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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCGTCTACGAGGCTTGTCGGAGGATGGCTGCACGCAGGGTGGACGCTGTGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgaggattttctttgatgtatgtcctcaataggtgttgaattggaaaattattcatttctcactcttttgctaacctccaatcag

Basic information

species Oryza sativa
transcript LOC_Os01g69900.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G133621_T02 (Zea mays), 5'ss of exon 2
AACCGTCTACGAGGCTTGTCGGAGGATGGCTGCACGCAGGGTGGACGCTGTGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgaggattttctttgatgtatgtcctcaa-taggtgttgaattggaa-aattattcatttctcactcttttgctaacctccaatcag----------
 |||||  ||||||||||||||||||||||  |||||||||| || || ||||| ||||||||||||||||||||||| || ||||||||||| |||||||||| |||| | ||| ||   || | |  ||   |   |  ||  || ||  || |     |   |  ||     |   | |   | | |           
GACCGTGCACGAGGCTTGTCGGAGGATGGCATCACGCAGGGTAGATGCCGTGTTACTGACCGACTCCAATGCTTTGCTCTGTGGGATCCTTACCGACAAGgtga-gaggctgttccttcgggttttttttcgtctctctactgtcttagagcaactccaagtgattagctaaaaagactaaccaaatttaccgatttagct

upper sequence: LOC_Os01g69900.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171622_T01 (Zea mays), 5'ss of exon 2
AACCGTCTACGAGGCTTGTCGGAGGATGGCTGCACGCAGGGTGGACGCTGTGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgaggattttctttgatgtatgtcctcaataggtgttgaattggaaaattattcatttctcactct--------tttgctaacctccaatcag
||||||  ||||||||||||||||||||||  |||||||||| ||||| ||| ||||||| |||||||| |||||||| || |||||||| || |||||||||| | |   || ||| | | | | |      |  |||  |  || ||   |    ||||||||||| |        |||    | | |   ||||
AACCGTGCACGAGGCTTGTCGGAGGATGGCGTCACGCAGGGTTGACGCCGTGCTGCTGACTGACTCCAACGCTTTGCTCTGTGGGATCCTCACCGACAAGgtgaggggatgttccttcgctttttttttcgtgtcagtgccgccttagatgttc--ccatttctcactgtatgctgtattttgggaacgctggtcag
















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|58655058|gb|CK043738.1|CK043738
EST:     TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAG                         GACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGA
genomic: TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGA
EST: gi|29626335|gb|CB631346.1|CB631346
EST:     TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAG                         GACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
genomic: TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
EST: gi|29668008|gb|CB664283.1|CB664283
EST:     TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAG                         GACATAACCACTAGAGTAATTGCTCGCGAATTGAAGCTAGAATAGACACCT
genomic: TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
EST: gi|29641958|gb|CB646965.1|CB646965
EST:     TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAG                         GACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
genomic: TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
EST: gi|29660358|gb|CB656633.1|CB656633
EST:     TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAG                         GACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT
genomic: TGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCT

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: 66 (upstream exon), 74 (downstream exon)
Score: 37

AACCGTCTACGAGGCTTGTCGGAGGATGGCTGCACGCAGGGTGGACGCTGTGTTGCTGACCGACTCCAATGCTTTGCTGTGCGGGATCCTTACTGACAAGgtgatgagga ... ctccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCTGTTTCAAAGGTCATGACAAGAAATCCTCTCTTTGTTCTGTCTGACACAC




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