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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcgacaactatatacagattttgcatcatattttacacatgattcttaccctgagaaacgctgcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAGGTGGTGTGTTCCTTGAACAACCGGGACGAATGCTTGGCATGTGGTAGTT

Basic information

species Oryza sativa
transcript LOC_Os02g56100.1
intron # 16
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|88509031|gb|CI436537.1|CI436537
EST:     GCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88508770|gb|CI436276.1|CI436276
EST:     GCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88480030|gb|CI417301.1|CI417301
EST:     GCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88505269|gb|CI432775.1|CI432775
EST:     GACACTACTCTCCTCAAG                         GATAACCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88470170|gb|CI407441.1|CI407441
EST:     GCGCTGCGGCCGATGCAATCAAATTCACANTGGACACTACTCTCCTCAAG                         GATAACCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88474972|gb|CI412243.1|CI412243
EST:     GCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: GCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88520109|gb|CI447763.1|CI447763
EST:     CTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: CTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88516157|gb|CI443811.1|CI443811
EST:     TTCACAGTGGACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
genomic: TTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG
EST: gi|88479118|gb|CI416389.1|CI416389
EST:     GACACTACTCTCCTCAAG                         GATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTGTAAAATGGCAGAG
genomic: GACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAG

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: 31 (upstream exon), 45 (downstream exon)
Score: 1

GGCCTGAAAACTGGAATGTATTATCTAAGAACACGCGCTGCTGCCGATGCAATCAAATTCACAGTGGACACTACTCTCCTCAAGgtgattcgac ... gcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAGGTGGTGTGTTCCTTGAACAACCGGGACGAATGCTTGGCATGTGGTAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgcatcatattttacacatgattcttaccctgagaaacgctgcatgtgcagGATAAGCAGCATAATGCAGAGGAAGAGGATGTCCAGTCTAAAATGGCAGAGGTGGTGTGTTCCTTGAACAACCGGGACGAATGCTTGGCATGTGGTAGTT
                         ttcttac  putative branch site (score: 1)
       atcatatttta  TA-rich tract