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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCGACTGAGGCTACTGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaacagtaaattttactttaaatattgcaagttaatgagaatgtatcattttatgttattgaaaagtgctgctaattgtcaaagaggttacca...

Basic information

species Oryza sativa
transcript LOC_Os06g35030.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g35030.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G814159_T01 (Zea mays), 5'ss of exon 8
GTTGCTCGACTGAGGCTACTGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaacagtaaattttactttaaatattgcaagttaatgagaatgtatcattttatgt-tattgaaaagtgctgctaattgtcaaagaggttacca
||| |||| ||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||| |||  | || ||| |  || ||||| |  |   |   |  |  | |  | | |    || ||  ||   |    |||   |||       ||  
GTTTCTCGTCTGAGGCTACTTGGTGATTATGTGCACTCCACATGCATCGCTTTTGTTGAGTTTGTCCAAgtaagttaaaatggaactttaaaatttaatatcgtcacaaacaaatcaatttttgtatcagacataatggcaaacacattaaatgaacaacacaaacact-
















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|58610994|gb|CK038706.1|CK038706
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTGCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|86498038|gb|CI140671.1|CI140671
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|88199202|gb|CI199052.1|CI199052
EST:     TGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|88247552|gb|CI247401.1|CI247401
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29664696|gb|CB660971.1|CB660971
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTATGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|27553952|gb|CA997852.1|CA997852
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCAT
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCAT
EST: gi|88246608|gb|CI246457.1|CI246457
EST:     TTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|218500791|gb|FG960831.1|FG960831
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29664748|gb|CB661023.1|CB661023
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|86593985|gb|CI260214.1|CI260214
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|86495703|gb|CI138336.1|CI138336
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|88243612|gb|CI244009.1|CI244009
EST:     GTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: GTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29673490|gb|CB669765.1|CB669765
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29637104|gb|CB642113.1|CB642113
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|396941304|gb|HO188513.1|HO188513
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29664747|gb|CB661022.1|CB661022
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|88236140|gb|CI235342.1|CI235342
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|38476666|gb|CF960799.1|CF960799
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|87022101|gb|CI259173.1|CI259173
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|86539456|gb|CI179662.1|CI179662
EST:     TGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|86535072|gb|CI175278.1|CI175278
EST:     GCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: GCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|29685221|gb|CB681496.1|CB681496
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
EST: gi|5003290|gb|AU068439.1|AU068439
EST:     TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAA                         GCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG
genomic: TGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCG

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: 69 (upstream exon), 62 (downstream exon)
Score: 40

GTTGCTCGACTGAGGCTACTGGGTGATTATGTGCACTCCACATGCATCGCGTTTGTTGAGTTTGTTCAAgtaagtaaaa ... gttcatgcagGCAGACTCTGCTATTCTTGCTCTGAGTTGCAGTGGCATGGTCCTTGGAGCGCTTCCCGTCAG




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