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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAACAGTCACAGAAATAGGTGATGATAAGAAAATCTTGAAGAAAGTTCTGACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaagcgtgatgcttactgatcttactattttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacag

Basic information

species Oryza sativa
transcript LOC_Os08g41390.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 6
AAAACAGTCACAGAAATAGGTGATGATAAGAAAATCTTGAAGAAAGTTCTGACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaagcg-tgatgcttactgatcttact-attttctttcctatatgtcagatagaggtcaacagtgtctgattactacctgtaatgacaaagttgcatttactgtttgacag
|| || ||||||||||| || ||||||||||||||| | ||||| ||||| | ||||||   ||| |||||||| ||||| || ||||| |||||| |||||||||  ||| | | |   |   | ||  || | ||  |  |  || |  ||     |    |      ||  |   |    | || | | || || ||   ||||||||| | |||
AAGACTGTCACAGAAATTGGGGATGATAAGAAAATCCTTAAGAAGGTTCTCAAGGAGGGAGAAGGTTATGAGCGTCCCAACGAGGGTGCTGTTGTTGAAGgtatgctcaagtggtcaaagtacttaattgtaatgatgctagtagctgttggttcttgactcctttcagttgattaggtttatcttgcactcactaaattatgtttactgtt-ggcag
















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|454468|gb|D28191.1|D28191
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAANGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58677816|gb|CK066503.1|CK066503
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58695757|gb|CK084444.1|CK084444
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58695816|gb|CK084503.1|CK084503
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|29630489|gb|CB635498.1|CB635498
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58686617|gb|CK075304.1|CK075304
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|58682283|gb|CK070970.1|CK070970
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|2427305|gb|C71768.1|C71768
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTNTTAAAG                         TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC
EST: gi|29628610|gb|CB633621.1|CB633621
EST:     GACGGAGGGTACAGGGTATGAGCGGCCCAATGAATGTGCAGTTGTTGAAG                         TCAAAATAACTGGAAAACTTCAAGATGGTACAATATTTACAAAGAACGGGC
genomic: GACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGC

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), 75 (downstream exon)
Score: 155

AAAACAGTCACAGAAATAGGTGATGATAAGAAAATCTTGAAGAAAGTTCTGACGGAGGGTACAGGGTATGAGCGGCCCAATGAAGGTGCAGTTGTTAAAGgtatgccaaa ... tgtttgacagTCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAG




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