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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactaaaacatctggagaacaattttcaaatttgtcagttgatctttgcttatgcttatgttctttctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAACCCAGAGTATCATGAAGATTAAGGGATAGATATGGCACACGCAAAATGC

Basic information

species Oryza sativa
transcript LOC_Os09g15750.1
intron # 24
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|88479370|gb|CI416641.1|CI416641
EST:     GAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: GAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88901735|gb|CI001843.1|CI001843
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88470132|gb|CI407403.1|CI407403
EST:     TGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: TGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|8857666|gb|AU094984.1|AU094984
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|12622674|gb|AU172887.1|AU172887
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88455294|gb|CI519315.1|CI519315
EST:     CCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGGAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: CCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86592847|gb|CI270404.1|CI270404
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86518551|gb|CI158757.1|CI158757
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|14191579|gb|AU183790.1|AU183790
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86492954|gb|CI135587.1|CI135587
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88506110|gb|CI433616.1|CI433616
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|8856938|gb|AU094256.1|AU094256
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86872143|gb|CI333304.1|CI333304
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|55410835|gb|CV723211.1|CV723211
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|89174234|gb|CI042127.1|CI042127
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|58591305|gb|CF989613.1|CF989613
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86478141|gb|CI120774.1|CI120774
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTCGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88269184|gb|CI380482.1|CI380482
EST:     ACGCCTTTATTACTTTCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88411733|gb|CI521456.1|CI521456
EST:     GAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: GAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|87016283|gb|CI271694.1|CI271694
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88249096|gb|CI248945.1|CI248945
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|29626609|gb|CB631620.1|CB631620
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86425366|gb|CI070463.1|CI070463
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88837459|gb|CI078819.1|CI078819
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|8527826|gb|AU092641.1|AU092641
EST:     ACGCCTGTATTACTTGCCGCNGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86430376|gb|CI082799.1|CI082799
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88260505|gb|CI362798.1|CI362798
EST:     CGCAGGGGAACGAGCAGAGGCTGGCAACTG-AAA                         ATATCTTCCACTGACACCAGTTCTTGAGGTTTTTGTGATCCTAAAAAATAA
genomic: CGCAGGGGAACGAGCAGA-GCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|86479306|gb|CI121939.1|CI121939
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88225411|gb|CI225327.1|CI225327
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|88283498|gb|CI404944.1|CI404944
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|13896674|gb|AU183010.1|AU183010
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
EST: gi|27920720|gb|CB096528.1|CB096528
EST:     ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAA                         ATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA
genomic: ACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAA

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: 20

TCGGTCAGGCGGGTCGACCCAAGACAATTACTGGATTCCAGACGCATTCAACGCCTGTATTACTTGCCGCAGGGGAACGAGCAGAGCTGGCAACTGAAAAgtaaactaaa ... ctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAACCCAGAGTATCATGAAGATTAAGGGATAGATATGGCACACGCAAAATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttcaaatttgtcagttgatctttgcttatgcttatgttctttctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAACCCAGAGTATCATGAAGATTAAGGGATAGATATGGCACACGCAAAATGC
               agttgat  putative branch site (score: 20)
                                 cttatgttctttct  putative PPT
                                          tttctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactaaaacatctggagaacaattttcaaatttgtcagttgatctttgcttatgcttatgttctttctatatgcagATATCTTCCACTGACACCAGTTCTTGAGGGTTTTGTGATCCTAAGAAATAACCCAGAGTATCATGAAGATTAAGGGATAGATATGGCACACGCAAAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA