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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCGGGATCTCAAGCCGGAGAACTTTTTGTTCCTCAGTAAAAGCGAGGACTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctcgaggcttcactatctcattacagaggaatggatcgcgagatatttcattgttccagtgtttgacttcatgaggattttgggtttacttag...

Basic information

species Oryza sativa
transcript LOC_Os01g43410.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43410.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G856738_T02 (Zea mays), 5'ss of exon 2
CACCGGGATCTCAAGCCGGAGAACTTTTTGTTCCTCAGTAAAAGCGAGGACTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctcgaggcttcactatctcattacagaggaatggatcgcgagatatttcattgttccagtgtttgacttcatgaggattttgggtttacttag----
|||||||| |||||||| ||||||||  ||||||||| ||| |  |||||||| |||||||||||||| |||||||| || ||||| ||||||||||| |||| ||||| ||   || |||   ||  | |      |||||||      |||  | || |     |||||||||  ||| |||| | |  || ||||      
CACCGGGACCTCAAGCCCGAGAACTTCCTGTTCCTCAATAACAAGGAGGACTCCCCGCTCAAGGCCACGGACTTCGGCCTCTCCGTCTTCTTCAAGCCCGgtgagtgcttgat-tttgacttcatctcttcttccatatggatcttaccgtatgcctttat---gatgtttgactagatgcggatgtggaattgacttgacccg

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G025387_T03 (Zea mays), 5'ss of exon 1
CACCGGGATCTCAAGCCGGAGAACTTTTTGTTCCTCAGTAAAAGCGAGGACTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctcgaggcttcactatctcattacagaggaatggatcgcgagatatttcattgttccagtgtttgacttcatgaggattttgggtttacttag---
|| |||||||||||||| ||||||||  ||||||||| ||| |  |||||||| |||||||||||||| ||||||||||| ||||| ||||||||||  |||| ||||| ||   || |||   ||  | |      ||| |||      ||      | |   | |||||||||  ||| |||| | |  || ||||     
CATCGGGATCTCAAGCCCGAGAACTTCCTGTTCCTCAATAACAAGGAGGACTCCCCGCTCAAGGCCACGGACTTCGGTCTCTCCGTCTTCTTCAAGCACGgtgagtgcttga--tttgacttcatctctgcttccatatgaatcttaccttacccttgtatatga-tgtttgactagatgtggatgtggatttgacttgaccg

upper sequence: LOC_Os01g43410.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA11G02260.1 (Glycine max), 5'ss of exon 1
CACCGGGATCTCAAGCCGGAGAACTTTTTGTTCCTCAGTAAAAGCGAGGACTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctcgaggcttcactatctcattacagaggaatggatcgcgagatatttcattgttccagtgtttgacttcatgaggattttgggtttacttag
||| | ||||||||||||||||||||  |||||||||| ||   |||| |||||||||| |||||||| ||||||||||| || || ||||||||||| |||  ||   ||   | | |   || | ||      |  ||    | | | | | ||  |  || |         ||||  |                   
CACAGAGATCTCAAGCCGGAGAACTTCCTGTTCCTCAGCAAGGACGAGAACTCGCCGCTTAAGGCCACGGACTTCGGTCTCTCTGTCTTCTTCAAGCCCGgttagt-tccgtttcgttaaattcgccttgttactgtctg--ctgtgtgctgtctcggttctcaacgaaccattttcagaacag----------------

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|29637710|gb|CB642719.1|CB642719
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGATGGAAGTGCGTATTATGTTGCACCTGAGG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
EST: gi|29681099|gb|CB677374.1|CB677374
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
EST: gi|29657259|gb|CB653534.1|CB653534
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGTTGGAAGCGCGTATTATGTTGCACCTGACG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
EST: gi|29657424|gb|CB653699.1|CB653699
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
EST: gi|29678241|gb|CB674516.1|CB674516
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
EST: gi|29668406|gb|CB664681.1|CB664681
EST:     CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTG                         GGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG
genomic: CTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGG

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), 61 (downstream exon)
Score: 40

CACCGGGATCTCAAGCCGGAGAACTTTTTGTTCCTCAGTAAAAGCGAGGACTCGCCGCTCAAGGCCACTGACTTCGGTCTTTCCGTTTTCTTCAAGCCTGgtgcgtgctc ... gatgttgcagGGGAGCATTTTAAGGACCTTGTTGGAAGTGCGTATTATGTTGCACCTGAGGTGCTGAAACGAAACTATGGAGCAGAGGCTGACATATGGAGTGCTGGCGT




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