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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTTATGAGCTATCCCCTGATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattgcctaggatgaaagaaatctgaagtatggcttcatttatattttattggcatttatttatttcggtgtgttatggtacgtataatggttag

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 12
GGTTTTATGAGCTATCCCCTGATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattgcctaggatgaaagaaatctgaagtatggcttcatttatattttattggcatttatttatttcggtgtgttatggtacgtataatggttag------------
| || |||||||  ||||||||| |||| ||||  || || || || ||||||||| | |||||||||||||||||||    |   |||      ||     || ||   |   ||   ||  |  | |  |  ||| |||  |      |   |   | |  |  ||              
GTTTCTATGAGCGGTCCCCTGATTTGCTAGAGGCTGCAGTAGCTCACATCCAGTTGGTCATTGTAACCAAgtgagtatcaattca-atgttgtttatgaagtgtgtgctgttcctttccttccacggtctctgttttttttttggaaaaaaaaatgattcttctttttttatactgctatag
















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|218483555|gb|FG957326.1|FG957326
EST:     CTTGAGGTGGC-GNGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: CTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|88355636|gb|CI628920.1|CI628920
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|58670583|gb|CK059269.1|CK059269
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|218498819|gb|FG964003.1|FG964003
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|29641670|gb|CB646677.1|CB646677
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAAGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|27410222|gb|CA923292.1|CA923292
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|58598568|gb|CK009096.1|CK009096
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
EST: gi|87023655|gb|CI286406.1|CI286406
EST:     GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAA                         GTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA
genomic: GATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCA

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: 70 (upstream exon), 70 (downstream exon)
Score: 103

GGTTTTATGAGCTATCCCCTGATCTGCTTGAGGTGGCGGTGGCCCATATCCAGTTGATAATTGTAACCAAgtgagtattg ... taatggttagGTTCATAGAGAAATTAGAGCAGGACATCCCTGGTGAGGGAGTGAAGGAGCAACTGTGCATCCTTTGCAATGTGTACGCGCTGTATCTTGTTCACAAGCAT




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