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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAGTTGCGAGGACAGAATTCACCAAGACTGGATTCTGATTCACCAGCAGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaacccacactcacctcatacacaaggaccaatctatttcaaatttgactaagtccatagacaaattagtttcatcaaatcaataattgaata...

Basic information

species Oryza sativa
transcript LOC_Os01g51840.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51840.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AC207628.4_FGT011 (Zea mays), 5'ss of exon 6
GCAAAGTTGCGAGGACAGAATTCACCAAGACTGGATTCTGATTCACCAGCAGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagtt-gaacccacactcacctcatac----acaaggaccaatctatttcaaatttgactaagtccatagacaaattagtttcatcaaatcaataattgaata
|| || |||||||  ||||||||||| || ||||||||||||||| | ||||| | |||||| ||||| || ||||| ||||| |||||   |||||| |||||||| |||| |||  |     || ||    |||||||             |  || |  ||||  |  | |  || ||| | |  |||    |  ||     
GCGAAATTGCGAGCCCAGAATTCACCCAGTCTGGATTCTGATTCAGCGGCAGAAAAGAATGGTTTCACCCGACGCCACTCTCTTCCTTCCAGTACAAAGAgtaagtttgaactcactgtgtttacagacgcgtacaaggaagtgagaggggtgatgttaaaaaagtaaagggtctgataagtattaaaaaaa-ggtgtttc----
















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|88993517|gb|CI110338.1|CI110338
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86881817|gb|CI324104.1|CI324104
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86864482|gb|CI334759.1|CI334759
EST:     AGACATGAATGGCTTCACACCCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86884489|gb|CI337057.1|CI337057
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86868088|gb|CI331855.1|CI331855
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|89168353|gb|CI109557.1|CI109557
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|88987370|gb|CI034334.1|CI034334
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86592238|gb|CI272584.1|CI272584
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86833517|gb|CI336306.1|CI336306
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGTTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86887777|gb|CI319727.1|CI319727
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|88983121|gb|CI020685.1|CI020685
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86833337|gb|CI334932.1|CI334932
EST:     AGACATGAATGGCTTCACACCCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|86868827|gb|CI334199.1|CI334199
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
EST: gi|38477194|gb|CF961327.1|CF961327
EST:     AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACA                         ACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA
genomic: AGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCA

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: 32 (upstream exon), 44 (downstream exon)
Score: 1

GCAAAGTTGCGAGGACAGAATTCACCAAGACTGGATTCTGATTCACCAGCAGACATGAATGGCTTCACACGCCGCCAGTCTCTACCTTCTTCTACAAACAgtaagttgaa ... catctatcagACAGAGCGATCAGAGCTGAATGGAGACGGTGGTGAGGACAACCAACTTCCATTTGAACGGTGCAACGTTGTGGTGGATGAAGTGCCCTGCTGTCCGTGAG




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