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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaaactcaatatataccagcagattttactgatcattgttaatttcatgcaccgccaggataaaatacatataatggcatcaccattttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG

Basic information

species Oryza sativa
transcript LOC_Os09g29404.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150796_T01 (Zea mays), 3'ss of exon 9
gtatccaaactcaatatataccagcagattttactgatcattgttaatttcatgcaccgccaggataaaatacatataatggcatcaccat-tttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG
||||  | |  |  || | |  |  | || |||    | |  | |  |||     | |    |   |||| | || |||| | || | ||| |||    |||||||| ||||||| |||||||||||||||||||| || ||||||| | |||| || |||||||| || ||||| ||||||||||||
gtattgacatcctgtagacat-aataaatcttatgcttgaccgatgtttttgataatctt--gtccaaaaaatatttaattgtataatcatatttcaatagGTTATTTTGGATGTAGTTTACAACCATACAAATGAAGCTGATGATGTTAACCCTTACATGACTTCCTTTCGTGGTATTGATAACAAG

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G385578_T01 (Zea mays), 3'ss of exon 7
gtatccaaactcaatatataccagcagattttactgatcattgttaatttcatgcaccgccaggataaaatacatataatggcatcaccat-tttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG
||||  | |  |  | || |       || ||  |  |||   ||  ||||    ||| | ||   |||| | || ||||   || |  || |||    |||||||||||||||| |||||||||||||||||||| || ||||||||| |||| || |||||||| || |||||| |||||||||||
gtattgacatcc--tgtagaatgatgaatctttttcttcagcattg-tttctaatacc-ctagtccaaaaaatatttaattctataatgatgtttcaatagGTTATTCTGGATGTAGTTTACAACCATACAAATGAAGCTGATGATGCTAACCCTTACATGACTTCCTTTCGTGGCCTTGATAACAAG

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 9
gtatccaaactcaatatataccagcagattttactgatcattgttaatttcatgcaccgccaggataaaatacatataatggcatcaccat-tttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG----------------------------------------------------------------------------------------------------
||||  | |  |  || | |  |  | || |||    | |  | |  |||     | |    |   |||| | || |||| | || | ||| |||    |||||||| ||||||| |||||||||||||||||||| || ||||||| | |||| || |||||||| || ||||| ||||||||||||                                                                                                    
gtattgacatcctgtagacat-aataaatcttatgcttgaccgatgtttttgataatctt--gtccaaaaaatatttaattgtataatcatatttcaataggttattttggatgtagtttacaaccatacaaatgaagctgatgatgttaacccttacatgacttcctttcgtggtattgataacaagGTGATTGCAGAATACCTCTTTACTTGCTGTTCTATCATTTAAGTTCCAAGTCCATGGAGAGACTTGTATGATGGGGTGTCATCAATCTCTGGACGAATTT

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 6
-------------------------gta--tccaaactcaatatatac----cagcagattttactgatcattgttaatttcatgc-accgccaggataaaatacata--taatggc-----------atcaccattttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG
                         |||  |    | |  |  ||| |    ||  | | ||| ||| |  |   | |||| ||   | |   ||  | |  || |||  |  |||            |||       | ||||||||||| |||||||||| ||||| ||||| |||||||| ||||||||    || || |  ||||| || |||||||| ||||| |||
gtagtaatgttaatatttccctagtgtaactttggagtggaagtatgctttacattataatttcctggttctgtcttattttatattatctaaagtcttatttatatacctcttggttctttccataaatcttatccatatgcagGTTATTTTGGATGTTGTCTACAATCATACTAATGAGGCTGATGATGCCTTTCCTTACACTACTTCATTTCGTGGCATAGATAATAAG

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 9
-gtatccaaactcaatatat--accagcagattttactgatcattgttaatttcatgcaccgccaggataaaatacatataatggcatcaccattttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG
  |  ||  ||||  |   |       |  ||||| |   |  || || |     || |  ||     ||  ||   ||||||| |||    |   | | ||||| ||| | ||||||||||| |||||||| |||||||| |||||||   |||| || |  ||||| || |||||||| ||||| |||
catggccttactctttggtttggtttccctatttttcactttcttcttgacagtctgaaatgctttt-tattatg-gtataatgacatt-ttaccctttacagGTCATTTTAGATGTTGTTTATAACCATACTAATGAGGCTGATGATGAAAACCCTTACACCACTTCATTTCGTGGCATAGATAATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcatgcaccgccaggataaaatacatataatggcatcaccattttgtgcagGTTATTCTGGATGTTGTTTACAACCATACAAATGAGGCGGATGATGCTCACCCGTATATGACTTCTTTCCGTGGCATTGATAACAAG
 tgttaat  putative branch site (score: 3)
                                          ccatttt  putative PPT
                   ataaaatacatataat  TA-rich tract