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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATCTCTGACTCTGGGCAGGTATCCTAGGCATGGTCATCAGAGATCCTCCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaacttgaatttcttcaatacacctatcaggtctgtgatgttcagttaaataatgcagcgtttggtggtaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g69040.1
intron # 4
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|89175684|gb|CI042705.1|CI042705
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|88830390|gb|CI010590.1|CI010590
EST:     TACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: TACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|86257319|gb|CI004137.1|CI004137
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|88991627|gb|CI019805.1|CI019805
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAACTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|38476075|gb|CF960208.1|CF960208
EST:     CAACATCAGCACCAGCCCTGTGATACATATAATTGACACACGCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAAGTTTCAATTG
genomic: CAACATCAGCACCAGCCCTGTGATACATATAATTGACACAC-CTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTG
EST: gi|89180157|gb|CI044436.1|CI044436
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|88525719|gb|CI452745.1|CI452745
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCGAT                         GCACTCCCTGAACCCGAGAAGGCCGTTGCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|88552796|gb|CI482839.1|CI482839
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
EST: gi|33794315|gb|CF323045.1|CF323045
EST:     CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAAT                         GCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC
genomic: CCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGC

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: 66 (upstream exon), 39 (downstream exon)
Score: 8

ACTATCTCTGACTCTGGGCAGGTATCCTAGGCATGGTCATCAGAGATCCTCCAACATCAGCACCAGCCCTGTGATACATATAATTGACACACCTAGCAATgtactcaaac ... ggtaatgcagGCACTCCCTGAACCCGAGAAGGCCGTTCCGAAGGAACCAACTTTCAATTGCCCTGTCTGCATGAACGAGCTGGTCGAACCGTCATCGACCATCTGCGGTC




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