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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctccatactgattactgtcttatcactaaaattttcag

Basic information

species Oryza sativa
transcript LOC_Os06g05860.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G443985_T01 (Zea mays), 5'ss of exon 13
CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcattcgct-------atagggcagttaaactttct----------gttaatacaaaaaaaaaaaa------actctgct----ccactgctctccatactgattactgtcttatcactaaaatt--ttcag
||||||| |||| ||||| ||||| |||||||||||||||||||| |||||||| ||  |||||||||| ||||||||||| ||||| ||||| || || ||||||||  | |          ||||||   ||   || |           | |   ||  |    | |       | ||||||    | | ||| |||| |||| |||  | |    || |   | |   |||||
CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcacacccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacctacttattctgcttgaactaatgccctccgtactaattgttttgcattcgcgtcactcacttcag

upper sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G816636_T02 (Zea mays), 5'ss of exon 13
CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctccatactgat-tactgtcttatcactaaaattttcag
||||||| | || ||||||||||| ||||||||||||||||||||||||||||||||  | || ||||| ||||||||||||||||||||||| || |||||||||||  |  |||   | |||   ||      ||  | | |  |||   || |   ||  ||   ||    | ||  |   | ||| ||   || |     | |||
CACACTGCTAGCTCACAGTGTGGTCCATGGAGCCATGGCTGGATACACTGGTTTCACCATCGGTCAAGTGAATGGTCGGCATTGCTATATCCCCTTCTACgtaagtcaccc--tatgaaggagtgggacacagaattctttctactaaattcaa-catcgcagcat--ctaataagacctacacattgttttga-accacccactccag

upper sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G443985_T04 (Zea mays), 5'ss of exon 13
CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctccatactgattactgtcttatcactaaaattttcag
||||||| |||| ||||| ||||| |||||||||||||||||||| |||||||| ||  |||||||||| ||||||||||| ||||| ||||| || || ||||||||  | |  |   | ||     |      ||  |   |    |   |   |||   |  |||    |  |||| ||| |||  | |  |||||     ||  
CACACTGCTGGCTCACAGCGTGGTCCATGGAGCCATGGCTGGATATACTGGTTTTACCATTGGCCAAGTGAATGGTCGGCACTGCTACATCCCATTCTATgtaagtcacac-ccctgccggagcagggcacggaattctttttaccgcattcatcatctcagcatctgagacc--tacttatt-ctgcttga--actaatgccctc--

upper sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 5'ss of exon 12
CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctc-catactgattactgtcttatcactaaaattttcag
||| || || || || || | |||||||||||  |||||||| |||| |||||||||||||||||  || |||||  | |||   || || || ||  | || ||||  ||   |      | | | || |     |     | |   | |  || |  |     ||  |  |      ||| || ||| |                  
CACGCTTTTAGCTCAAAGCGCGGTTCATGGAGTGATGGCTGGTTACAATGGTTTCACTGTTGGCCTTGTCAATGGAAGACATACTTACATTCCCTTCAATgtgagtc--tcaggaccaaatactcatacctgagcatctcttacatttatatcaatttgggaatcctaataacatggtttgaatattgtgtag----------------

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|88578300|gb|CI687223.1|CI687223
EST:     GTTTCACTGTTGGCCAAGTANATGGTCGGCATTGCTATATCCCGTTTTAC                         AGGATCACAGAGAAGCAGAACAAAGTTTCAATTACCGATAGGATGTGGGCA
genomic: GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
EST: gi|313080385|gb|HO213393.1|HO213393
EST:     GTAAATGGTCGGCATTGCTATATCCCGTTTTAC                         AGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
genomic: GTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
EST: gi|29663408|gb|CB659683.1|CB659683
EST:     GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTAC                         AGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
genomic: GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
EST: gi|58675106|gb|CK063793.1|CK063793
EST:     GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTAC                         AGGATCACAGAGAAGCAGAACCAAGTTTCAATTACTGATAGGATGTGGGCA
genomic: GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
EST: gi|58662977|gb|CK051663.1|CK051663
EST:     GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTAC                         AGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA
genomic: GTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCA

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: 47 (upstream exon), 71 (downstream exon)
Score: 55

CACACTGTTGGCACACAGTGTGGTTCATGGAGCCATGGCTGGATACACTGGTTTCACTGTTGGCCAAGTAAATGGTCGGCATTGCTATATCCCGTTTTACgtaagtcatt ... aaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCAAGACTTCTCTCCTCAACCAACCAGCCAAGTTTCCTCAGCAAGAAAGATG




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