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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag

Basic information

species Oryza sativa
transcript LOC_Os10g32880.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag
|||||||| |||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||| | |  |      |  || |  |||| ||||   ||||| |||  | |||| ||||   |  ||||||| |||||
TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatttagataaaagctacgtgcacaatgacaaatttatttagt-ttctaatat---ttccatcactttacag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G037698_T02 (Zea mays), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag
|| ||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |  |      |  || || |||| | |||| | ||| |||    |||| |||| | |  ||||||| | |||
TCGAATGTCGCGAAGTTTGAGGGGCATGTAGGACCAGTCACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTAGCGgtatgtaatttagataaaagctatgtgcacagtgttaagtttgtttagc-ttctaatat-tttgccatcactttgcag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AC205703.4_FGT004 (Zea mays), 5'ss of exon 4
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag
|||||| | |||||||||||||| ||||| ||||| || |||| |||||| ||||||||||||||||||||||| |||||| | |  |      |  || |  |||| ||||   ||||| |||  | |||| ||||   |  ||||||| |||||
TCAAATATCGCAAAGTTTGAGGGTCATGTCGGACCGGTCACTGTTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCGgtacgtaatttagataaaagctacgtgcacaatgacaaatttatttagt-ttctaatat---ttccatcactttacag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G26870.1 (Glycine max), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag
 |||||||||| | |||||| || |||| ||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||| |        ||  | | |  | |  ||| |   ||| |    |||| | |  | | |      | | |||||
GCAAATGTTGCTAGGTTTGATGGACATGCTGGGCCAGTAACTGCCATATCTTTCTCTGAGAATGGATACTTCCTTGCGgtatgcaagaaaatgtaacg-agtaagtatgatgattgttttatacagtatttttaattgtattcttaaattctacag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA20G21330.1 (Glycine max), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccatagtgcaatctgcaaaatgttgaatttcttttt----tattctgatatatgtatcatcactgtacag
 |||||||||| | |||||| || |||| ||| ||||| ||||| || || |||||||| ||||| |||||||||||||||||         | | || ||   | ||| | |     || ||| |    |||||| || | |        | |  ||||
GCAAATGTTGCTAGGTTTGACGGACATGCTGGGCCAGTAACTGCCATATCTTTCTCTGAGAATGGATACTTCCTTGCGgtatgtgag-----aaaatgtaactagtaaagtatgatgattgtttatacagtattcttat-tgtactcttaaatttgacag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT2G33340.1 (Arabidopsis thaliana), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctc-catagtgcaatctgcaaaatgttgaatttcttttttattctgatatatg-tatcatcactgtacag----------
 ||||||| || |||||||| || ||   |||   ||| || ||||| || ||||||||||||||||||||||| |||||  | |  |    || | | | |   | | |   |  |  ||   || |  |   ||  ||| | |  |   ||| | |          
GCAAATGTGGCTAAGTTTGATGGACACACTGGGGAAGTTACAGCTATATCTTTCTCTGAAAATGGTTACTTCCTCGCGgtgagtactttgaacaaaatacgagaag-agagaatacagcttaagttatgcttacatgaatgattttctttttgtcctggaattgacag

upper sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 5'ss of exon 14
TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatctctccat-----agtgcaatctgcaaaatgttgaatttcttttttattctgatatatgtatcatcactgtacag
 ||||||| ||||  ||||| ||||| |||||  | || |||||||| || ||||| ||||||||||||||||||||||||||  | |  | |      |||| | | ||  |     |||  | | ||| |  | |  |||   |    |   |      
GCAAATGTGGCAAGATTTGACGGGCACGTTGGGGCTGTAACTGCTATATCTTTCTCAGAAAATGGTTACTTCCTTGCGgtatgtgttttcctaattagaagtgta-tatgtgaggaagtgacatacatttctgattttttatgcttgatgtttttag----

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|4879072|gb|AU063371.1|AU063371
EST:     TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG                         ACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
genomic: TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatct ... cactgtacagACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
EST: gi|4879056|gb|AU063355.1|AU063355
EST:     TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG                         ACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
genomic: TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatct ... cactgtacagACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
EST: gi|58686960|gb|CK075647.1|CK075647
EST:     TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG                         ACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
genomic: TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatct ... cactgtacagACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
EST: gi|25797187|gb|CA753148.1|CA753148
EST:     TNGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG                         ACTGCTGCTCTTGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC
genomic: TTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatct ... cactgtacagACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAAC

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), 68 (downstream exon)
Score: 39

TCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCGgtatgaatct ... cactgtacagACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAACTTTAGGACGATATCACCTTATGACTCAGACACGCCAACAAATTCTG




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