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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggcctgggcagctgattgaagtgctgccaattcttacgttacagaagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA

Basic information

species Oryza sativa
transcript LOC_Os04g57140.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 6
----------gtactggcc-tgggcagctgattgaagtgctgccaattcttacgttacag------aagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
           || |   | | |  |||| | |||||  |||||| ||  |  ||||  |      ||||||||||||||||     ||  || || ||||| |||  | ||||||| ||||||||||| ||||| ||||||||||| || || |||||||||||| |||| || |||||||| || || ||||| || ||||| ||  |||| |
gtactggttgatagtattcatagctagctaactgaaggactgccagtttgtgtgttattgttactcaagtaatattgtttccagaatagatctaacaaatatcatttttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTCGGCAGGGATGATGCTTCACAACTCTCTGCTCTTCAGATCTTGGTTGAGATTGGATTCATTGATA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
gtactggcctgggcagctgattgaagtgctgccaattcttacgttacagaagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
                   | |||||   ||||| ||  |  ||||   ||||||| ||| |||      || ||| || | ||  |||| | ||||||| ||||||||||| ||||| ||||||||||| || || |||||||||||| |||| || |||||||||||||| ||||| || ||||| ||  | ||||
-----------------gtactgaaggattgccagtttgtgtgttattcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 11
-gtactggcctgggcagctgattgaagtgctgccaattcttacgttacagaagtaatattgtttccttggaagtgctgac--taatataattgcta-tgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
     |         ||   | | |||   | | |  |   |  | | |    |||| ||||  || |   | |  ||    || |  |  || |  | ||| | ||||||||||||||||| ||||| || || || || |||||||||||||| ||||| |||||  | ||||| || |  || ||||| ||| ||  ||
aaagataaagaaataagacaactaaagaatt-caagattagatatgataatcctaat-ttgtgaccatatcatttttgttgatactggatgtgttggtacagATGCAACATGATTATATTTTGGGAAATTACCCTGTTGGAAGGGATGATGCTGCTCAGCTTTCTGCCTTACAAATCTTAGCTGAGATTGGATTTCTTAGCA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
------------gtactgg--cctgggcagctgattgaagtgctgccaattcttacgtta--cagaagtaatattgtttccttggaagtgctgactaatataattgctat-gcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
             |  ||   |||   | | |||   ||||    | | ||  |     |  | | | | |  ||       | ||  |||||| || |  |  || | |  ||| | ||||||||||||||||| ||||| || ||  | || |||||||||||||| ||||| |||||  | ||||| ||||  || ||||| ||| |  |||
gtatgccttttcattatgaaaccttacctgatgac--aagtatatctagtttatgtacaaagctgcaattaccttcaagttatagatttgctga-tactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA

upper sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 5
gtactggcctgggcagctgattgaagtgctgccaattcttacgttacagaagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
         || |||  |  || |  || || || || || |   ||| |||       | || | |     |||||||  | |||     ||||||| | |||||||| ||| |  ||||||||||||| || || ||||| |||||||||||||| | |||  |||||||  | || |  ||||| |||||  | |
--------gtgagcattttcttcat-tggtgacatttatttccacacaaaag-------gcttgcctttcgttgctgacacacata-----tatgcagCTGCAACATGACTATTTGCTAGGAAACTATCCTGTTGGGAGGGACGATGCTGCACAGCTTTGTGCCTTGCAAATTCTTGTTGGGATTGGGTTTGTCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacagaagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA
                                 gactaat  putative branch site (score: 2)
                                    taatataattgctat  TA-rich tract