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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacagtctcttcgctatgaattattaactagctgattgatatcaactactttacgcatatagtctgggtgtgcctctacagcgttatgctcttttcttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCACCACCCAATTGATCGTTCTGCTCCCGATCCCTCTGCAAACTGGGAGCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g42970.1
intron # 10
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|86487942|gb|CI130575.1|CI130575
EST:     GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|38481213|gb|CF965302.1|CF965302
EST:     GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|87024730|gb|CI259445.1|CI259445
EST:     CTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: CTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|218499838|gb|FG962434.1|FG962434
EST:     GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|86540396|gb|CI180602.1|CI180602
EST:     GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|86540864|gb|CI181070.1|CI181070
EST:     GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: GACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
EST: gi|88850558|gb|CI093239.1|CI093239
EST:     ATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT                         TTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC
genomic: ATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCAC

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: 29 (upstream exon), 75 (downstream exon)
Score: 3

GTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGATgtatgacagt ... cttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCACCACCCAATTGATCGTTCTGCTCCCGATCCCTCTGCAAACTGGGAGCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacgcatatagtctgggtgtgcctctacagcgttatgctcttttcttaatgcagTTCTACATGAAGACAGGATTTTGCAAGTTTGCTGACCGATGCAAGTTTCACCACCCAATTGATCGTTCTGCTCCCGATCCCTCTGCAAACTGGGAGCCTG
                                            tcttaat  putative branch site (score: 3)
                                 ttatgctcttttctt  CT-rich tract
                                         ttttcttaat  TA-rich tract