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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttgactatctaaattgtttgttgttgctatgtactaattacccttgcatttgggagctcataagtcataacattacttttctcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCTTGGTGTCCATTACTGTTCTGGGTCATAGAGTTTCCAATCTTTGGCAATT

Basic information

species Oryza sativa
transcript LOC_Os09g15170.1
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|88692716|gb|CI736291.1|CI736291
EST:     GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAG                         ATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
genomic: GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
EST: gi|88360507|gb|CI608433.1|CI608433
EST:     GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAG                         ATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
genomic: GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
EST: gi|88363819|gb|CI610579.1|CI610579
EST:     GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAG                         ATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
genomic: GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
EST: gi|88362037|gb|CI607037.1|CI607037
EST:     GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAG                         ATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
genomic: GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
EST: gi|86903814|gb|CI302460.1|CI302460
EST:     GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAG                         ATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT
genomic: GGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCT

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: 30 (upstream exon), 66 (downstream exon)
Score: 2

AAAACTAGTTCTTGATTGGTTCTTGTCATCTTTGGGAGGACATTGCTCTGGGTGTGTGTCAAGATTGTGCTGGGAGCATAAAGCTGGGATCTTTGGCCAGgttcttgact ... tcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCTTGGTGTCCATTACTGTTCTGGGTCATAGAGTTTCCAATCTTTGGCAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacccttgcatttgggagctcataagtcataacattacttttctcttttgcagATTGTAGAGGGCTTCTGGTTCTTGTCACTGGGGGTGCTTTAGAGCATTTCTTGGTGTCCATTACTGTTCTGGGTCATAGAGTTTCCAATCTTTGGCAATT
                                  cattacttttctcttt  CT-rich tract
                              ataacattactttt  TA-rich tract