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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatccattttcccctctatctcgccacatttcctgtgcgtgcatttgctcgtttgccgtaatctttactcactaccttagcaccttgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGAAGTATTAGTAGCTCCCACTTTTATGCGACCTGTGCGATAACAGGACGCC

Basic information

species Oryza sativa
transcript LOC_Os02g40680.1
intron # 6
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|89178486|gb|CI015191.1|CI015191
EST:     CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
EST: gi|88262730|gb|CI366504.1|CI366504
EST:     CGATCAAATTGATTGGGACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
EST: gi|38476753|gb|CF960886.1|CF960886
EST:     CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
EST: gi|218495835|gb|FG960251.1|FG960251
EST:     CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
EST: gi|58596171|gb|CK006699.1|CK006699
EST:     CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
EST: gi|88988639|gb|CI039058.1|CI039058
EST:     CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAG                         GTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA
genomic: CGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGA

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: 72 (upstream exon), 69 (downstream exon)
Score: 4

TTTCAGCGGAAACTGGAAGGTATGAAAAGGAAGATTGTTGAGAACATTGACGATCAAATTGATTGGAACGTCAATGGACACCACAAGCGGTTAGCATCAGgtaatccatt ... tgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGAAGTATTAGTAGCTCCCACTTTTATGCGACCTGTGCGATAACAGGACGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttgctcgtttgccgtaatctttactcactaccttagcaccttgcctcgcagGTTTCACTGCCAGAACAGAAGACAGTCAAGATGTTGTGAATGTCTTAAAGAAGTATTAGTAGCTCCCACTTTTATGCGACCTGTGCGATAACAGGACGCC
                         tactcac  putative branch site (score: 4)
                                          ccttgcctc  putative PPT
                  taatcttta  TA-rich tract