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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACCTTTTGAGCACATCTCATTTAGGGAGTTAGCGGCTAGAGGATTCAGCAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctccatgcactagccattacaaagttgtgttcttattgtttttgcggtgttcataagatgatttttatgtgttcatttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g33300.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g33300.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G002978_T02 (Zea mays), 5'ss of exon 6
CCACCTTTTGAGCACATCTCATTTAGGGAGTTAGCGGCTAGAGGATTCAGCAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctccatgcactagccattacaaagttgtgttcttattgtttttgcggtgttcataaga-tgatttttatgtgttcatttc--ttgcag-----------
 |  | |||||||||||||| |||||||||||||| || |||||| ||| || |||||| ||||||||  | ||||||||| |||| || || ||||||||| ||   |  |     | | |||     ||     ||    |||     ||  | ||||  || | |||||    |  |||  ||  || ||            
GCTTCATTTGAGCACATCTCCTTTAGGGAGTTAGCAGCAAGAGGAATCACCAAAATGGACATGACAGCAGTAACATGTTGTGAGGAGAACAACATTCCTGgttagtacctct-tgtcaactattct---gtcccactccagatgtaggc-cgtaggtcatttgactcattttagcctcctcaactcaattccatcctgctaagag
















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|86517958|gb|CI158164.1|CI158164
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGCCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
EST: gi|163926185|gb|EG712845.1|EG712845
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
EST: gi|86538570|gb|CI178776.1|CI178776
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
EST: gi|87039017|gb|CI193639.1|CI193639
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
EST: gi|25806638|gb|CA762599.1|CA762599
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG
EST: gi|58595083|gb|CF993391.1|CF993391
EST:     CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTG                         TTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTAGTG
genomic: CAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTG

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: 55 (upstream exon), 75 (downstream exon)
Score: 29

CCACCTTTTGAGCACATCTCATTTAGGGAGTTAGCGGCTAGAGGATTCAGCAGAATGGATATGACAGCGATTACATGTTGTCAGGAAAATAATATTCCTGgtcagcctcc ... tttcttgcagTTGTCATCTTCAACATGTTAGAGCCTGGCAATATCTCCAAAGCAATTTGTGGGGATCAAGTAGGTACATTAGTTGACCAATCAGGAAGGATTACATAAAC




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