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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgttctcttcgaacgggaattgtttacataaatagttagtagaagaagagtttgaacagtaactggaaattttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA

Basic information

species Arabidopsis thaliana
transcript AT1G53880.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G53880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 3'ss of exon 2
gtcagtgttctcttcgaacgggaattgtttacataaat-agttagtagaagaagagtttgaacagtaactggaaattt-tgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
|| |        |   |    |  || |||| |||||| ||    |  |     || |      ||      |  ||| ||||||| || | || |||||||||||| || || ||||| || |  ||||| |||||||||||||| |||||||  ||||||||||| || ||| | |||||| 
gttatctagaattataatatagttttttttatataaatgagactttccacctttagctaatttcgtggaacaatgtttgtgcagGCTCGTAAGACAATTGCAATGCTCAGCCAGGATTTTATTTCAGATGGTTGTACTATTCTGGTACATGGTTATTCCAGAGTTGTTTTGGAAGTTCTAAAGC

upper sequence: AT1G53880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G084647_T02 (Zea mays), 3'ss of exon 2
------------gtcagtgttctctt-cgaacgggaattgtttacataaatagttagtagaagaagagtttgaacagtaactggaaattttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
              ||    | ||            | | | |  | ||  | ||| |          ||           | |   |||| ||||| || | || |||||||||||||||||| ||||| || | ||||||||||||||| || |||||||| |  |||||||| ||  | ||| | |||||| 
gttatccacatatccaaaactttccaattgttatctagtttctgtacaagaatttaatccttttgttcttatgcttcggggtcgtgttttttcagGCTCGCAAGACAATTGCAATGCTTAGTCAGGATTTTATTTATGATGGGTGTACTATACTTGTCCATGGGTATTCCAGAGTAGTACTGGAAGTTCTAAAGC

upper sequence: AT1G53880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G45180.1 (Glycine max), 3'ss of exon 2
------gtcagtgttctcttcgaacgggaattgtttacataaatagttagtagaagaagagtttgaacagtaactggaaattttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
        ||    || || |   |     || ||| | |   |   |       |   | |||      |  ||     ||||||||||||| |   | ||||||||| | ||||| ||||| ||||||||||| ||||| ||| |||| |||||||| |||||||| || |||||| | || ||  
gcaacttccaactctcgctgcactctaattttcttttctttcctcactctctt--gcccattttcctttctttct-----ttttgcagGCCCGCAAAGTTATTGCAATGTTGAGTCAGGATTTTATATTTGATGGCTGTACAATTTTGGTTCATGGTTTTTCCAGAGTCGTCTTTGAAGTCCTGAAAC

upper sequence: AT1G53880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G42430.1 (Glycine max), 3'ss of exon 2
----gtcagtgttctcttcgaa-cgggaattgtttacataaatagttagtagaagaagagtttgaacagtaactggaaat-tttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
     |      ||||    |  |     || ||| | |   |   |         | | |        |   ||    | |||||||||||| |   | ||||||||| | ||||| ||||| ||||||||||| || || ||| |||| |||||||| ||||||||||| |||||| | |||||  
gcaaattccaactctcactaactctaattttcttttctttcctcactctcgtgcccatattcctttttttttttgtccttctttgcagGCCCGCAAAGTTATTGCAATGTTGAGTCAGGATTTTATATTTGATGGCTGCACAATTTTGGTTCATGGTTTTTCCAGAGTTGTCTTTGAAGTCCTAAAAC

upper sequence: AT1G53880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g00390.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------gtcagtgttctcttcgaacgggaattgtttaca---taaatagttagtagaag----aagagtttgaacagtaactggaaattttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
                                                    ||| | || | | |     | |||| |   ||    ||||| | |    |||    || |  ||  |   || |    |  ||  ||||| || |  || |||||||||||| |||||||||| ||||||||||| ||||| ||| |||| ||||||||||| |||||||| || ||| | || ||||
gtatattgattatatatttatttttttccctttttccatggtaataattgtttcactattgtgt-catgttgcaattatccccaatgcaaatattcaaattaagcacaaaaacctttcaacttaccccttatattgacagGCACGCAGAATCATTGCAATGCTTGGTCAAGATTTTATATTTGATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacataaatagttagtagaagaagagtttgaacagtaactggaaattttgcagGCCCGAACGATAATTGCAATGCTTAGTCAAGATTTCATATTTGATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGA
                                  cagtaac  putative branch site (score: 2)
     ataaatagttagta  TA-rich tract