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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtgattttagtgttgatgtttaggtggttataggtttggatcctgctgtgagtaactcgtagatcctgatcctgattgattgtatttatgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGATGAGCGTGGTGGGCTTTGATCTAGGGAATGAGAGCTGCATTGTGGCCGTC

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
intron # 1
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|88356810|gb|CI619296.1|CI619296
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88344861|gb|CI624512.1|CI624512
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|29680265|gb|CB676540.1|CB676540
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88826135|gb|CI776700.1|CI776700
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|58664216|gb|CK052902.1|CK052902
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88400214|gb|CI590904.1|CI590904
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|58689129|gb|CK077816.1|CK077816
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88454101|gb|CI693642.1|CI693642
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCC----                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88328439|gb|CI676644.1|CI676644
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCC----                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88366431|gb|CI610726.1|CI610726
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88361642|gb|CI680209.1|CI680209
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCC----                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|58662624|gb|CK051310.1|CK051310
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         T
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcag-
EST: gi|58662624|gb|CK051310.1|CK051310
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         T
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcag-
EST: gi|29678338|gb|CB674613.1|CB674613
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88742162|gb|CI765670.1|CI765670
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88377659|gb|CI605494.1|CI605494
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88354443|gb|CI624833.1|CI624833
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGACAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88443569|gb|CI597036.1|CI597036
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88424653|gb|CI606452.1|CI606452
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88356212|gb|CI627660.1|CI627660
EST:     TCTACAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|88406030|gb|CI591425.1|CI591425
EST:     TCTAGAAGCTTCCAGACCCTTCGGGGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|58653851|gb|CK042531.1|CK042531
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAG                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
EST: gi|58673971|gb|CK062657.1|CK062657
EST:     TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAT                         GAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT
genomic: TCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGAT

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: 74 (upstream exon), 74 (downstream exon)
Score: 42

GCGAAGGCGATTCAGGCGAGAAGAGAGAGAGAGAGCGCGAGGCCGGCGGTTCTAGAAGCTTCCAGACCCTTCGGCGCGAGCGAGCTCACCTCCCCCGTAGgtacggccca ... atgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGATGAGCGTGGTGGGCTTTGATCTAGGGAATGAGAGCTGCATTGTGGCCGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgtgagtaactcgtagatcctgatcctgattgattgtatttatgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGATGAGCGTGGTGGGCTTTGATCTAGGGAATGAGAGCTGCATTGTGGCCGTC
                                attgattgtatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtgattttagtgttgatgtttaggtggttataggtttggatcctgctgtgagtaactcgtagatcctgatcctgattgattgtatttatgtgcgcagGAGCTGTTCATTAGATCTGAATAAGGGGGATTGAAGCAGTGAGGAGAAGATGAGCGTGGTGGGCTTTGATCTAGGGAATGAGAGCTGCATTGTGGCCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- tgtgatt
- - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - - -gatcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg