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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagcttttgcatatcagaattattgctagccatataattcatttttccatccttacatgttctacttttgatatatcaattcaatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g44660.1
intron # 8
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|163921168|gb|EG710157.1|EG710157
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|163927859|gb|EG714239.1|EG714239
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88557502|gb|CI487915.1|CI487915
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88545586|gb|CI475155.1|CI475155
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|163920287|gb|EG709539.1|EG709539
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88830004|gb|CI074676.1|CI074676
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88551563|gb|CI481630.1|CI481630
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|25806219|gb|CA762180.1|CA762180
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88839839|gb|CI017604.1|CI017604
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|86498135|gb|CI140768.1|CI140768
EST:     TCGAGAAATCTTTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|86864180|gb|CI334017.1|CI334017
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
EST: gi|88556421|gb|CI486745.1|CI486745
EST:     TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTG                         AATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT
genomic: TCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCT

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: 61 (upstream exon), 40 (downstream exon)
Score: 7

GAACAACAACATCGAGAAATCTCTAAAAGATTACTCCGAGGCATTTGATATTGTCTACTTGgtgaggcagc ... ttcaatgcagAATGACGCGCCAATGGTGGGAGTTGTTGAGCTTGTATCTGAACTATGTCCTTAACCAAATGATGTTTTGCTGAGCTTAGAAGCCGCATCCGCCTCCCGCT




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