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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGACACCATTGCCCTCGTCAAGAAGACGCTGATGAACGAGCATTCTGGTATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcatttcattgacaagtttcctgttaaactaggctaatgaagttccatctgattcctgatattatgctagtgttgctgatgagctctcgtctgttttgtacag

Basic information

species Oryza sativa
transcript LOC_Os01g57890.1
intron # 11
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|88437835|gb|CI533792.1|CI533792
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88464638|gb|CI534775.1|CI534775
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88295270|gb|CI525423.1|CI525423
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|3762562|gb|AU029314.1|AU029314
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88257569|gb|CI360155.1|CI360155
EST:     TATGTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|86601822|gb|CI258498.1|CI258498
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88464137|gb|CI529526.1|CI529526
EST:     ACGGGGTT-GCCCGGTTCCACCCCTAGATTCANG-AAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGGCAGAGAAAAATCAAGAACATGCGAAGGG
genomic: ACGGGGTTAGCCC-GTTCCACCCCTAGATTCA-GAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGT-GCAGATAAAAATCAAGAACATGCGAAGGG
EST: gi|88413679|gb|CI526241.1|CI526241
EST:     TATTTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88256296|gb|CI358684.1|CI358684
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|89197716|gb|CI012497.1|CI012497
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88467463|gb|CI537105.1|CI537105
EST:     TATTTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88466502|gb|CI532309.1|CI532309
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88976303|gb|CI024520.1|CI024520
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|86526010|gb|CI166216.1|CI166216
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88449418|gb|CI533977.1|CI533977
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88320608|gb|CI525550.1|CI525550
EST:     ATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: ATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|86601815|gb|CI258491.1|CI258491
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|86525942|gb|CI166148.1|CI166148
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88375714|gb|CI525808.1|CI525808
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88437947|gb|CI536106.1|CI536106
EST:     TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: TATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
EST: gi|88254185|gb|CI352811.1|CI352811
EST:     CACCCCTAGATTCAGAAAAACACCAGAG                         GGAGAAAAGGG-GGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG
genomic: CACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGG

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: 73 (upstream exon), 60 (downstream exon)
Score: 14

ACTGACACCATTGCCCTCGTCAAGAAGACGCTGATGAACGAGCATTCTGGTATCTACGGGGTTAGCCCGTTCCACCCCTAGATTCAGAAAAACACCAGAGgtaatcattt ... ttttgtacagGGAGAAAAGGGAGGTCCGTGTGCAGATAAAAATCAAGAACATGCGAAGGGGATTCATCGGCTCCGATCACCCTGCATCTCCCAGAATTTGCTGAATTAAT




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