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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttacctgaaaatctgtaatagtgtttttctgttctgtgtctgatgatggcagtaggctgatcagtaagtcggcatttctgtaattttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCG

Basic information

species Oryza sativa
transcript LOC_Os02g52650.1
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|86903730|gb|CI300584.1|CI300584
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACC
EST: gi|88311190|gb|CI570264.1|CI570264
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88302173|gb|CI668019.1|CI668019
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88383946|gb|CI631836.1|CI631836
EST:     CGTGCGAACTGGCTGGCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|33673864|gb|CF302103.1|CF302103
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88347524|gb|CI637464.1|CI637464
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|33683439|gb|CF311678.1|CF311678
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88341656|gb|CI641408.1|CI641408
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88336163|gb|CI647357.1|CI647357
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|58590186|gb|CF988494.1|CF988494
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|33672022|gb|CF300261.1|CF300261
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88288599|gb|CI663388.1|CI663388
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88339332|gb|CI633903.1|CI633903
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88571596|gb|CI662969.1|CI662969
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88332746|gb|CI660264.1|CI660264
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|33799384|gb|CF325551.1|CF325551
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
EST: gi|88335275|gb|CI650240.1|CI650240
EST:     CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCAC                         ATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC
genomic: CGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGC

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: 75 (upstream exon), 73 (downstream exon)
Score: 37

ATGTTTTTCAGTCTCCACGAGCTCGGATTGCAGTGCGAGCTAGCACCGAGCGTGCGACCTGGCTGCCTGGGCTCGATCCACCTCCTCACCTCGACGGCACgtcagttacc ... ttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatggcagtaggctgatcagtaagtcggcatttctgtaattttggttgtagATTACCTGGCGATTTCGGATTTGATCCCCTGGGTCTCGGGGAGGAACCGGCAAACTTGAAATGGTATGTTCAAGCCGAACTTGTGCACTGCCGGTTTGCG
              ggctgat  putative branch site (score: 37)
                                 atttctgtaatttt  TA-rich tract