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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaatgggtgtgcttgtttgtgtcatacggtaacagttgttgaattttagctgctgttatacaggatctatgaattgtgagaatggcagtaatatatttggggttaaattgtctttggtgtgctcataactgttcgaattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g64920.1
intron # 3
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|88346773|gb|CI657324.1|CI657324
EST:     TGCGAATTTCCTTGGTATAACGCCCTCCGGTTGANACGGAGGCAATTCAG                         GGTAGAGGTAGCTACGATGA
genomic: TGCGAATTTCCTTGGTATAACGCCTTC-GGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGA
EST: gi|88372509|gb|CI610832.1|CI610832
EST:     TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG                         GGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGAT
genomic: TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGAT
EST: gi|300215704|gb|HO088330.1|HO088330
EST:     TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG                         GGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCCGTCTCATTGTTGAT
genomic: TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGAT
EST: gi|87009560|gb|CI309081.1|CI309081
EST:     TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCNATTCAG                         GGTAGAGGTAGCTACGATGAGCGTGT
genomic: TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGAGCGTGT
EST: gi|29687390|gb|CB683665.1|CB683665
EST:     TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAG                         GGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGAT
genomic: TTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGAT

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: 65 (upstream exon), 50 (downstream exon)
Score: 7

ACCTGGCCGAGATTGCGAATTTCCTTGGTATAACGCCTTCGGTTGACACGGAGGCAATTCAGgtgagagaaa ... cgaattgcagGGTAGAGGTAGCTACGATGAGCGTGTAGAGCTTCTCTGTCTCATTGTTGATCTAGTTGAAGCTAGCTGCTATGCTGACAATCCAGAGTGGAG




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