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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcttctgtgctttatttctgtttcctcaaaacctccactccttttggctcattatataaggtgttttatctgataagtaaaatgttgaaagaagttgcaattcctattagtttgttcagactgcttaaagcagtaatttatcctttgatctagcgaaattttaatatttcacacttctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACTGGCCAGTTGGAATGACTTTTCTTTACGGCCAAATCTCAACATCTTCACA

Basic information

species Oryza sativa
transcript LOC_Os05g06330.1
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|88675544|gb|CI729657.1|CI729657
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|89165925|gb|CI103015.1|CI103015
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|29662376|gb|CB658651.1|CB658651
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|88554107|gb|CI484267.1|CI484267
EST:     GAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: GAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|66912666|gb|CX099514.1|CX099514
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|9788921|gb|BE530931.1|BE530931
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|86834648|gb|CI340765.1|CI340765
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         TTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|27920538|gb|CB096346.1|CB096346
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|89171366|gb|CI720425.1|CI720425
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|29658153|gb|CB654428.1|CB654428
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|86506896|gb|CI149529.1|CI149529
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|86541829|gb|CI182035.1|CI182035
EST:     CACATTGAAGTTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCGTGAACTGAC
genomic: CACATTGAAG-TCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGC-TGAACTGAC
EST: gi|88256301|gb|CI358689.1|CI358689
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAAAACTTGATGGTGACGA-GAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|88670529|gb|CI724645.1|CI724645
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|9886387|gb|BE607479.1|BE607479
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|29662375|gb|CB658650.1|CB658650
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
EST: gi|33801514|gb|CF326629.1|CF326629
EST:     TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAG                         GTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT
genomic: TCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACT

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: 69 (upstream exon), 55 (downstream exon)
Score: 48

AGTTAAGCTAAAAATGCAAGGTGCCTGCAGTGGATGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTCATGCATTATGTCCCTGAGgtatctcttc ... tctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACTGGCCAGTTGGAATGACTTTTCTTTACGGCCAAATCTCAACATCTTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtaatttatcctttgatctagcgaaattttaatatttcacacttctttggcagGTGAAAGGAGTAGAGCAAGAACTTGATGGTGACGAGGAAGCTGAACTGACTGGCCAGTTGGAATGACTTTTCTTTACGGCCAAATCTCAACATCTTCACA
                            ttttaat  putative branch site (score: 48)
                                    tttcacacttcttt  CT-rich tract
                         aaattttaatatttca  TA-rich tract