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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttttttcgaatagttattacctcgccgtcatgcctgattagttgttaacaagaccatactactggtcag

Basic information

species Oryza sativa
transcript LOC_Os02g39570.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G007647_T01 (Zea mays), 5'ss of exon 8
TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttttttc---gaatagttattacc--tcgccgtcatgcctgattagttgttaacaagaccatactactggtcag
||||||| | || ||||| || ||||||||||| |||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||     || || | ||     |     |  |  | | ||| || ||||||||    ||||    |||||
TGGACTTTGCTCGCATACCCTCTCCATCCTTGTGAATGATTGTCCTGGTGTTCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATATACAGgttttctttttttttcgaaaaagctcttcttgttgaatatagtagcaggttaattattaacaagtgggtact---tgtcag

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G407044_T02 (Zea mays), 5'ss of exon 9
TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttttttcgaatagttattacctcgccg----tcatgcctgattagttgttaacaagaccatactactggtcag
||||||||| || |||||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||    ||   |   |  || |  |    |  |||| |  ||||| || |||||  ||||||    |||||
TGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATATACAGgttttctttttcgacaaagttccctttcttgttgaatatagtgccaggctagttattgacaagtgcatact---tgtcag

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA05G30130.1 (Glycine max), 5'ss of exon 8
TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttttttcgaatagttattacctcgccgtcatgcctgattagttgttaacaagacca-tactactggtcag--------------------------------------
|||| |||||||||| ||  ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || || |||||||||||||| |   ||  |||| |  |    ||     |  |||    |   | ||  ||| |  |  || |                                         
TGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACATTCAGgttttctttttattttatt-ttataatatttgtgta----caaattgcaagcacataaatccaatgtttttgatttctctgttttctcatcttgaatctgctttgttatttccag

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G13290.1 (Glycine max), 5'ss of exon 8
TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttttt----tcgaatagttat---tacctcgccgtcatgcctgattagttgttaacaagaccata--ctactggtcag-------------------------
|||| |||||||||| ||| ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || || ||||||| |||||||    |  |||| || |    |  | ||   ||  |  |   | |  ||        |      | ||  ||                           
TGGAATTCGATCACACACTTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACATTCAGgtttgcttttttattttataatatttgtgtacaaattgcaagcacacaagtccaatcctttttggtttctctgttttctcatcttcttgaatctgctttgttatttccag

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|29676546|gb|CB672821.1|CB672821
EST:     TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAG                         AGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
genomic: TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
EST: gi|32948291|gb|BP184863.1|BP184863
EST:     TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAG                         AGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
genomic: TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
EST: gi|32948361|gb|BP184933.1|BP184933
EST:     TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAG                         AGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
genomic: TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
EST: gi|86522997|gb|CI163203.1|CI163203
EST:     TCGCAGAGGCTACAATATACAG                         AGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
genomic: TCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
EST: gi|33682200|gb|CF310439.1|CF310439
EST:     TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAG                         AGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA
genomic: TTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACA

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: 73 (upstream exon), 73 (downstream exon)
Score: 53

TGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATATACAGgttttctttt ... tactggtcagAGTCTTGCTGTAGGCCCAGCTGAAAAGTCAGGCCTTTCGCGTATTACAACAGTTGCTCCTGGAACAGATGAATCCATTGAGAAGTTAGTTCAGCAGCTTA




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