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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g10690.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G462207_T01 (Zea mays), 5'ss of exon 1
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| | |||||||||||| || ||||  |||||||| ||||||||||||||||| ||| || ||  |||||||||| ||| || | ||  ||||||| | |||||  |  || ||   |||| |||  || ||  ||  |  |||||||  | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || |||||| |||||  | | |||||
CCTAATAATGGTGGATCTCTAGCTAACATGTGGGGCCGTGCATCAGCTAAACCTAAGCCTTCAAGTACCACTAATTCTATAGCTGTAGAAAGTGTTTCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttgtgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcatgttgttaatatgttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G021033_T01 (Zea mays), 5'ss of exon 4
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| | |||||||||||| || ||||  |||||||| ||||||||||||||||| ||| |||||  |||||||||| |||||| | ||  ||||||||| |||||  |  || ||   |||| |||  || ||  ||  |  |||||||  | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || ||||||  ||||  | | |||||
CCTAATAATGGTGGATCTCTGGCTAACATGTGGGGCCGTGCATCAGCTAAACCTAAGCCTCCAAGTACCACTAATTCTACAGATGTAGAAAGTGTTGCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttgtgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcatgctgttaatatgttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G148626_T02 (Zea mays), 5'ss of exon 5
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| | |||||||||||| || ||||  |||||||| ||||||||| ||||||| ||| |||||  |||||||||| |||||||| ||  ||||||||| |||||  |  || ||   |||| |||  || |||  |  |  |||||||  | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || |||||   ||||  | |||||||
CCTAATAATGGTGGATCTCTGGCTAACATGTGGGGCCGTGCATCAACTAAACCTAAGCCTCCAAGTACCACTAATTCTACAGTTGTAGAAAGTGTTGCAGgtatctc--actaatggtcatatttaatt-cttcatgct--tttcttgtgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcacgctgttaatattttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G086707_T01 (Zea mays), 5'ss of exon 1
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| | |||||||||||| || ||||  |||||||| ||||||||||||||||| ||| |||||  |||||||||| |||||| | ||  ||||||||| |||||  |  || ||   |||| |||  || ||  ||  |  |||||||  | | | |   |   || | ||| |||||||       |||   |    ||||||| || ||| || ||||||  || |  | | |||||
CCTAATAATGGTGGATCTCTGGCTAACATGTGGGGTCGTGCATCAGCTAAACCTAAGCCTCCAAGTACCACTAATTCTACAGCTGTAGAAAGTGTTGCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttgtgtataactctcagcacacatctagtcatgta------tataaacccttctaagcatgctactgtagatctcatgctggtaatatgttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G113515_T01 (Zea mays), 5'ss of exon 1
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgtt-ttcag
|| | |||||||||||| || ||||  |||||||| ||||||||||||||||| ||| |||||  |||||||||| |||||| | ||  ||||||||| |||||  |  || ||   |||| |||  || ||  ||  |  |||||||  | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || ||||||  ||||  |  | |||| 
CCTAATAATGGTGGATCTCTGGCTAACATGTGGGGCCGTGCATCAGCTAAACCTAAGCCTCCAAGTACCACTAATTCTACAGCTGTAGAAAGTGTTGCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttgtgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcatgctgttaataatgttcaa

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G043623_T01 (Zea mays), 5'ss of exon 2
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcat-acaaacattcatgtttcttttctttgt--tatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| ||||||||||||||||| | ||  |||||||| ||||||||||| ||||| | | |||||   ||||||||| |||||| | || |||||||||| ||||||   | |||||  ||| | ||    ||||||||  | || ||||| |  | | | |   |   || | ||| || |||| | |||    | | |    | |||| ||  |  ||  || ||  ||||  | |||||||
CCTAGTAATGGTGGATCACTGGTTAACATGTGGGGTCGTGCATCAGCAAAACCTATGCCTCCAAGCACCACTAATTCTACAGCTGTAGCAAGTGTTGCAGgtattatctcacaaatgttcgtattcaaattctttgtgctttactttctcgtttataattctcagcacacatctagtcctgtata-tcaaccctttta---caggcatgctaatatagaactaatgctgttaatattttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G435338_T01 (Zea mays), 5'ss of exon 10
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcat-acaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| ||||||||||||||||| ||||  |||||||| ||||||||||| ||||| ||| |||||  |||||||||| |||||| | || |||||||||| ||||||   | |||||  ||||| ||    ||||||||  |  || ||||  | | | |   |   || |  ||||| |||| | |||    | |      |||||| ||  |  ||  |||||  ||||  | |||||||
CCTAGTAATGGTGGATCACTGGCTAACATGTGGGGCCGTGCATCAGCAAAACCTAAGCCTCCAAGTACCACTAATTCTACAGCTGTAGCAAGTGTTGCAGgtattatctcacaaatgttcatattcaaattctttgtgct--ttacttgtgtataactctcagcacacatataatcttgtata-tcaacccttta----caagcatgctattatagaactcatgctgttaatattttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AC204061.3_FGT001 (Zea mays), 5'ss of exon 1
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag-------------------------
|  | |||||||||||| || ||||  |||||||| ||||||||||||||||| ||| |||||  |||||||||| |||||| | ||  ||||||||| |||||  |  || ||   |||| |||  || ||  ||  |  |||||||  | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || ||||||  ||||  | | |||||                         
CTTAATAATGGTGGATCTCTGGCTAACATGTGGGGCCGTGCATCAGCTAAACCTAAGCCTCCAAGTACCACTAATTCTACAGCTGTAGAAAGTGTTGCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttgtgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcatgctgttaatatgttcagctactcttgatgcacaaatatgcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G076582_T01 (Zea mays), 5'ss of exon 1
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcatacaaacattcatgtttcttttctttgttatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| | |||||||||||| || ||||  |||||||| | ||||||||||||||| ||| |||||  |||||||||  |||||| | ||  ||||| ||| |||||  |  || ||   |||| |||  || ||  ||  |  ||||||   | | | |   |   || | ||| || ||||       |||   |    ||||||| || ||| || ||||||  ||||  | | |||||
CCTAATAATGGTGGATCTCTGGCTAACATGTGGGGCCTTGCATCAGCTAAACCTAAGCCTCCAAGTACCACTAACTCTACAGCTGTAGAAAGTGCTGCAGgtatctc--actaatggtcatatttaatt-ctccgtgct--tttcttatgtataactctcagcacacatctagtcctgta------tataaacccttctaagcatgctactgtagatctcatgctgttaatatgttcag

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G481471_T01 (Zea mays), 5'ss of exon 3
CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcat-acaaacattcatgtttcttttctttgt--tatattttcttgcatgttaattcaaatgcatacctaatcatgtaaaatcagatatgtcaagttaagcatacttctgaagttctcatcttgttgctgttttcag
|| |||||||||||||| || ||||  |||||||| ||||||||||| ||||| | | |||||  |||||||||| |||||| | || |||||||||| ||||||   | |||||  ||| | ||    ||||||||  | || ||||| |  | | | |   |   || | ||| || |||| | |||    | |  ||    |||| ||  |  ||  || ||  ||||  | |||||||
CCTAGTAATGGTGGATCGCTGGCTAACATGTGGGGCCGTGCATCAGCAAAACCTATGCCTCCAAGTACCACTAATTCTACAGCTGTAGCAAGTGTTGCAGgtattatctcacaaatgttcgtattcaaattctttgtgctttactttctcgtctataattctcagcacacatctagtcctgtata-tcaaccctttacag----gcatgctaatatagaactaatgctgttaatattttcag

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|27921126|gb|CB096934.1|CB096934
EST:     ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTG                         TTACAGCTGATGCACAAATATGTGCAAAGGAAGAGGCAAATGCTGATAGTA
genomic: ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcata ... ctgttttcagTTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
EST: gi|88220274|gb|CI219834.1|CI219834
EST:     ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTG                         TTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
genomic: ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcata ... ctgttttcagTTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
EST: gi|87021826|gb|CI277993.1|CI277993
EST:     ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTG                         TTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
genomic: ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcata ... ctgttttcagTTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
EST: gi|58600250|gb|CK010778.1|CK010778
EST:     ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTG                         TTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA
genomic: ACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcata ... ctgttttcagTTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTA

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), 25 (downstream exon)
Score: 4

CCCAGTAATGGTGGATCACTTGCTACGATGTGGGGACGTGCATCAGCTAAACCCAAGACTCCAGCTACCACTAATCCTACAGTTTTACCAAGTGTTGCTGgtattgcata ... ctgttttcagTTACAGCTGATGCACAAATATGTGCAAAGGAAGAAGCAAATGCTGATAGTAGTGATGATGAACAAGCTGTACACTACAAGCGTGGCTCTAGTGCAAATAA




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