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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggtcgtctcctctcttctaccgttccataatttcctcatcatgccgatcatcttctattttgacaccacgtcatttcatccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGCCGTCATCGGGTTCTCATCGTCGTTCCGACCGAACCGAACCACCCCAAGC

Basic information

species Oryza sativa
transcript LOC_Os08g12449.9
intron # 1
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|88358004|gb|CI650740.1|CI650740
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         CCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC
EST: gi|218485628|gb|FG954877.1|FG954877
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         CCACGGGAACGCAGAGCTCACCGACGATGCTCTGGAGCGCGCACTGGACGC
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC
EST: gi|218501117|gb|FG969544.1|FG969544
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         CCACGGGAACGCAGAGCTCACCGACGATGCTCTGGAGCGCGCACTGGACGC
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC
EST: gi|218497006|gb|FG952577.1|FG952577
EST:     TCGCCATTGTGCT                         GCACGGGAACGCAGAGCTCACCGACGATGCTCTGGAGCGCGCACTGGACGC
genomic: TCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC
EST: gi|218482913|gb|FG954573.1|FG954573
EST:     CCTTGCCGCCGGCCGTGAAGACGACGTGCCGTTGCCATCGCCATTGTGCC                         G
genomic: CCTTGCCGCCGGCCGTGAAGACGACG-GCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|218482913|gb|FG954573.1|FG954573
EST:     CCTTGCCGCCGGCCGTGAAGACGACGTGCCGTTGCCATCGCCATTGTGCC                         G
genomic: CCTTGCCGCCGGCCGTGAAGACGACG-GCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|218482913|gb|FG954573.1|FG954573
EST:     CCTTGCCGCCGGCCGTGAAGACGACGTGCCGTTGCCATCGCCATTGTGCC                         G
genomic: CCTTGCCGCCGGCCGTGAAGACGACG-GCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|218482913|gb|FG954573.1|FG954573
EST:     CCTTGCCGCCGGCCGTGAAGACGACGTGCCGTTGCCATCGCCATTGTGCC                         G
genomic: CCTTGCCGCCGGCCGTGAAGACGACG-GCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|88584998|gb|CI702597.1|CI702597
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         G
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|88584998|gb|CI702597.1|CI702597
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         G
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|88584998|gb|CI702597.1|CI702597
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         G
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|88584998|gb|CI702597.1|CI702597
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         G
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcag-
EST: gi|2312233|gb|C28388.1|C28388
EST:     ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCC                         CCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGN
genomic: ACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGC

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: 67 (upstream exon), 74 (downstream exon)
Score: 15

TGAGCCGAGCAAACCGAGGGGGAGAGCTCCGGCTTTTCTTTTCCATCTCGACCTTGCCGCCGGCCGTGAAGACGACGGCCGTTGCCATCGCCATTGTGCCgtggtcgtct ... tccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGCCGTCATCGGGTTCTCATCGTCGTTCCGACCGAACCGAACCACCCCAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcatcatgccgatcatcttctattttgacaccacgtcatttcatccactgcagCCACGGGAACGCAGAGCTCGCCGACGATGCTCTGGAGCGCGCACTGGACGCCGTCATCGGGTTCTCATCGTCGTTCCGACCGAACCGAACCACCCCAAGC
                        ttttgac  putative branch site (score: 15)
                                        tttcatcc  putative PPT
                   ttctatttt  TA-rich tract