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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCATTGCTCGAACATACTCCCCGAACAGCACAAGCACAGAAAGTCCTGAGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaagaaagacacccgaacctgttgcatgcatcttgtggtgtgttgtctgtctgtcttacaccatttgccgctgttgtag

Basic information

species Oryza sativa
transcript LOC_Os04g59624.2
intron # 19
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|88843458|gb|CI372358.1|CI372358
EST:     ACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: ACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88408359|gb|CI551488.1|CI551488
EST:     AAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88289874|gb|CI525206.1|CI525206
EST:     GGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: GGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|2799889|gb|AA752878.1|AA752878
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86592938|gb|CI270495.1|CI270495
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88428353|gb|CI562619.1|CI562619
EST:     GCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: GCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88255155|gb|CI353979.1|CI353979
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88251173|gb|CI349403.1|CI349403
EST:     AGGAAATCAAGTCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGA-GCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86880798|gb|CI339145.1|CI339145
EST:     AGGAAATCAAGGTCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88380646|gb|CI521215.1|CI521215
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88321350|gb|CI535302.1|CI535302
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88274845|gb|CI388303.1|CI388303
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86853050|gb|CI324752.1|CI324752
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86592859|gb|CI270416.1|CI270416
EST:     GGAAATCAAGCCCAAAATCAACCGGCTTTCGCAAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: GGAAATCAAGGCCAAAATCAACCGGCTTTCGC-AAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88438952|gb|CI531132.1|CI531132
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88425141|gb|CI562456.1|CI562456
EST:     CGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: CGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86428913|gb|CI075594.1|CI075594
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|86845891|gb|CI347130.1|CI347130
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88829261|gb|CI074131.1|CI074131
EST:     AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: AGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
EST: gi|88440667|gb|CI552133.1|CI552133
EST:     ATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACG                         GTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA
genomic: ATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATA

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: 15 (upstream exon), 67 (downstream exon)
Score: 2

GTTCATTGCTCGAACATACTCCCCGAACAGCACAAGCACAGAAAGTCCTGAGGAAATCAAGGCCAAAATCAACCGGCTTTCGCAAACCCTTGCAAACACGgtgggagcaa ... gctgttgtagGTGCTTGTGGCGAAGCTACCAGATCGTGGAGACAAGATAAGGAGGCAGATAAATGAGCTGGACGAAAAGCTGACCGTGATCGAGTCTTCTCCGGAGCCAT




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