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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacactttgggtagtatcatggtgggatttccagtcttttcgacgtgtcgtgtcaccggatccatttctttgttgccgttgttgttgttgctgtttggttggttgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGCTGCTAGAGAGACGAAGCTCGGTGCGACGGTCGCAGAGTATGGTGAGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g55520.1
intron # 1
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|88405494|gb|CI588700.1|CI588700
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGAAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88693904|gb|CI737942.1|CI737942
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|66923711|gb|CX110559.1|CX110559
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGGGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88395907|gb|CI593109.1|CI593109
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88300627|gb|CI587431.1|CI587431
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88406812|gb|CI604006.1|CI604006
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTAAAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88718166|gb|CI741676.1|CI741676
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88370681|gb|CI592447.1|CI592447
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
EST: gi|88294896|gb|CI604768.1|CI604768
EST:     TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAG                         CTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC
genomic: TTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGC

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: 73 (upstream exon), 39 (downstream exon)
Score: 7

GGCTCTCTCTGCGTGGGTGTTCTGCAGCGCCAATCCTGGATCATCATCGTTTGCTTCTGCACACGTCGCTCGAGGCCGCAGAAAGCTGCGTCCTTTACAGgtatatacac ... tgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGCTGCTAGAGAGACGAAGCTCGGTGCGACGGTCGCAGAGTATGGTGAGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatccatttctttgttgccgttgttgttgttgctgtttggttggttgccgagaagCTGGCCACGGTGGAGTTGATCGGTTGATGGCAGCGAGCGGCGGTGGGTCGCTGCTAGAGAGACGAAGCTCGGTGCGACGGTCGCAGAGTATGGTGAGCGA
     atttcttt  TA-rich tract