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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCCTTTTATTATGGGTTATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcgtattcctaagaagtttgccttagtatgccagtggctagagctgtgcactgattttgctgccgctgtcctaatttcag

Basic information

species Oryza sativa
transcript LOC_Os11g16370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 4
GAGTCCTTTTATTATGGGTTATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcgtattcctaagaagtttgc-cttagtatgccagtggctagagctgtgcactgattttgctgccg-------ctgtcctaatttcag
||||||||||||||||| ||  | ||||| ||||| |||||||||||||||||||| |||||||||||||||   || | |  |   |  |   ||    ||| ||| | |||  | |||| | |||||||| | |||||| |       || | |  |||||||
GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTCCATGTTCATGATTATAATTTTGATCATCCAGgtcgaattcatccttacacaagaattatatttactatcctagtcccaagagttctgcactgaatgtgctgctgtatctatcttttcctatttcag

upper sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 3
GAGTCCTTTTATTATGGGTTATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcgtattcctaagaagtttgcct-tagtatgccagtggct---agagctgtgcactgattttgctgccg---ctgtcctaatttcag
||||||||||||||||| ||  | ||||| ||||| || ||||| ||| |||||||||||||||||||||||  ||| | |  | | |  |   ||   | || | | | | | ||    |||| | |||||||| | |||||| |   || | |  |||||||
GAGTCCTTTTATTATGGATTGACGGATGAAGAATTAGTACATGTCCATAATTATAACTTTGATCATCCAGgt-cgattcatccttccacaagaattatatgtactgtcctactagccccaagagttctgcactgaatatgctgctgtgtcttttcctatttcag
















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|88301528|gb|CI597221.1|CI597221
EST:     ATCTGATGAGGAATTGGTC-ATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTA
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTA
EST: gi|117233504|gb|CT842322.1|CT842322
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
EST: gi|58689975|gb|CK078662.1|CK078662
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
EST: gi|58655184|gb|CK043864.1|CK043864
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
EST: gi|58653267|gb|CK041947.1|CK041947
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATAC
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATAC
EST: gi|58693385|gb|CK082072.1|CK082072
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
EST: gi|58662773|gb|CK051459.1|CK051459
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
EST: gi|58666921|gb|CK055607.1|CK055607
EST:     ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAG                         ATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG
genomic: ATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATG

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: 46 (upstream exon), 63 (downstream exon)
Score: 37

GAGTCCTTTTATTATGGGTTATCTGATGAGGAATTGGTCCATGTTCATGATTATAACTTTGATCATCCAGgtatgatgcg ... ctaatttcagATGCATTTGATACGGAGTTACTACTCTCTTGTATGGAGAACTTGAAACATGGCAAGGCTGTGGACATTCCTAATTATAACTTCAAAACATATAAGAGTGT




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