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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA

Basic information

species Arabidopsis thaliana
transcript AT2G45150.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 2
-----gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctat-tgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
       ||    | |          | |||   |  || | ||||   | | || |     |  || ||        | | |  ||   |||| |||       || |    ||| |||||    ||  || | |   |  |||||||| ||||||||||| |||||||| ||||||||||||||||| ||||| ||||||||| | ||  |               
ggttcataaaaagttgagcagcaaagtttttaccagttcaagagtttgtactgttaa-----atttcactatagcaagcgaat--aggattcctcttg------cttatgcagTATGTGTTTTGCCAGAAATTGCATACAGTTGGCCAATACTTCTTGGTGGGCAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATTTCTATTAGTAG---------------

upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
gcaagctctcgccttttctcctcttttatatctcta-aagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
               || |  |  || |  ||  || ||| |||  |  ||   |     || | | |||||       |  ||    ||  |||        | | |    | | |    ||| || | |   |  |||||||||||||||||||| |||||||| ||||||||||||||||| ||||| |||||  || | ||  |  | |||||  | ||
--------------atttttattattgaagtccttacaaggtcatgtcgttctagtgtttctattt-ctttgctaccagtaggaccctctcctga--------tatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA

upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G027043_T01 (Zea mays), 3'ss of exon 2
------------------------------------------gcaagctctcgccttttctcctcttttatatctctaaagttcagatta--ttga--ggcc----aagctctctgctttgtcctacttcagatgtccttttgaccagt-----tttttttcctat------tgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
                                              ||| |    ||| || || ||  ||||   ||| ||    ||||  | ||  ||||    ||| ||    | || |  | |||   || || ||   ||| ||       |   |  |||      |||||    |||||| | |      |||||||||||||| ||||| |||||||| ||||||||||||||||| ||||| |||||  || | ||  |  | |||||  | ||
gtaagttgcttggttggatcgtctttttttgctcttgtgctaatgtgctgtttaatttgctactgttg-atatagataatgtgtgtattaaatggattggccttacaaggtcatgtcattctagtgctttctatttctttgctacctgtaggaccctccctgatatacagtgtgttttgccagGTATAGCATACCGTTGGCCAATTCTTCTCGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA

upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA-
              | | |  |  |||||||   | |    || | | ||||   |    | |   || || | |   | ||    || | || ||   ||  |    |||| ||| | |||| || |||   |||||||| || ||||||||||| |||||||||||||||||||| ||||||||||| |||||| |  | ||| | || |||||  | || 
-------------atatattattatttatattcattag---cataattttgaactccctattttctctgtggcttgaattagg---ccctatgtcc---ttaatagattattattt-tgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT

upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G30030.2 (Glycine max), 3'ss of exon 4
gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
              | | |     |||||||   | |   |   ||| |  |  ||    | |||   | |    | ||  ||  |   | |    | |   ||     ||| ||| | |||  || |||   |||||||| || || |||||||| |||||||||||||||||||| ||||||| ||| |||||| |  | ||| | ||||||||  | ||
--------------tatattagtatttatattcattagcat--aattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagatt-----attattt-tgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA

upper sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
   | | |  || | |   ||      | | || |   ||  | |||  |||| |   |   |||||||| | ||    ||| |||  |  | |||||  || |||         |   |||| || |||| | | |||||  ||||||||||||||||||||||||||||||| || ||||||| ||| ||||||||| ||||| || |||||||  ||||
--gaacacctgcatgtgggccc-----acagcttt---gtgtatatt-ctgagcctgtgga-tctgctttatgctttgccagctgtt-tcctaaccagggttattt---------ttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
                     ttttgac  putative branch site (score: 3)
                               ttttttttcctattgt  putative PPT
                               ttttttttcctatt  TA-rich tract