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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccgaacaaactattctggaataccttctaatgaaggataatgtcactaagcaaacaccatggaattcctcataccctcacactaaatt...

Basic information

species Oryza sativa
transcript LOC_Os08g40530.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 27
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccgaacaaactattctggaatacct--tctaatgaaggataatgtcactaagcaaacaccatggaattcctcataccctcacactaaatt----
|||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||| ||||||||||| | || ||| | || |||| | | || | | || | | | |||||| | | | | |
GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgttt------ggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacacattga

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AC214484.3_FGT001 (Zea mays), 5'ss of exon 1
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttt-------ttccccgaacaaactattctg-----------gaatacctt--ctaatgaaggataatgtcact------aagcaaacaccatggaattcctcataccctcacac--taaatt-------------------------------------------------------
||||||||||| || |||||||| ||||||| |||||||||||| |||||||| ||||||||||||||||||||||| ||||||| |||||||| ||||||||||| || || | || ||| || | ||| || | || ||||| |||| || |||| || ||| |||| | || ||| |||
GCCGATATAGGCCTTTCAATGGGTATTTCAGAGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacac-attgaagtcctgactcctgaacatagcaaacatgcatgccttttttttggtataatgtgcatttctaggctataattcttgttgcag

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 5'ss of exon 27
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccg--aacaaactattctggaataccttctaatgaaggataatgtcactaagcaaaca-ccatggaattcctcataccctcac-actaaatt------------------------------------------------------------------------------
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GCCGACATTGGTCTTTCAATGGGTATAGCAGGAACGGAAGTCGCGAAAGAAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAGgttcgattcgatcagtcattcctctaatctagagttcctcatgttca-gctttgtaac-ccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctag

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccgaacaaactattctggaataccttctaatgaaggataatgtcactaagcaaacaccatggaattcctcataccctcacactaaatt
|| ||||| ||||| ||||||||||| |||||| || || ||||||||||| || ||||||||||| ||||||||||||| |||| ||||| ||||| | | |||| || ||| | || || || | | | |
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagat--------aacagc---ttttggtgcgagtctgaaggatcgaaattcttgcag----------------------------------------

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|29665351|gb|CB661626.1|CB661626
EST:     AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG                         GTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
genomic: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttttt ... ttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
EST: gi|29681421|gb|CB677696.1|CB677696
EST:     AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG                         GTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
genomic: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttttt ... ttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG

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: 71 (upstream exon), 47 (downstream exon)
Score: 18

GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttttt ... ttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG




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