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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaatgtgttctgatcagtgagatgtactaggaatactaaaataaaggacacattgatattataaaaaggcaagatttctgagtaaactgaagatgatatatctctttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATCACGGACATCTTCTCGACTATTTAACCATGCACCATCACCGAGATTTCGC

Basic information

species Oryza sativa
transcript LOC_Os05g26914.1
intron # 2
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|58680824|gb|CK069511.1|CK069511
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58662397|gb|CK051077.1|CK051077
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58685204|gb|CK073891.1|CK073891
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58673557|gb|CK062243.1|CK062243
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58608089|gb|CK036122.1|CK036122
EST:     GATTTCTGGTGTCAAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGGTAGTTTACAATC
genomic: GATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|29685207|gb|CB681482.1|CB681482
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58608887|gb|CK036920.1|CK036920
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCAAAAAGTGG                         TAGTGGAGGCAGGCTTAAACAC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACAC
EST: gi|58692323|gb|CK081010.1|CK081010
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|29620923|gb|CB625934.1|CB625934
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCAAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|88451449|gb|CI565502.1|CI565502
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTACACACCTTGTATCAC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCAC
EST: gi|29680449|gb|CB676724.1|CB676724
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|58605038|gb|CK033071.1|CK033071
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTAGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|29681007|gb|CB677282.1|CB677282
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|29680374|gb|CB676649.1|CB676649
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
EST: gi|29635402|gb|CB640411.1|CB640411
EST:     CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGG                         TAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC
genomic: CTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATC

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), 55 (downstream exon)
Score: 60

TGGCCCCCAAACTTGGGGAAAAACCTCAGCTGTTGCCCAGGTCACCTGCACTTACAAGAGTTATTTATGCTGATCCAAGATTTCTGGTGTCGAAAAGTGGgtatgtgaat ... ttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATCACGGACATCTTCTCGACTATTTAACCATGCACCATCACCGAGATTTCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaaaggcaagatttctgagtaaactgaagatgatatatctctttttgtgcagTAGTGGAGGCAGGCTTAAACACCTTGTATCACCTACTGCTAGTTTACAATCACGGACATCTTCTCGACTATTTAACCATGCACCATCACCGAGATTTCGC
                                      tatctcttttt  CT-rich tract
                                   atatatctcttttt  TA-rich tract