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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTACTTCGTTATATCCACCAGGACCTCAAACAATAGGGGGTTGGCAGAGAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctatcattctcatattagcgatttattgtgtatctgatgttgatgtttttcctaactagataaattatttaccaattttag

Basic information

species Oryza sativa
transcript LOC_Os02g11820.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G341732_T01 (Zea mays), 5'ss of exon 1
CTTTACTTCGTTATATCCACCAGGACCTCAAACAATAGGGGGTTGGCAGAGAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctat--cattctcatattagcgatttattgtgtatctga--tgttgatgtttttcctaactagataa--attatttaccaattttag
||||||| |  |||||||||||  | ||||||  ||    || ||||||||| | ||||| |||||||||||||| ||||||| |||||   ||| | ||||||| ||  |||||| || |  |  |  |||| || | ||||  ||||  ||| |||      || ||||  | |  |   |||||  ||
CTTTACTGCACTATATCCACCATCAACTCAAATGATGCCTGGCTGGCAGAGAGCTCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgtcattctaatttgtgtaacatattatgcacctgagctgttactgtctttttatcttacataaggaatgctcttcaattccag

upper sequence: LOC_Os02g11820.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G043056_T02 (Zea mays), 5'ss of exon 10
CTTTACTTCGTTATATCCACCAGGACCTCAAACAATAGGGGGTTGGCAGAGAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctat--cattctcatattagcgatttattgtgtatctga-----tgttgatgtttttcctaactagataaattatttaccaattttag
||||||| |  |||||||||||  | ||| ||  ||    |||||||||||| | ||||| |||||||||||||| ||||||| |||||   ||| | ||||||| ||  |||||||||||  |  |  ||||||| | ||||     |  ||   ||||  || ||   |  |||  | | |||       
CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgtcattctcatatgtgtaacatattgtgcacctgagttggtactgcctttttatcttacacaaggaatactcttccag------
















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|58674115|gb|CK062801.1|CK062801
EST:     GCCATATCAGACTGCAATG                         GGAATGCAAGCATATCCTCATGATGGCATTTGCTCAACCTGCATATCAACA
genomic: GCCATATCAGACTGCAATGgtatctatca ... ccaattttagGGAATGCAAGCATATCCTCA-GATGGCATTTGCTCAACCTGCATATCAACA
EST: gi|86837601|gb|CI345784.1|CI345784
EST:     GAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATG                         GGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA
genomic: GAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctatca ... ccaattttagGGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA
EST: gi|86596732|gb|CI286645.1|CI286645
EST:     GAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATG                         GGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA
genomic: GAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctatca ... ccaattttagGGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA
EST: gi|29678350|gb|CB674625.1|CB674625
EST:     AACACCCNCA-TTTGGAATGGGATATGCCATGCCATATCAGACTGCAATG                         GGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA
genomic: AACACCC-CAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctatca ... ccaattttagGGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAA

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: 74 (upstream exon), 63 (downstream exon)
Score: 30

CTTTACTTCGTTATATCCACCAGGACCTCAAACAATAGGGGGTTGGCAGAGAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctatca ... ccaattttagGGAATGCAAGCATATCCTCAGATGGCATTTGCTCAACCTGCATATCAACAACCTGTATATCCGCAACAGCAACATGCATACCCCCAACCTGCGAAAGCAT




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