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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCAAATGTGGAAGGAAGAATCGTTAATGTTTCATCAGAGGGGCACAGGTTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatatatggttcaatcttgtgttgtacag

Basic information

species Oryza sativa
transcript LOC_Os09g39670.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G009940_T02 (Zea mays), 5'ss of exon 4
AATCAAATGTGGAAGGAAGAATCGTTAATGTTTCATCAGAGGGGCACAGGTTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaacttttatgcactttgtttttcttttccttgttaacttccttcaaaggaattgtactgtactaatata-tggttcaatcttgtgttgtacag
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AATCAAATTTGGAAGGAAGAATTGTCAACGTGTCATCAGAGGGGCACAGACTTGCATATCGGGAAGGAATCCGTTTTGACAAGATCAACGATGAATCAGTgtatgtaattgctgtgc--tgtgattatgttctacggtctaatttacttt----gttttgaagaaaacctagccacttgttcaatcttgtgttgtgcag
















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|86828431|gb|CI278560.1|CI278560
EST:     CATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: CATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|58677683|gb|CK066370.1|CK066370
EST:     TGTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|5003515|gb|AU068664.1|AU068664
EST:     TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
EST: gi|5002903|gb|AU068012.1|AU068012
EST:     TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGNCGAGTCGGA                         GTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA
genomic: TTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCA

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), 75 (downstream exon)
Score: 50

AATCAAATGTGGAAGGAAGAATCGTTAATGTTTCATCAGAGGGGCACAGGTTTGCATATCGGGAAGGCATCCGCTTTGCCAAGATAAATGACGAGTCGGAgtatgcaact ... tgttgtacagGTACAACTCCATTGGAGCATATGGGCAGTCAAAGCTTGCAAACATTTTGCATGCGAATGAACTTGCTAGGAGATTTAAG




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