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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgcttatgactcctactaactgacatgtgaacagtgggcattttctgacaacaatttgaataaattacag

Basic information

species Oryza sativa
transcript LOC_Os01g56490.1
intron # 31
splice site 5'
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|58662695|gb|CK051381.1|CK051381
EST:     GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|86826737|gb|CI364258.1|CI364258
EST:     CTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: CTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|88838574|gb|CI375122.1|CI375122
EST:     TGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: TGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|88267518|gb|CI379453.1|CI379453
EST:     AAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: AAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|88465709|gb|CI524659.1|CI524659
EST:     GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|33810375|gb|CF331078.1|CF331078
EST:     GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|33812341|gb|CF332060.1|CF332060
EST:     GTCACCCC-AAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|218495798|gb|FG954256.1|FG954256
EST:     GACTTGAGCACTCAGACGTCATCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGA
EST: gi|33810373|gb|CF331077.1|CF331077
EST:     GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTC
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTC
EST: gi|86887682|gb|CI311889.1|CI311889
EST:     GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
EST: gi|9865065|gb|AU100815.1|AU100815
EST:     GACTTGAGCACTCAGNCGTCACCCCAAAAAGGTCATGCTTGTCCAATCAG                         AACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA
genomic: GACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTA

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: 71 (upstream exon), 21 (downstream exon)
Score: 4

AAAGATGTTTATGGACCATGGGAACAATGCCTAGGACTTGAGCACTCAGACGTCACCCCAAAAAGGTCATGCTTGTCCAATCAGgtatacgctt ... taaattacagAACCGCAATTCTTTCGATAAGGCTGTGAAGATTTTCAACTAGAGGTGGTTAAATTATCACATTTATGTGATGTATCCAGAGCTCTCACCTGCCGTAGTAC




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