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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAATCAGAAAGCCCTCGCAGGCTCTTCTATTTGGCATTGCCTCCATCTGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttctttactattccatacgttattctttttggaatttatacaagctatgcgctctagttgaacaaaagcaatgaagcataaagttagtggaaaattcaggtcttcttggaagcatttcttcatcaagattcattttctttgcataaatgttctgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g40874.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40874.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G130230_T03 (Zea mays), 5'ss of exon 5
AACAAATCAGAAAGCCCTCGCAGGCTCTTCTATTTGGCATTGCCTCCATCTGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaa-gtttctttactattccatacgttattctttttggaattt-atacaagctatgcgctctagttgaacaaaagcaatgaagcataaagttagtggaaaattcaggtcttcttggaagcatttcttcatcaagattcattttctttgcataaatgttctgtttgcag
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AAGAGTTCAGGAAGCTATCGCAGGCTCTTTTATTTGGCATTGCCTCCATCTGTCTACCCTTCAGTGTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaaagtttctttcctatgctggatttttttattcttataagctgatgcaaat------ctttagtttagtaacaaacaagtatggtggagttagttgaagcttc----------------------------------------------------------------
















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|29663317|gb|CB659592.1|CB659592
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|86850539|gb|CI307768.1|CI307768
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|29614696|gb|CB619709.1|CB619709
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|58608815|gb|CK036848.1|CK036848
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|58670061|gb|CK058747.1|CK058747
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGACAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|29680803|gb|CB677078.1|CB677078
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
EST: gi|117243651|gb|CT843162.1|CT843162
EST:     TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCAT                         CTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT
genomic: TGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACT

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: 75 (upstream exon), 74 (downstream exon)
Score: 64

AACAAATCAGAAAGCCCTCGCAGGCTCTTCTATTTGGCATTGCCTCCATCTGTCTACCCTTCAGTCTGCAAAATGATCAGAACATATTGCATGAATCCATgtaaagtttc ... ctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACTCTGCAGAAGAATTAAGTGCCCAACTTGGGGAGCTATTTGACGAAAACCA




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