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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCTAAACGAGAAGAGTGACGTCTACAGTTTTGGAGTGCTACTCTTGGAAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgcacaatctcatatctgtcacccttgctgcccggtcgccattattttcttaatatggagttctcacatttaaaagcagtaaaacagtttatt...

Basic information

species Oryza sativa
transcript LOC_Os01g41730.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g41730.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 5'ss of exon 7
GCAGCTAAACGAGAAGAGTGACGTCTACAGTTTTGGAGTGCTACTCTTGGAAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgcacaatctcatat-ctgtcacccttgctgcccggtcgccattattttcttaatatggagttctcacatttaaaagcagtaa--aacagtttatt----------
   | |||| |||||||||||  ||||||| ||||| || || ||  |||||||||| || ||||||||||||||| ||||||| || ||| |  |||||||     | | |  ||  ||    ||    | |   |  ||  ||| |   |     | |||||  ||   |       || |||  | |  | | ||| ||           
CTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGATCCAGTTGACTATGGCCGGCCTGCTAATGAGgta---tttctctgtccaatgcattggggacttctttctcctttcgtcgaaagg---taaatatacaggcttgttcaagaagagctatgataagctgttcatgctcatggcag
















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|86257385|gb|CI007928.1|CI007928
EST:     GACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAG                         GTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG
genomic: GACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgc ... ctgtttgcagGTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG
EST: gi|89180073|gb|CI044352.1|CI044352
EST:     AAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAG                         GTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG
genomic: AAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgc ... ctgtttgcagGTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG
EST: gi|86528880|gb|CI169086.1|CI169086
EST:     AAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAG                         GTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG
genomic: AAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgc ... ctgtttgcagGTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAG

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: 64 (upstream exon), 54 (downstream exon)
Score: 3

GCAGCTAAACGAGAAGAGTGACGTCTACAGTTTTGGAGTGCTACTCTTGGAAGCAGTGACCGGAAGGGATCCAGTTAACTATGGTCGACCTACCGATGAGgtggacatgc ... ctgtttgcagGTGCACCTGCTGGAGTGGATCAAGCTGATGGCTAGCAGCAGAAGAGCCGAGGAGGTAGTAGACCCTGCGATGGAGGCCAAGCCAACCAAACGGCAGCTGA




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