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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCACGCCTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacacacacaactctgcagatcgatttgcagatgaaaattattgcagcaacatctgactcatctcattgatctccataactctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g39300.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G137868_T04 (Zea mays), 5'ss of exon 2
GAAGCACGCCTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac-acacaactctgcagatcgatttgcagatgaaaattattgcagca----acatctgactcatctca----ttgatctccataactctgcag------
| |||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||| ||||||||||||| || ||| || | | ||| ||| || || || | | |||| | | |||| | || || || | | | ||| |
CAGGCACGCGTGGAAGCGGTACAACCTCAGTCTCGGCCTCGGCCTCAACAAGGTCGCCGGGAAGGTCTTCAGGATCGGCCATCTCGGCAACCTCAACGAGgt-agcgcactgcagagtttggcaattcgtttaattaattaa--tcagtgcaacgtactatatcttgatgctcccaaacattatttttttttcttcttctttgtcag

upper sequence: LOC_Os08g39300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G359559_T01 (Zea mays), 5'ss of exon 1
GAAGCACGCCTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac-acacaactctgcag-----atcgatttgca----gatgaa--aattattgcagcaacatctgactcatctcattgatctccataactctgcag--------------
| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||| ||||||||||||| ||| ||| || | | || ||| ||| | | || ||| | |||| | | | || ||| || || | | || | |
CAGGCACGCGTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGGAAGGTCTTCAGGATCGGCCATCTCGGCAACCTCAACGAGgt-agtgcactgcagggttgcgttaccgttatatattggcaattcgtttaattaatcagtgcaacgtactatatcttgtcttgatgctcccaaaaaaaattcttctcttctttgtcag

upper sequence: LOC_Os08g39300.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G119511_T01 (Zea mays), 5'ss of exon 1
GAAGCACGCCTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacacacacaactctgcagatcgatttgcagatgaaaattattgcagcaacatctgactcatctcattgatctccataactctgcag--------------------
| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| |||||| ||||||||||||| ||| ||| | || || | || |||| | | || ||| ||| || | || | | ||
CAGGCACGCGTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGGAAGGTCTTCAGGATCGGCCATCTCGGCAACCTCAACGAGgt-agtgcactgcaggacgggttgagttatataataatagcaattcgttaattaatcactgcaacatactat-atcttgaatgatgccccaacatttttccttctttgtcag

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|16753675|gb|BM038054.1|BM038054
EST:     GCAAGNTGTTCAGGATC-GCCACCTCGGCCACCTCAACGAG                         CTGCTATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: GCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|16578334|gb|BI812429.1|BI812429
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|18385541|gb|BM418740.1|BM418740
EST:     A-GTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|16577686|gb|BI811781.1|BI811781
EST:     A-GTCGCCGGCAAGGTGTTCAGGATC-GCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|16579460|gb|BI813555.1|BI813555
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTC-GCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|58688176|gb|CK076863.1|CK076863
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC

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: 75 (upstream exon), 72 (downstream exon)
Score: 368

GAAGCACGCCTGGAAGCGGTACAACCTCAGCCTCGGCCTCGGCCTCAACAAGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC




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