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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttctgcttcattttcattttactttgttattgatggttttgttttatctttcgatttgtgatgtcgggaaagctgggcatcatttgctcctgactttcttgttttccagTTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTAAGTTCATAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g08990.1
intron # 5
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|29627798|gb|CB632809.1|CB632809
EST:     CCTGAAGGAAAACATGGAAGCCATAGTTGAACAGCGATATCATATAAATG                         TTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTA
genomic: CCTGAAGGAAAACATGGAAGCCATAGTTGAACAGCGATATCATATAAATGgtttgttttc ... tgttttccagTTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTA
EST: gi|29674312|gb|CB670587.1|CB670587
EST:     TCTGAAGGAAAACATGGAAGCCATAGTTGAACAGCGATATCATATAAATG                         TTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTA
genomic: CCTGAAGGAAAACATGGAAGCCATAGTTGAACAGCGATATCATATAAATGgtttgttttc ... tgttttccagTTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTA

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: 61 (upstream exon), 71 (downstream exon)
Score: 29

GGGTGGTTGTTTCAACTGAAGAGATTCAGTCAATGGTCACTGATATCCTGAAGGAAAACATGGAAGCCATAGTTGAACAGCGATATCATATAAATGgtttgttttc ... tgttttccagTTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTAAGTTCATAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgatgtcgggaaagctgggcatcatttgctcctgactttcttgttttccagTTGGCAGCTTGTGCGGACAGGTTAGGAAGTGGCACCCCTGGGGCGATGCTAAGTTCATAAAG
                                 tcctgac  putative branch site (score: 29)
                                ctcctgactttcttgt  CT-rich tract
                        atcattt  TA-rich tract