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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttgcagcaagtcatctattattaaaaagtgaattaagtcctattttcaatcattttgtttattgcaatttgcctttttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG

Basic information

species Oryza sativa
transcript LOC_Os01g21420.1
intron # 15
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|88517893|gb|CI444782.1|CI444782
EST:     AAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: AAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88471315|gb|CI408586.1|CI408586
EST:     CACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: CACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88529689|gb|CI458027.1|CI458027
EST:     ATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: ATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88511081|gb|CI438587.1|CI438587
EST:     TCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: TCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|86869190|gb|CI335757.1|CI335757
EST:     ATCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: ATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88282667|gb|CI404063.1|CI404063
EST:     ATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: ATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88556121|gb|CI486430.1|CI486430
EST:     GATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: GATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88524724|gb|CI453668.1|CI453668
EST:     GATCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: GATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88304531|gb|CI518187.1|CI518187
EST:     CTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: CTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88273153|gb|CI388609.1|CI388609
EST:     AGATCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: AGATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|88852428|gb|CI374196.1|CI374196
EST:     AGATCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: AGATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
EST: gi|86865003|gb|CI344551.1|CI344551
EST:     AGATCAATATCAAGATCACGGACTCCTGTTTCTTCA                         CCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC
genomic: AGATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGC

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: 68 (upstream exon), 63 (downstream exon)
Score: 19

ATCAATATCAAGATCACGGACTCCTGTTTCTTCAgtaagtcttg ... tttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaagtcctattttcaatcattttgtttattgcaatttgcctttttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG
                                     tttgccttttttt  CT-rich tract
          tattttcaatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttgcagcaagtcatctattattaaaaagtgaattaagtcctattttcaatcattttgtttattgcaatttgcctttttttggcagCCTTCTCGTGGAAGATCTGTTAGTAAAAGCCCAAGCAGGAGCTTATCCCGCTCTCCCTCTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT