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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctaccagtaaaaaagaaaagggaaaagtttcatctgttgcactatatgcaatattccatatatggcttatgaattttgcaatatatcacaggtctcttctgtcaatccactgaatattttcatattgttattgtgatttatttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCCTTGGTTGCTCTTGTG

Basic information

species Oryza sativa
transcript LOC_Os05g49270.1
intron # 13
splice site 3'
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|87009920|gb|CI277421.1|CI277421
EST:     CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
EST: gi|86501749|gb|CI144382.1|CI144382
EST:     CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
EST: gi|87021810|gb|CI277977.1|CI277977
EST:     TGGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: T-GGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
EST: gi|86890215|gb|CI321392.1|CI321392
EST:     TGCAGTTGCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: TGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
EST: gi|29687040|gb|CB683315.1|CB683315
EST:     CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: CTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
EST: gi|86890239|gb|CI321416.1|CI321416
EST:     GCTGTTGTATTTTTCCTCAAG                         GATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC
genomic: GCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCC

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: 60 (upstream exon), 45 (downstream exon)
Score: 7

ATCTCTTCTGCTGGGATGACTCTAAGCCTCCTTGCAGTTGCTGTTGTATTTTTCCTCAAGgtaagttcct ... tttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCCTTGGTTGCTCTTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtcaatccactgaatattttcatattgttattgtgatttatttgtttcagGATAGCATTTCACAAGATTCTCACATGTACTACACCTTAAGTATGATCTCCTTGGTTGCTCTTGTG
                                             tttgtttc  CT-rich tract
                 aatattttcatattgt  TA-rich tract