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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactgattcaaatggacattttacactgaattccagaatgctgggttcttttgacatgaaaattttcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGACATCAGAGCCCAACCAGAAACGGCTCCAACGCATGCGCTACAATGTAACA

Basic information

species Oryza sativa
transcript LOC_Os04g31690.2
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|88958626|gb|CI096142.1|CI096142
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|29631481|gb|CB636490.1|CB636490
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|86522333|gb|CI162539.1|CI162539
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|313079778|gb|HO213217.1|HO213217
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|86887856|gb|CI297967.1|CI297967
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|38474121|gb|CF958253.1|CF958253
EST:     TTTCCGTGCCATGTTGTTTCATCATCATCCTACGGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: TTTCCGT-CCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|58594719|gb|CF993027.1|CF993027
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|5038575|gb|AU070685.1|AU070685
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|27546938|gb|CA767312.2|CA767312
EST:     ATTTCCATCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
EST: gi|86837004|gb|CI347551.1|CI347551
EST:     ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTT                         GCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC
genomic: ATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGAC

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: 52 (upstream exon), 60 (downstream exon)
Score: 31

AGGATGAAGTATTTCTTATGAACTGAAATAATACGCCATGTATATTCCATATTTCCGTCCATGTTGTTTCATCATCATCCTACTGCATTCTGGCATGCTTgtaagtactg ... tcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGACATCAGAGCCCAACCAGAAACGGCTCCAACGCATGCGCTACAATGTAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacactgaattccagaatgctgggttcttttgacatgaaaattttcacttgcagGCTGGGAGCCTTTGTAAATCGAAGAGGAATAGGGAGGACCCTTTTTGTGACATCAGAGCCCAACCAGAAACGGCTCCAACGCATGCGCTACAATGTAACA
                            ttttgac  putative branch site (score: 31)
                                          ttttcactt  putative PPT
                                   atgaaaatttt  TA-rich tract