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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtctataccctgaacacacaagaaatcccaatgatcatagttggtaccttctttgtgaggagatcataactgatacttatggttcatttttatcattttcagACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATTCTTCGGTTGTTTAGGAGCCATGATGCAGTTGGGATTCAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g25820.1
intron # 7
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|58665614|gb|CK054300.1|CK054300
EST:     TTGTCCATGGAACGTGCTTGTATCTAAGCAGGAAATGGTACAAGAAGACG                         ACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATT
genomic: TTGTCCATGGAACGTGCTTGTATCTAAGCAGGAAATGGTACAAGAAGACGgtaaaagtct ... tcattttcagACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATT
EST: gi|29679760|gb|CB676035.1|CB676035
EST:     TTGTCCATGGAACGTGCTTGTATCTAAGCAGGAAATGGTACAAGAAGACG                         ACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATT
genomic: TTGTCCATGGAACGTGCTTGTATCTAAGCAGGAAATGGTACAAGAAGACGgtaaaagtct ... tcattttcagACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATT

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), 68 (downstream exon)
Score: 16

TGCCTTCTGGTTTACCCACCACCTGTTTGTCATTGTGTACACTTTGCTCTTTGTCCATGGAACGTGCTTGTATCTAAGCAGGAAATGGTACAAGAAGACGgtaaaagtct ... tcattttcagACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATTCTTCGGTTGTTTAGGAGCCATGATGCAGTTGGGATTCAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttgtgaggagatcataactgatacttatggttcatttttatcattttcagACATGGATGTACCTCGCTGTTCCTGTTGTCCTGTATGTAAGTGAGCGTATTCTTCGGTTGTTTAGGAGCCATGATGCAGTTGGGATTCAGAAG
                                       tttttatcattttc  CT-rich tract
                                   ttcatttttatcattt  TA-rich tract