTCATGCCCAACCAgtatggcaat ... ctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATCCATGATGCTGGAAGTATGATCAGTTATCACAAGAACCTCACAGGCCAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttacaatattttcatcttacaactttaatttattacatacgctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATCCATGATGCTGGAAGTATGATCAGTTATCACAAGAACCTCACAGGCCAGG
        aatattttcatcttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcaatcatttagtgacgacccagaattagatagaattttacaatattttcatcttacaactttaatttattacatacgctcatgatagGTAAGCTCAATTGGCTCGTGGCTTATATGCACCAACGTGTTGGATTTCATCCATGATGCTGGAAGTATGATCAGTTATCACAAGAACCTCACAGGCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC