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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaactatattttgtaacagttgtggaatactaaagttaaggctaccttgtttagtaaatattctatgaatttgaaatagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG

Basic information

species Oryza sativa
transcript LOC_Os09g24220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G421541_T02 (Zea mays), 3'ss of exon 4
gtacaactatattttgtaaca-gttgtggaatactaaagttaaggctaccttgtttagtaa--------atattctatgaatttgaaatagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
|||||  |||||||||  ||| |||      |||| || |     |||  || |||||| |        |||   |||||||||||| ||||||||||||||||| ||| ||||||| ||||||||||||||||| |||||||| |||||||||||||| ||||||                                                                                 
gtacatttatattttgccacaagttacttggtacttaaat-gcaactattttatttagtgattacaataataaaatatgaatttgaa-tagATGGGCAAATTCTACGAACTATTTGAGATGGATGCACATGTTGGAGCAAAGGATCTTGATCTTCAGTACATGAAG---------------------------------------------------------------------------------

upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 4
---------gtacaactatattttgtaacagttgtggaatactaa--agttaaggctaccttgtttagtaaatattctatgaatttgaaatagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
         |   || | |  || ||  || |  |  | | || |  |||||   | |  |    || |   |  ||  |    ||||   ||||||| ||||| |||||  | ||||| |||||||||||||| || || || ||||||||  | ||||||||||||                                                                                 
gtttgagttggttaagttttgttggtgccattattccattccttacaagttacaaccaaatgaaatatttt-tcctccctattgttgatgcagATGGGTAAATTTTATGAGCTTTTTGAGATGGATGCACATGTAGGTGCGAAAGAGCTTGACTTGCAGTATATGAAG---------------------------------------------------------------------------------

upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0005g01370.t01 (Vitis vinifera), 3'ss of exon 4
gtacaac-tatattttgt--aacagttgtggaat-actaaagttaaggctaccttgtttagtaaatattctatgaat-ttgaaatagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
||| ||  || ||   |   |||  |  |  | |    |  || |    | |  |     |  |||||| |||   | || ||| |||||||||| || |||||| | |||||||||||||| ||| | || ||||| ||||||||| | || |||||||||                                                                                 
gtataagataaataaagctaaactatcataaacttgtcagggtcactagtgcaattaaatgataatattttatctttgttcaaacagATGGGCAAGTTTTATGAACTTTTTGAAATGGATGCGCATATAGGAGCAAAAGAGCTTGATTTGCAATATATGAAG---------------------------------------------------------------------------------

upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtacaacta-tatttt-gtaacagttgtggaatactaaagttaaggctaccttgtttagtaaat-----attctatgaatttgaa--atagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
         ||| |   | || ||| ||  ||         | ||| |  | | | | |  |||| |||  ||       |  || ||||       |||||||| |||||||||||  | |||||||||||||||||| | || || |||||||| ||  | ||||||||||||                                                                                 
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG---------------------------------------------------------------------------------

upper sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ29124 (Selaginella moellendorffii), 3'ss of exon 7
gtacaactatattttgtaacagttgtggaatactaaagttaaggctacct-tgtttagtaaatattctatgaatttgaaatagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
                     ||  ||  || | |   ||| | || |   |||||||    | | ||      |      ||||||| || ||||| ||| | ||||| ||||||||||||||||| ||  | || |||||||| ||||| ||||||                                                                                 
---------------------gtgatg--atgcgatgcttatgcctgctagtgtttagc---tgtgctgcatgct----gcagATGGGGAAGTTCTACGAAATGTTTGAGATGGATGCACATGTTGGAGCTCAAGACCTTGATCTGCAGTACATGAAG---------------------------------------------------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
      gcttgat  putative branch site (score: 5)
                                    ttctcttctgcttatt  putative PPT
                             tagtaaatt  TA-rich tract