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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCGGCTGAAGCAATGGAGCTCCCGTGCCCGAGGCTGCTGCTGCTTCTTCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggttttctttttttctcaagatttggattcttcagggtttctgggtgtgcatttggggatatggtggtttaccttcttggtttgcttcag

Basic information

species Oryza sativa
transcript LOC_Os03g18370.1
intron # 1
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|117246185|gb|CT862605.1|CT862605
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88433062|gb|CI569731.1|CI569731
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGAGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGAATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88360811|gb|CI625117.1|CI625117
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCA
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCA
EST: gi|88385734|gb|CI566596.1|CI566596
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88311304|gb|CI570378.1|CI570378
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88345043|gb|CI625889.1|CI625889
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88341081|gb|CI638637.1|CI638637
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
EST: gi|88387528|gb|CI583046.1|CI583046
EST:     TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAG                         GGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT
genomic: TCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTT

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: 19 (upstream exon), 74 (downstream exon)
Score: 4

CCTGCGGCTGAAGCAATGGAGCTCCCGTGCCCGAGGCTGCTGCTGCTTCTTCGTCTTCTTGTGTTCTTGGTTGCGGTTTCTTGGCCGCTCTGCGGCGCAGgtttggtttt ... tttgcttcagGGACTGAAGGCCTCGGAGTTGGAGAGGAGGGGTTGAGCAGCATTGGTGCTTCTTCTGGTTCTAG




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