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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTATGAAACATCTCGGACTATCTGCACCAGTATATGCCACAGAACCTGTATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttctagtgtccattttaacctcttgtttgtttcattgcatatagtggatctaaccattctttattttcctttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g39590.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39590.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G036050_T05 (Zea mays), 5'ss of exon 2
TGCTATGAAACATCTCGGACTATCTGCACCAGTATATGCCACAGAACCTGTATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttctagtgtccattttaacctcttgtttgtttcattgcatatagtggatctaaccattctttattttcctttgcag---------------------------------------------------------------------------------------
 ||||||||||| || || || ||||||||||| ||||| |||||||| || ||||| |||||| |||| ||| |||||||  | ||  | || ||| |||||||| |  | |||     | |   |    |       | || ||   | |   |  ||      | || | |||||  |                                                                                         
CGCTATGAAACACCTTGGGCTGTCTGCACCAGTTTATGCAACAGAACCCGTGTTTAGGCTTGGCCTTTTGACCATGTATGACCATTTCCTGTCTCGATGGgtaagcgtcatggtgcttgatattttcctagggcgtacacttttcaaccactcctttaaaatgccatatagtctccttccctccctcccaatatgctaaagaaaactggacttcactttgtagtctatatttgttcagtgtacccttacctgttaatctttcttttgcag
















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|88405194|gb|CI685648.1|CI685648
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCAT
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCAT
EST: gi|88408643|gb|CI686148.1|CI686148
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
EST: gi|88379027|gb|CI681857.1|CI681857
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CNAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
EST: gi|29665117|gb|CB661392.1|CB661392
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
EST: gi|88592675|gb|CI710796.1|CI710796
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CCAGTTTCAGATTTTGACTTGTNTACTTTGGACGATAT
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATAT
EST: gi|88579866|gb|CI691857.1|CI691857
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CAAGTTTCAGATTTTGACTTGTTTACTTTGGACGAT
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGAT
EST: gi|88344480|gb|CI677535.1|CI677535
EST:     TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGG                         CCAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC
genomic: TATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTC

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: 70 (upstream exon), 41 (downstream exon)
Score: 9

TGCTATGAAACATCTCGGACTATCTGCACCAGTATATGCCACAGAACCTGTATTTAGACTTGGCATTTTAACCTTGTATGATTACTTTATATCACGACGGgtaagctttc ... tcctttgcagCAAGTTTCAGATTTTGACTTGTTTACTTTGGACGATATTGATGCTGCATTCCAAAATGTTGTTAGATTGAAGTACTCACAGAACCACCTTTTGAATG




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