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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgcactcatgggtaaagttactgtatgctgtgtgtaacaaagctctgaaattctatttattttgtactaactgtaatcatgtattccgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g42530.1
intron # 4
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|88733555|gb|CI756732.1|CI756732
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGT
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGT
EST: gi|87030406|gb|CI252683.1|CI252683
EST:     CAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGCCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: CAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|38479329|gb|CF963460.1|CF963460
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|218479973|gb|FG945844.1|FG945844
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|88329358|gb|CI653273.1|CI653273
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|88326643|gb|CI658364.1|CI658364
EST:     TGGGATACAGCTGGTCAGGAGAAATCCGGTGGACTCAGGCATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTA
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTA
EST: gi|88825209|gb|CI775774.1|CI775774
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|88696329|gb|CI739904.1|CI739904
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTC
EST: gi|2311042|gb|C27197.1|C27197
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCCGATGGNTACTTCTCGGCTG
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTC-GATGT-TACTTCTCGGCTG
EST: gi|88346234|gb|CI634107.1|CI634107
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|88352570|gb|CI654395.1|CI654395
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|25802747|gb|CA758708.1|CA758708
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|56158064|gb|C72115.2|C72115
EST:     TGGGATACAGCTGGTCAGGAGAA-TTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTC
EST: gi|325493512|gb|JG458036.1|JG458036
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTC
EST: gi|428684|gb|D24836.1|D24836
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATA
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATA
EST: gi|88720998|gb|CI744297.1|CI744297
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAA
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAA
EST: gi|88290672|gb|CI667045.1|CI667045
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
EST: gi|55442434|gb|CV734535.1|CV734535
EST:     TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTA                         TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC
genomic: TGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGAC

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: 72 (upstream exon), 72 (downstream exon)
Score: 59

TCCACCCCTTGGATTTCTTCACTAACTGCGGCAAGATCCGCTTCTACTGCTGGGATACAGCTGGTCAGGAGAAATTTGGTGGACTCAGGGATGGTTACTAgtaagtatta ... cgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctgaaattctatttattttgtactaactgtaatcatgtattccgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG
                       tactaac  putative branch site (score: 59)
      aaattctatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattgcactcatgggtaaagttactgtatgctgtgtgtaacaaagctctgaaattctatttattttgtactaactgtaatcatgtattccgcattgtagTATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG

tgattgc
- - - - - - - - - - - - -tgtatgc
- - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat