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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT

Basic information

species Arabidopsis thaliana
transcript AT2G38960.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 6
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
     | |    || | | | | || || |      || |||     | ||||   |  || | | ||| || | |      |||| |  ||  |   |  ||||||||| ||||| ||||| || |||||||| || ||  ||||||||||||| ||  |||| |||||||||||||||||||| ||||| ||| ||||  ||
----gtgtgtgttcatgttattcatgttttcagttcataata-----tgcact---tgtctgattcaaaatcatatc-----cttggaatgttattt-tcacagTGCAATTATGGATTGTGTTGGATGTGAGAAGTGTCGATTATGGGGAAAGCTCCAAGTTCTTGGTCTCGGTACTGCATTGAAGATTCTTTTCTCTGTTGAT

upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 7
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
       ||| | | | |  |   | ||||  |    | ||   |||   |   | ||  | |   |  |   |  |||   | || | | | ||   |   |||||||| ||||||||||| || || ||||| ||||| || ||||||||||| ||  |||  ||||| || |||||| |||||||||| ||| ||||  ||
-----gtttgtgacatatttcctgtgttctcaacttctcatttcattag-atgcatta--tgaaccacttgaatccttacc-catgtaacattttatttattagTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCATGGTCTTGGAACTGCACTGAAAATTCTTTTCTCTGTTGAT

upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 7
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
       ||| | | | |  ||  | |||||      | |||| ||    |   || |      ||  || |||    ||   |   ||  ||||| |||  |||||||| ||||||||||| || || ||||| ||||| || ||||||||||| ||  |||| || || || |||||  |||||||||| ||| | ||  ||
-----gtttgtgacatatttctggtgttcttatt---tcataagatacatatgaaccac-----ttgtatccttacccatg--taacattttcttg-att--agTGCAATTATGGACTGTGTTGGATGCGAGAAGTGCCGACTGTGGGGAAAGCTCCAAGTTCTTGGCCTTGGAACTGCTCTGAAAATTCTTTTCTCCGTTGAT

upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G10830.2 (Glycine max), 3'ss of exon 7
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagc---taagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
    | ||||    ||  |  || | ||||  |  | ||||  || || |||      ||   | | |||  |  ||    ||    |  ||  | ||| | ||||||||||| ||||| |||||||| ||||||||||| ||  ||||||| || |||||| |||| |||||||| |||||||| || ||||| ||| ||||  ||
---ttacttg--ctctccatttattattct--actactgattcaacttacacactgctgcttttgatttatctcattgacaatggaatatatttttttggaatgcagTGCAATGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGCAAACTTCAGGTTCTTGGTCTCGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G23150.2 (Glycine max), 3'ss of exon 7
--gtccttct-tgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
   ||||| |    || ||  |  || | ||||  |  | ||||  || || ||||       | | |||  |  ||    ||    ||     |  || | ||||||||| | ||||| |||||||| ||||||||||| ||  ||||||| ||||||||| |||| ||||| || |||||||| || ||||| ||| ||||  ||
cactccttttacttgttctccatttattattct--actactgattcaacttacactt-----ttgatttatctcattggcaatggaatgttattttgtggaatgcagTGCATTGATGGATTGTGTAGGATGTGAGAAATGTCGATTATGGGGTAAGCTTCAGGTTCTTGGTCTTGGAACTGCATTAAAGATTCTCTTCTCTGTTGAT

upper sequence: AT2G38960.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 7
gtccttcttgagtcctttaactaattttcttgagcaatgataaaatttccactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
    |||   |  | ||| | |    |  ||||    ||     | |   | ||||| | | |      | |   |     | ||   ||   || ||||| |||||| | ||||||||||| ||||||||||| || || || ||||||||||||||| |||  ||||| || |||||||||||||| || ||| || |  ||
aattttcactatgcatttcaatgtgatctttgattgctgc----actattattgactggttcatgcctgtgccaatgatacaattatttctgttttcattgtagTGCATTGATGGACTGTGTTGGCTGTGAGAAGTGTCGACTTTGGGGAAAGCTTCAGGTTCATGGTCTTGGAACTGCATTGAAAATCCTTTTCTCTATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgactagctaagttaaattcttttttattacttgaatcgtcttgcattgcagTGCAATAATGGACTGTGTAGGCTGTGAGAAATGCCGTCTATGGGGAAAGCTTCAGATTCTCGGTCTCGGTACTGCATTGAAAATTCTATTCACTGTCAAT
 cactgac  putative branch site (score: 2)
                                       tcgtctt  putative PPT
           taagttaaattctttt  TA-rich tract