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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgctttttgctgcctcccattcctcacttctctacctgtcattaatctggtttattccaatttcgtgttgatttcgctaaccaattatgctgctatgtcgttggttgattcgcgtcatcctttgcttgctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAGGTGACAATAGGTCCCTGGATAGACAACGGCTTCTACTACGACTTCGACA

Basic information

species Oryza sativa
transcript LOC_Os02g33500.1
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|29624982|gb|CB629993.1|CB629993
EST:     TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACC                         TGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
genomic: TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
EST: gi|58604883|gb|CK032916.1|CK032916
EST:     TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACC                         TGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
genomic: TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
EST: gi|29643996|gb|CB649003.1|CB649003
EST:     TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACC                         TGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
genomic: TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
EST: gi|29613162|gb|CB618175.1|CB618175
EST:     TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACC                         TGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
genomic: TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
EST: gi|58611796|gb|CK039508.1|CK039508
EST:     TGCTCCCCAACAACGAGTCCTCCGACCGACTGCTCCGCATCCGGCACACC                         TGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG
genomic: TGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAG

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: 71 (upstream exon), 61 (downstream exon)
Score: 20

GGCGGGATCCGACGGCAAGGGGGATGGGATTGGGGAGGAGGAGCGCGTCGTGCTCCCCACCAACGAGTCCTCCGACCGCCTGCTCCGCATCCGCCACACCgtacttgctt ... gctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAGGTGACAATAGGTCCCTGGATAGACAACGGCTTCTACTACGACTTCGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatgctgctatgtcgttggttgattcgcgtcatcctttgcttgctgctctagTGTGCGCATGTGATGGCCATGGCCGTCCAGAAGCTGTTCCCCAACTCCAAGGTGACAATAGGTCCCTGGATAGACAACGGCTTCTACTACGACTTCGACA
                    ggttgat  putative branch site (score: 20)
                                              ctgctct  putative PPT