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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaccttgcaatcttgagccaggcagatcgttcatcttcagtttgattgaacaaattcttcaacttgtagGGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATCAGACATGAGACCAATATGGGATGGGCACAGCAGTGATGACATGTGTCAG

Basic information

species Oryza sativa
transcript LOC_Os08g32600.1
intron # 12
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|58653648|gb|CK042328.1|CK042328
EST:     GAAACCTCTGAGCTTCCGGCATACGATAGGCCAACTGGTGACCT                         GGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATC
genomic: GAAACCTCTGAGCTTCCGGCATACGATATGCCAACTGGTGACCTgtaagtacct ... caacttgtagGGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATC
EST: gi|58655950|gb|CK044630.1|CK044630
EST:     GAAACCTCTGAGCTTCCGGCATACGATATGCCAACTGGTGACCT                         GGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATC
genomic: GAAACCTCTGAGCTTCCGGCATACGATATGCCAACTGGTGACCTgtaagtacct ... caacttgtagGGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATC

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: 44 (upstream exon), 8 (downstream exon)
Score: 2

GAAACCTCTGAGCTTCCGGCATACGATATGCCAACTGGTGACCTgtaagtacct ... caacttgtagGGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATCAGACATGAGACCAATATGGGATGGGCACAGCAGTGATGACATGTGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagccaggcagatcgttcatcttcagtttgattgaacaaattcttcaacttgtagGGGCTTGAATCATTCTGGCAACCCAAGTAACTTGAATTCCTATAAGTCATCAGACATGAGACCAATATGGGATGGGCACAGCAGTGATGACATGTGTCAG
                         gtttgat  putative branch site (score: 2)
                                        ttcttc  putative PPT
                                  aacaaatt  TA-rich tract