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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGCCAGTGTCACTGAGGATCTTTCCAGGTGTTTAATCAGAGACAACAATCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatctgtccttaccagttgactttaacctgcaattaaacttgtatcctccattatatctttcatacattgtgtgactcaagatagattttgcacgttacctatcttccag

Basic information

species Oryza sativa
transcript LOC_Os05g05160.1
intron # 9
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|58676444|gb|CK065131.1|CK065131
EST:     TCTAAAATCACAGGATACTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GGGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|88828566|gb|CI073436.1|CI073436
EST:     TAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|89177111|gb|CI043614.1|CI043614
EST:     AAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: AAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|58685382|gb|CK074069.1|CK074069
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|86898584|gb|CI292404.1|CI292404
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|58668494|gb|CK057180.1|CK057180
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|38477994|gb|CF962127.1|CF962127
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|58690737|gb|CK079424.1|CK079424
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|58686748|gb|CK075435.1|CK075435
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
EST: gi|58604748|gb|CK015276.1|CK015276
EST:     TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAG                         GTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA
genomic: TCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTA

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: 75 (upstream exon), 72 (downstream exon)
Score: 58

ACAGCCAGTGTCACTGAGGATCTTTCCAGGTGTTTAATCAGAGACAACAATCTAAAATCACAGGATTCTGCTTCAGTCGGTGCAAGCAGAATCCCTCAAGgttagcatct ... tatcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTAACTGTTCGACATCCGCTGCTGAGCAACAATATGAGCAGCGAAGGGTTGT




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