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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccggccgaactccaccttggattcatcggtggcgcttccgccgttggtttgatcgctgacaccgttattgttgttgtggtggtgtatgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g56210.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56210.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G051756_T01 (Zea mays), 5'ss of exon 2
CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccggccgaactccaccttggattcatcggtggc-gcttccgccgttggtttgatcgctg--acaccgttattgt-tgttgtggtggtgtatgtgtgcag
|||||| |||| |||||||||||||||||||| |||||||||||||| ||||||||||||  ||||||||| ||||||||||||||||||||| | |||||||||| ||| | |  |          ||       |||  |  |  | |   |  |  |   | |   |   | ||| || | |||    | ||  |||||||||
CTGTTCCTGCTAGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCTCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagc-ccgcctgtgcatggatgcatatgagattatggttggattggtcaccgactccagttccgttgcgttgatatggtgtattggatcgatg-gtgtgtgcag

upper sequence: LOC_Os02g56210.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G150209_T02 (Zea mays), 5'ss of exon 3
CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccggccgaactccaccttggattcatcggtggc-gcttccgccgttggtttga--tcgctgacaccgttattgt-tgttgtggtggtgtatgtgtgcag
|||||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||  ||||||||| ||||||||||||||||||||| | |||||||||| ||| | |  |          ||       |||  |  |  | |   |  |  |  || ||  |   | ||| || | |||    | ||  |||||||||
CTGTTCCTGCTGGAGCAGGCGCACTGGTTCTATGAGGACAACTCCGTTGAGCACAACCCCAACCTCAAGTCCCTCTCCTTCAAGGACTTCACTTCCCTCAgtaagc-ccgcctgtgcatggatgcatatgagattatggttggattggtcaccgactccagttcccttgcgttgatatggtgtattggatcgatg-gtgtgtgcag

upper sequence: LOC_Os02g56210.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ34514 (Selaginella moellendorffii), 5'ss of exon 2
CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccggccgaactccaccttggattcatcggtggcgcttccgccgttggtttgatcgctgacaccgttattgttgttgtggtggtgtatgtgtgcag
|| ||||| |||||||| || ||||||||||||||||||||| || | ||||| ||  | ||| | || |||||  | ||    || |||||| | ||||||||| |    ||   ||||   ||     | | | |  |  || |  | | |                                                 
CTCTTCTTACTGGAGCAAGCTCACTGGTTCTACGAGGACAACACCATGGAGCAGAATGCTTCCTTGAAATCGCTAACATTGCGAGAGTTCACTGCTCTCAgtaagatttctcc---ctcctttttctcccctttgcttacattttcttcctag-------------------------------------------------

upper sequence: LOC_Os02g56210.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ10144 (Selaginella moellendorffii), 5'ss of exon 2
CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccggccgaactccaccttggattcatcggtggcgcttccgccgttggtttgatcgctgacaccgttattgttgttgtggtggtgtatgtgtgcag
|| ||||| |||||||| || ||||||||||||||||||||| || | ||||| ||  | ||| | || |||||  | ||    || |||||| | ||||||||| |    ||   || |   ||   | | | | |  |  || |  | | |                                                 
CTCTTCTTACTGGAGCAAGCTCACTGGTTCTACGAGGACAACACCATGGAGCAGAATGCTTCCTTGAAATCGCTAACATTGCGAGAGTTCACTGCTCTCAgtaagatttctcc---cttctttttctctccttggctcacattttcttcctag-------------------------------------------------

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|58604557|gb|CK015085.1|CK015085
EST:     GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
genomic: GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
EST: gi|58599901|gb|CK010429.1|CK010429
EST:     GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
genomic: GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
EST: gi|58653383|gb|CK042063.1|CK042063
EST:     GCACAAGCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACC
genomic: GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
EST: gi|58597464|gb|CK007992.1|CK007992
EST:     GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
genomic: GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
EST: gi|218484683|gb|FG956662.1|FG956662
EST:     TCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
genomic: TCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA
EST: gi|58599652|gb|CK010180.1|CK010180
EST:     GCACAAACCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCA                         TGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGGGCGCACCTTGATGACT
genomic: GCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACA

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: 51 (upstream exon), 70 (downstream exon)
Score: 31

CTGTTCTTGCTGGAGCAGGCGCACTGGTTCTACGAGGACAACTCCGTCGAGCACAACCCCTCCCTCAAGTCGCTCTCCTTCAAGGACTTCACTACGCTCAgtaagctccg ... atgtgtgcagTGTTCAATAGCTGTGCTGCGCTCAGGCCATACCGCGCGCACCTTGATGACATTTACAAGGATTTCACTCACTATAAGTTCCGTGTCCCTGTCTGCGGCGC




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