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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtggcatatctaatcaagtaattacacaacgagcttgatgtttcttttacttctcaagattcagaacagtgctgtttcttttttcctttaatga...

Basic information

species Oryza sativa
transcript LOC_Os10g33930.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33930.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G069976_T01 (Zea mays), 5'ss of exon 21
TGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattg-tggcatatctaatcaagtaattacacaacgagcttgatgtttcttttacttctcaagattcagaacagtgctgtt----tcttttttcctttaatga
|||||||||||| || || ||||| || ||||| |||||||||||||| |||||||||||||||||||| || ||||| |||||||||||| |||||||||||     | |  ||||||   || |     |||||    | || |  |        | ||||||||| || | |   ||||     ||        |||||   
TGGAGTTGATATTGGTTCATCAACGGTGGCACGAGGTGTGGTGAGCCTAGTGCTTGGCTACTTGAACAATCTTGTGATCGAAATGGCCTTCTTGGTACAGgtatccaatcgtgtatctagctaatt-----cacaaaacccctgttcatatgaaatttcctcaagattgagcatacatctgtaaagatcacagaagatttaagac

upper sequence: LOC_Os10g33930.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT2G28320.1 (Arabidopsis thaliana), 5'ss of exon 20
TGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaa--ttgtggcatatctaatcaagt--aattacacaacgagcttgatgtttcttttactt-----ctcaagattcagaacagtgctgtttcttttttcctttaatga
 || |||||||| || || ||||| |||||| | || || ||||| ||||| ||||| ||| | ||||| || |||||||||||||||||| |  |||||||||  |  |  |  ||||   |  ||  || |  |   | |  | | ||  | || |  ||      | |||  |  ||   | |       ||| ||| ||      
GGGCGTTGATATTGGGTCATCAACTGTTGCAAGAGGAGTTGTGAGTCTTGTTCTTGGTTACCTCAACAAACTCGTGATTGAAATGGCCTTCTTAATACAGgtaaactaattaccaatctttcctggtttaaatctaagtcaacttcggtgggtattctggttacatattgaagcattggatttgagtgagcaatttcttctttgtgcag

upper sequence: LOC_Os10g33930.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 5'ss of exon 20
TGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtggcatatctaatcaagtaattacacaacgagcttgatgtttcttttacttctcaagattcagaac-agtgctgtttcttttttcctttaatga--
|||| | || || || || |||||||||||| |||| ||||| || ||||| || || ||| | ||||| ||||| ||||||||| | || ||| |||||||||       || |||  || |    |  ||        |  |  | ||| ||| || | | |  ||||  | |||  | |      |       | |    
TGGAATCGACATTGGGTCATCAACAGTTGCAAGGGGCGTGGTCAGTCTTGTTCTCGGTTACCTTAACAATCTGGTTATTGAAATGACATTTCTGATACAGgtaacacaactatgtct--tccacatgtggcatgtgttcttcaaattatctcttagttat-atgcctcagcgccagttttatcgagagtagaagcaatttgaa

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|88224051|gb|CI223900.1|CI223900
EST:     TGCTCGGTTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAG                         GGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG
genomic: TGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtgg ... tgtcgtgcagGGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG
EST: gi|88837249|gb|CI078609.1|CI078609
EST:     TGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCCTCCTGGTACAG                         GGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG
genomic: TGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtgg ... tgtcgtgcagGGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG
EST: gi|163928467|gb|EG715447.1|EG715447
EST:     TGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAG                         GGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG
genomic: TGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtgg ... tgtcgtgcagGGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTG

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: 63 (upstream exon), 63 (downstream exon)
Score: 14

TGGAGTTGATATAGGCTCGTCAACAGTTGCACGGGGTGTGGTGAGCCTTGTGCTTGGCTACTTGAACAACCTGGTGATTGAAATGGCCTTCCTGGTACAGgtaattgtgg ... tgtcgtgcagGGCAACACGCAAGAAGAGCTCCCGGAGTTCCTCCTGGGCACCTGCCGACTGAACTACCTCGACGCGTCCAAGGCAGTGTCCATAGACGAGTGCTGAAGGC




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