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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttggcaacttaaccataccgaggttgcagtttagaaattctggccatcaatcatactcatatgcatgattccaacattttgttcttatctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTGTCCCAGGTTCCTTTCGCCGTGGCTTTCACAGCTTATATTATATACGCGA

Basic information

species Oryza sativa
transcript LOC_Os01g57710.1
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|86505990|gb|CI148623.1|CI148623
EST:     GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAG                         GGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCAGCCTG
genomic: GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAGgtatgccccc ... atctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTG
EST: gi|87015232|gb|CI275422.1|CI275422
EST:     GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAG                         GGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTG
genomic: GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAGgtatgccccc ... atctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTG
EST: gi|86496301|gb|CI138934.1|CI138934
EST:     GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAG                         GGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTG
genomic: GGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAGgtatgccccc ... atctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTG

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: 37 (upstream exon), 68 (downstream exon)
Score: 12

CGGCGACGCGGGGTTCCCGTGGAAGGACGTGTCAGTGCTTGTCATGGTCTGGCTCTGCTTCTTCGTGCTCCATGTCTTCATTGGCGATAAGCATGGAAAGgtatgccccc ... atctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTGTCCCAGGTTCCTTTCGCCGTGGCTTTCACAGCTTATATTATATACGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggccatcaatcatactcatatgcatgattccaacattttgttcttatctgctcagGGTATGATCAGGATAAAACCCTGTGGAGTTGCATACTGGTTGATCACCCTGTCCCAGGTTCCTTTCGCCGTGGCTTTCACAGCTTATATTATATACGCGA
                                   ttttgttcttatct  CT-rich tract
                               aacatttt  TA-rich tract