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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacag

Basic information

species Oryza sativa
transcript LOC_Os01g56630.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G079389_T01 (Zea mays), 5'ss of exon 13
TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacag
|| | ||| |||||||| ||||| || ||||||||||||||||| || || || | ||| || ||||||||||||||||| ||||||||||||||||||  || |  ||| ||   ||||||         | |||  || ||  ||||||      |  | | || ||||
TCTATAGAGCTTCACATATATACAGATTTCTTAAGAATTGTTCTGGAGATAATTATTGCCATCCTTACATATGCATTGCCCAGAAATCCTGAGgtatgtattggcctgcagttcagtttactgg-------acaggaggactagcactgcta-----acatttttctacag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 13
TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacag
|| ||||| |||||||| ||||| || ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||| |||||||| |||||||||  || |  ||||||   ||||||    |           || ||  ||||||||||| || | | |  ||||
TCTACAGAGCTTCACATATATACAGATTTCTTGAGAATTGTTCTGGAAATAATCAATGCAATCCTTACATATGCATTGCCCAGAAATCCCGAGgtatgtattggcctgcaattcagtttacttgaca----------ggactagcactgcttctaacatttttgt--acag

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA10G00550.1 (Glycine max), 5'ss of exon 13
TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctgactagcaattatatttactctgtacctcatagggagaatactactgcttctaatatgtgtatcaacag-------------------------------------------------------------
||  ||||  | || || ||||| |||||||| ||  |||| |||||||| || ||||||||||| || |||| | |||||  |||||||||||||     | |    |   |  ||| | |  | |  | | |    |   ||  ||  || || |  |  |  ||||||                                                             
TCAGCAGAGTTGCAGATATATACTGACTTCTTGAGGCTTGTACTAGAAATTATAAATGCAATTCTGACTTATGTACTGCCTCAAAATCCTGAGgtacaatttaatgttcctcttgattaatt--gaaaattaaaatatgcgcac--ctattttta-tgcggttcccaacagtcaaaaactacatttgcattctgatcttttacatcaaacgtcttgcttgtgactgagacag

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|58684083|gb|CK072770.1|CK072770
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|426809|gb|D22882.1|D22882
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAG                         GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC
genomic: TAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAAC

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: 54 (upstream exon), 71 (downstream exon)
Score: 8

TCCACAGAACTTCACATCTATACCGACTTCTTAAGAATTGTTCTAGAAATCATCAATGCAATTCTTACATATGCATTGCCTAGAAATCCTGAGgtatgtgctg ... gtatcaacagGTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA




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