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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaaatgttgagatgactttatttgtttgaacacataatgtatcaactttgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT

Basic information

species Oryza sativa
transcript LOC_Os03g17540.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G154883_T03 (Zea mays), 3'ss of exon 7
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaaatgttgagatgactttatttgtttgaacacataatgtatcaactttgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT
                                                                                          |    |||||    |  |||| |  | |      | ||| ||       ||      |     || |||| ||| |||  | ||||||||||||| |||   |||| |||| || |||||||| ||| |||||||||| |||| |||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
------------------------------------------------------------------------------------------ggcactgtatc---tcaaaatatctacacctaaatgttttttc-----tattgaaggttcttgttatggt-tattacttggcacttacatcaattgcaattttctt-cagCCAAACATATGGAATTCTTGGGAGTTCAAGTGGGATGGATAACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT

upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G154883_T02 (Zea mays), 3'ss of exon 8
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaaatgttgagatgactttatttgtttgaacacataatgtatcaactttgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT
                                                                                          |    |||||    |  |||| |  | |      | ||| ||       ||      |     || |||| ||| |||  | ||||||||||||| |||   |||| |||| || |||||||| ||| |||||||||| |||| |||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||       
------------------------------------------------------------------------------------------ggcactgtatc---tcaaaatatctacacctaaatgttttttc-----tattgaaggttcttgttatggt-tattacttggcacttacatcaattgcaattttctt-cagCCAAACATATGGAATTCTTGGGAGTTCAAGTGGGATGGATAACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTG-------

upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 8
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaa--------atgttgagatgactttatttgtttgaacacataatgtatcaactt--tgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT
|| ||| || |||| ||||     ||| | |  ||  | ||||   ||    |||  |  |||     | | | | | | | ||| | |   ||   || |   |||||        ||||  |  |  ||  |  |  |    |    | || |    |||  | |||| ||| |||  | ||||||||||||| |||   |||| |||| || |||||||||||| ||| |||||| |||| ||||||||||||||||||||| ||||| |||||| ||||||||||||||||||||||||       
gtatgttttccaattatat---cgctatattcatc--tctgtaatgttt--aattatatgttaaaaacacacatataggtttctg-tgactattgcttaatagtttgaaggcaatgtatgtcaaagtatctacacctaatgtttcttccattgaaggttcttgttatggt-tattacttggcacttacatcaattgcaattttctt-cagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG-------

upper sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0040g03050.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaaatgttgagatgactttatttgtttgaacacataatgtatcaactttgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT
                                                                                    | | || || ||||  ||| |||     ||   |||  |  ||     | ||    |  |||  ||    ||  ||   |   |  |||  |   ||  |||     |   | |||  |  ||| |||||| | | ||||| |||||||| ||| |  ||||||| ||||||||||| |||||  | |||||  |||||||||||||||       
------------------------------------------------------------------------------------gtttat-ctcttgttatcatttgt----ttattatgtatccatcctcctaaattgtttttgttaca----tgaagtaatttgattagtatct-tgtcttttatgcttcctgtgcagTTAGTCATCTGGATTGCTTAGGAGTGCAGGTGGCCTGGATCTCTGGACCTTGGTTTCTTTCCATTTTTGTGAATATTATTCCATGGGAAAGTG-------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaactttgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT
                          tacttac  putative branch site (score: 1)
                                            ccctctttc  putative PPT
                                 atcaatta  TA-rich tract