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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgtcttcgccatttccttttattctgttgtctgagaaggagattctgtttgaagctcaactaatttggtcatgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G50310.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G100815_T01 (Zea mays), 3'ss of exon 14
---------------------------------------------------------------------------------------gtaagattgtcttcg------ccatttccttttattctgttgtctgaga--aggagattctgtttgaagctcaactaatttggtcatgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG
                                                                                        || |  |||  |||       |||  ||    |||| |||  |||     |  | |  |    |   | |   || || |  || | |  || |  |  |||||||||||| |  |||  |||||||| ||| | ||||||||||||||||||||||||||||| ||||| || ||||| ||||| |||
gtaatgttgtacttagttttgtttattttctgtcacttctagatttattgctttccttttcattagctggctcctgtccatatcatcatatgtctgttctcgaacaaatcatggccaaccattc-gttacctgcagttaacaaaaccaagatattgttttgcttatattttcttttgtttattctgaaagCCTGGAGAATCACTGAGAGATTTCTACAAGAGGACAAATATGTACTGGCAAATGGCTGCCTATGAGCACACTCAACACACTGGAAAG

upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 17
--gtaagattgtcttcgccatttccttttattctgttgtctgagaaggagattctgtttgaagctcaactaatttggtca---tgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG
   |  | ||||| |   | |||      ||      |  |   |     ||| |  |||   | |   |   ||  |     | ||||||  |   ||||| |||||| | |||||||||||||| | ||| ||||||||||| ||||||||||| ||| | || ||||| ||||| ||||| || 
gtatctggttgtcatgtgcctttaaacgcatctctgggctttcaattagtatttttcttgtcccactgttttcttaattgaattcttgttgcatccaaagCCAGGAGAATCCTTGAAGGATTTCTACAGGCGTACAAATATGTATTGGCAAATGGCAGCCCATGAACATACTCAACACACTGGAAAA

upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 17
----gtaagattgtcttcgccatttccttttattctgttgtctgagaaggagattctgtttgaagctcaactaatt--tggtcatgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG
    ||    |     |          ||  | ||  || | |       |       ||      |||||| |||  |  |||| ||||  | | |||||||||||||||| |||||||| ||||||||||| || ||| |||||||||||||||| ||  | ||||| || ||||| ||||| |||
ttttgtgttgtgcatctaaaggcacatttaaactccattcttttcatctcatccatcattactttgtcaactgattgcttatcat-ttgtattttgtgaagCCTGGAGAAACCTTGAAGGACTTCTATAAGCGTACCAATTTGTACTGGCAAATGGCAGCACATGAGCACACTCAACACACTGGAAAG

upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S15_393V6.2 (Physcomitrella patens), 3'ss of exon 18
-----------gtaagattgtcttcgccatt-tccttttattctgttgtctg---agaaggagattctgttt----gaagctcaactaatttggtcat-gttgttg-----------------------------tctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG-------------
            | || |    ||     || |||   |  |||| || |||   ||| || |||  | |||    ||||||    || || | |  |  ||  ||                             |   || |||| |||||||  ||||||||||| | |   || ||||| ||||| ||||||||||| ||||||||||| || ||||||||||||||              
gtacgtgcactattagttgacatttatgtttctccggcttatctgctgcctgtaaagagggggataatttttcaacgaagctagtttatttcgtttctcattactggagcaacatgaactgacattagaatgaaatgactgcagCCAGGAGAAAGCTTGAAGGATTTTTTTGCTCGAACAAACATGTATTGGCAAATGGCAGCCTACGAGCACACTCAACATACTGGCAAAGAACTACGGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaggagattctgtttgaagctcaactaatttggtcatgttgttgtctttgaagCCTGGAGAAACTTTGAAGGATTTCTATAAGCGCACAAATATGTACTGGCAAATGGCTGCCTACGAGCATACCCAACATACTGGCAAG
                        aactaat  putative branch site (score: 2)
                                           ttgtcttt  putative PPT
                        aactaattt  TA-rich tract