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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATCAATTCCGAGTCGGATCCGGCTCTAAATGCTGAACATAGGAACACGAGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagcttactactattcagctattcaatttgcagatatttgttgtttcctcaaaacacaggtaacatttccttgcaactcgcag

Basic information

species Oryza sativa
transcript LOC_Os12g01170.1
intron # 5
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|89187213|gb|CI047280.1|CI047280
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88544420|gb|CI472517.1|CI472517
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88531358|gb|CI459827.1|CI459827
EST:     TCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: TCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|13165397|gb|AU174194.1|AU174194
EST:     GTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: GTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88217599|gb|CI217448.1|CI217448
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86500721|gb|CI143354.1|CI143354
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88846847|gb|CI005826.1|CI005826
EST:     GGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: GGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86503159|gb|CI145792.1|CI145792
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86524884|gb|CI165090.1|CI165090
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|29678194|gb|CB674469.1|CB674469
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88542597|gb|CI471936.1|CI471936
EST:     TGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: TGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|58693613|gb|CK082300.1|CK082300
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86525225|gb|CI165431.1|CI165431
EST:     TCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: TCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88976248|gb|CI024465.1|CI024465
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|66914385|gb|CX101233.1|CX101233
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|157651056|gb|EX450690.1|EX450690
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86261453|gb|CI017195.1|CI017195
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|88530451|gb|CI458846.1|CI458846
EST:     TTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: TTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|29678195|gb|CB674470.1|CB674470
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86504868|gb|CI147501.1|CI147501
EST:     AGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|58685986|gb|CK074673.1|CK074673
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG
EST: gi|86870305|gb|CI319411.1|CI319411
EST:     AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTAT-GGAAG                         GCCAATGCCATCGTCACAGATGTCAG
genomic: AGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG

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: 71 (upstream exon), 26 (downstream exon)
Score: 59

TAATCAATTCCGAGTCGGATCCGGCTCTAAATGCTGAACATAGGAACACGAGGAGGCCACCGTCGTCTTCTTCAGTTACAGGCTTGCCTCCTATGGGAAGgtaacagctt ... caactcgcagGCCAATGCCATCGTCACAGATGTCAG




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