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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTATTTTTTTACCATTGGCGGCTCGGCTGCATCCCCAAGTGAAGAAGAGAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcgatgccctttctttctctttggttatttactgttgctttagatatatgtatatgcgtctaaataatgttgttgcctttttgatcccctttg...

Basic information

species Oryza sativa
transcript LOC_Os08g03570.1
intron # 2
splice site 5'
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|29639521|gb|CB644530.1|CB644530
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|88452971|gb|CI574518.1|CI574518
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|58693033|gb|CK081720.1|CK081720
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|88360439|gb|CI608441.1|CI608441
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|88395966|gb|CI593168.1|CI593168
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|29660517|gb|CB656792.1|CB656792
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|117233153|gb|CT848014.1|CT848014
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
EST: gi|58695746|gb|CK084433.1|CK084433
EST:     GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTG                         GGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA
genomic: GAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTA

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), 63 (downstream exon)
Score: 25

ATTTATTTTTTTACCATTGGCGGCTCGGCTGCATCCCCAAGTGAAGAAGAGAATTCGTACATGATTCCGCTAAACAGGAGGGCGAGTCAGACTAGGGGTGgtagatctcg ... atgttgatagGGATGGAGTACTTCGATGCTAGGCGGAAGCCTCATAATGTTGGGAAAGTTATTGCAGCTCTGGTCCTCACAACACTATGTATATTTATTTTGAAGCAATC




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