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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcaaaatggaacatttctgggatgtgagatactctgtttcgatcattattagatgcctacaacccatgtaattttttcttttttctttacctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAAAATGCAGCAGTGGTAGGCTGTCAATGTACTGGACCAACTATCCTGATAA

Basic information

species Oryza sativa
transcript LOC_Os01g35580.2
intron # 5
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|88966558|gb|CI353110.1|CI353110
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88472347|gb|CI409618.1|CI409618
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|86508583|gb|CI151216.1|CI151216
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|89165456|gb|CI102546.1|CI102546
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|89161945|gb|CI102293.1|CI102293
EST:     TGACTTGGGGGTTGGATATGCGAACTTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: TGACTTGGGGGTTGGATATGCGAAC-TACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|87026087|gb|CI250103.1|CI250103
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88269358|gb|CI380656.1|CI380656
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88842916|gb|CI371816.1|CI371816
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCGATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|86595066|gb|CI260305.1|CI260305
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|86427245|gb|CI072342.1|CI072342
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88201871|gb|CI202226.1|CI202226
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|89189825|gb|CI049364.1|CI049364
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88248052|gb|CI246670.1|CI246670
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|157649986|gb|EX449620.1|EX449620
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|88978248|gb|CI384711.1|CI384711
EST:     CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCGATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
EST: gi|109712352|gb|CI104960.1|CI104960
EST:     CCAGTCTCCTTACCAGGCATAA                         TTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA
genomic: CCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAA

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), 75 (downstream exon)
Score: 32

GCTGGAGAGACGTCTGAAGGCGGAGTTCAAGAAAGTGAATGAGCAGCAATCTGACTTGGGGGTTGGATATGCGAACTACCAGTCTCCTTACCAGGCATAAgtaagttgtg ... acctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAAAATGCAGCAGTGGTAGGCTGTCAATGTACTGGACCAACTATCCTGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattattagatgcctacaacccatgtaattttttcttttttctttacctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAAAATGCAGCAGTGGTAGGCTGTCAATGTACTGGACCAACTATCCTGATAA
                       tgtaattttttctttt  CT-rich tract
                      atgtaattttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcaaaatggaacatttctgggatgtgagatactctgtttcgatcattattagatgcctacaacccatgtaattttttcttttttctttacctttgtagTTTCCAAGGTGCCAATTATGTTTCTTTACCTCTGGAATCTACAGTCACGAAAATGCAGCAGTGGTAGGCTGTCAATGTACTGGACCAACTATCCTGATAA

- - -aaatggaa
- - - - - - - - - - -ggatgtg
- - - - - - - - - - - - - - - - - -ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctac