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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG

Basic information

species Arabidopsis thaliana
transcript AT4G17150.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 6
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgca--atgaaactttaactcctttttcaatt----agGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
   | | ||| ||| |   ||  |   ||| | |   |    ||  | |   ||| | ||   || ||||||  ||  ||  ||  ||  | |||  |||    |||||||  ||||||||||||||||||| ||| ||||||| | ||  || |||||| |||| ||||||||  ||  |||| ||
-tagtttcatgttaattgtctgctaagtta-agtgcctaactgcccact---gac-tgttgcaatacttgcatcatataatgtttgctattatttatattgttcagGTTAAGATGGCTGTGCAGTACATGCGCCGTGTAATTCAAAGAAGAGCTAAGTTTGATATAATGGATCTTGATGTTGTTCAG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 6
aagggtccatattagtctccttatc--cattacaatcaatggtagcgt----attctagacattttcttatgcttgcaatgaa--actttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG-
       ||| |||   |||||     ||  | | || |||  | | |    |   | |   |  |  ||   ||  | ||      | | | | || |     | |||||||  ||||||| |||||||||||||| || ||||||||||  || |||||| | || |||||||| ||| || ||||| 
------tcatctta-catccttgctagcacaagagtctatgaaatcctcgagaccattgctgtaattgtaaagttttattgggttgttctgaattctgtcctt-tcagGTTAAGATGGCTGTACAGTACATGCGGCGAATCATTCAGAAAAGAGCTAAGTTTGACATAATGGATCTAAAT-GTTTTAAGG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G00770.1 (Glycine max), 3'ss of exon 7
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcc--------tttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
     ||| |   |  |  | |    || | || | || |  |  ||   | ||  ||||||  ||  |  | | |  |||  | ||         |   |||||||||||||| ||||||| ||||||||||||||  | ||| |||| ||||| |||||| |||||||| |||| || ||| |  ||
--aaatcctt--caagcaacatggaaataa-aacctatagctgt-taacttgga--ttttctggtgtgtttattaagtcttgtattctgctggatttgcctcaattagGTTAAAATGGCTGTACAGTACATGCGGCGGGTTATTGAGAAGAAGGCAAAGTTTGATATTATGAATCTGAACTGTTTGCAG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G02050.1 (Glycine max), 3'ss of exon 7
-aagggtccatattagtctccttatccattacaatc-aatggtagcgtattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
   |     | | | |||| ||   |  | | | |       |  |   || | |  |  |     ||  ||  ||    ||   |     | | ||||||||||||| ||||||| || |||||||||||  | ||| |||| |||||||||||| |||| ||||| || || ||| |   |
atggcagttaaacttgtcttctagactgtaatattttggacattactagttttggttaagtctgactgtctgagattttgct--gatctggtctacaattagGTTAAAATGGCTGTACAATACATGCGGCGGGTTATTGAGAAGAAGGCGAAGTTTGATATCATGGACCTGAACTGTTTGCTG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 7
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttcttatgcttgcaa----tgaaactttaactccttt--ttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
     ||| |   |  |  | |    || | || | || |  |  ||   | ||  || |  | || ||   |    | | | | |      |||   |||||||||||||| ||||||| |||||||||||| |  | ||| |||| ||||| |||||| |||||||| |||| || ||| |  ||
--aaatcctt--caagcaacatggaaataa-aacctatagctgt-taacttggattttctggtgtgtttattaagtcttatattctgctggatttgcctcaattagGTTAAAATGGCTGTACAGTACATGCGGAGGGTTATTGAGAAGAAGGCAAAGTTTGATATTATGAATCTGAACTGTTTGCAG

upper sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 5
aagggtccatattagtctccttatccattacaatcaatggtagcgtattctagacattttc--ttatgcttgcaa-tgaaactt---taactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
     ||  |   |||     | |  |||    || |   |    ||   | |||||||    || || ||     ||| | ||   | |     ||| ||||||||||||| ||||||| || |||||||||||  | ||| |||| ||||| |||||| |||| ||||| || || ||| |   |
-----tcagtggcagttaaact-tggattgtcttctagactgtgatacgttggacatttctagttttggttaagtctgagattttgctgatctgctttacaattagGTTAAAATGGCTGTACAATACATGCGGCGGGTTATTGAGAAGAAGGCAAAGTTTGATATCATGGACCTGAACTGTTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctagacattttcttatgcttgcaatgaaactttaactcctttttcaattagGTTAAAGTGGCTGTGCAGTACATGCGGCGTATAATTCAGAAAAAGGCGAAGTTTAATATTATGGATCTCAATTGTGTTAAG
                                 ctttaac  putative branch site (score: 3)
                                 ctttaactcctttttc  CT-rich tract
                                           tttttcaatta  TA-rich tract