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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTACCACTTTGCAAAGGACACCATGAACCTTGCATTCCAAGGTCTGTGAAGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAGgtatttaacttcagaatcaactgctcaattcacatccgaggaacaatcataaaggtagttcatattgacagaggatgaaaagcattggcattgtgctgtaaccaccatgtattgtctatgacag

Basic information

species Oryza sativa
transcript LOC_Os09g36530.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36530.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G103458_T01 (Zea mays), 5'ss of exon 9
CCTACCACTTTGCAAAGGACACCATGAACCTTGCATTCCAAGGTCTGTGAAGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAGgtatttaact--tcagaatcaactgctcaattcacatccgaggaaca-atcataaaggtagttcatattgacagaggatgaaaagcattggcattgtgctgtaaccaccatgtattgtctatgacag
 ||||||| ||||||||| ||   |||||| |||||||| |||||||||||||| ||| ||||||| || ||  | |||||||||||||| ||||||||||||      |  | | |||  |||||| | |  ||||   |  | ||   |||  |||  |   ||  |  ||  |     |   | ||   |    | | || |||                    
ACTACCACGTTGCAAAGGGCATAGTGAACCATGCATTCCGAGGTCTGTGAAGAAGGGCCCTAATATAGGCCGTTTGTTCTATGTCTGTGCTCGTGCTCAGgtacacgtgtacttacaatttactgcttagtagacataacatcatcatgccattcagg-ggcgaatcctaccatggcgcaca---ccttaaga----gatatacccat-------------------
















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|88261828|gb|CI365404.1|CI365404
EST:     AGAAA-GCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCA-                         GGACCTGCATCAAACCAAGAACCAAATTGTGGTCACTTTCAGTGGGCCACT
genomic: AGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAGgtatttaact ... tctatgacagGGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
EST: gi|88969421|gb|CI382959.1|CI382959
EST:     TTCTATTTCTGTGCCCGTGCTCAG                         GGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
genomic: TTCTATGTCTGTGCCCGTGCTCAGgtatttaact ... tctatgacagGGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
EST: gi|88271762|gb|CI387815.1|CI387815
EST:     TTCTATGTCTGTGCCCGTGCTCAG                         GGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
genomic: TTCTATGTCTGTGCCCGTGCTCAGgtatttaact ... tctatgacagGGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
EST: gi|86437027|gb|CI118749.1|CI118749
EST:     AGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAG                         GGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT
genomic: AGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAGgtatttaact ... tctatgacagGGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACT

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), 73 (downstream exon)
Score: 4

CCTACCACTTTGCAAAGGACACCATGAACCTTGCATTCCAAGGTCTGTGAAGAAAGGCTCTAATATTGGTCGCCTATTCTATGTCTGTGCCCGTGCTCAGgtatttaact ... tctatgacagGGACCTGCATCAAACCAAGAAGCAAATTGTGGTCACTTTCAGTGGGCCACTGTTAAGTCTAAAGAGAAACGCCGGTGACTAATTTCTCTTTTATCGCATA




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