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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCGTGTATGAAGAAGGCGACGCAAGGTCAGCTTTGATTGCCATGGTTCAGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgacatcttccccctcttctatctgaaatacttatttatttccagtgtattcctcttatttctgattgatctgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g61880.2
intron # 10
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|86481607|gb|CI124240.1|CI124240
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|88270393|gb|CI385651.1|CI385651
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86865969|gb|CI335558.1|CI335558
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86887101|gb|CI325916.1|CI325916
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|87039381|gb|CI194003.1|CI194003
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|29688221|gb|CB684496.1|CB684496
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86519889|gb|CI160095.1|CI160095
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86484673|gb|CI127306.1|CI127306
EST:     CATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: CATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86480722|gb|CI123355.1|CI123355
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86834297|gb|CI344057.1|CI344057
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|88962578|gb|CI097730.1|CI097730
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|86478047|gb|CI120680.1|CI120680
EST:     AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|87028963|gb|CI351266.1|CI351266
EST:     TCACGTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTT
genomic: TCAC-TTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGG-CAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTT
EST: gi|86881864|gb|CI324129.1|CI324129
EST:     ACTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGG                         ATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: AGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
EST: gi|88259648|gb|CI363941.1|CI363941
EST:     CTCCGCCAGCA-G                         ATTCCCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG
genomic: CTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTG

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), 69 (downstream exon)
Score: 15

CAGCGTGTATGAAGAAGGCGACGCAAGGTCAGCTTTGATTGCCATGGTTCAGTCACTTCAACATGCCAAAAATGGTGTGGATATCGTCTCCGGCAGCAGGgtattcgaca ... tctgttgcagATTCGCACACATTTTGCGAGGCCTAACTGGAGAAAGGTGTTCTCTGACTTGGCGAATGCCCACAAAAACTCACGCATAG




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