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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagctttttcttgaaaacaattttcagagcaagaccacaaataactctggatccaatccgcttggttttacaaggaaacctatcacacaatgggttctattcctgttttctgataagaaccactttattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG

Basic information

species Arabidopsis thaliana
transcript AT5G61980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 9
gcaagctttttcttgaaaacaattttcagagcaagaccacaaataactctggatccaatccgcttggttttacaaggaaacctatca-cacaatgggttctattcctgttttctgataagaaccactttattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG
                                                                            | || ||||   || |||  |   | |  |    ||   |  | |   |  |  |||    |  |||  |||  |  ||||||||||||||||| ||||| ||||| |||||||| | ||| ||||| 
----------------------------------------------------------------------------gtaatctattgtcataatttgcattttgacatccttagtaatatatgaatgtggttcaaggttccact-gttgctgtttctttcagGGATATGAGCTACTCCATCAGATGGAGCCATATATCAATCAA

upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 6
gcaagctttttcttgaaaacaattttcagagcaagaccacaaataactctggatccaatccgcttggttttacaaggaaacctatcacacaatgggttctattcctgttttctgataagaaccactttattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG
                                                                            | | |   |  || | |      |  |     | | | ||  |||  | |    | | |  |     | ||  | ||| |  ||||||||||||||| | |||||||||||||| | ||||||||||
----------------------------------------------------------------------------gtacctccttgcatattttaccttggtgtaactatgttat--gaatgaatgagattgat--cctgtcaattgctacttgt--cagGGATATGAACTATTGCATCAAATGGAGCCATATATTAATCAG

upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 9
gcaagctttttcttgaaaacaattttcagagcaagaccacaaataactctggatccaatccgcttggttttacaaggaaacctatcacacaatgggttctattcctgttttctgataagaaccactt--tattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG
                                                                           | | | |  |  ||  ||   |  ||||    |||   | | |    ||  |   ||||    | || |   | |||  ||  ||||||||||||||||||||||||| ||||| || | ||| ||||| 
---------------------------------------------------------------------------gtacatccttgccattattt-tcatattgacatttctaggttatgtacatgtgtgattcaaactttctctgttgctt--tttcttcagGGATATGAACTACTACATCAGATGGAACCGTATATCAATCAA

upper sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G090752_T01 (Zea mays), 3'ss of exon 1
gcaagctttttcttgaaaacaattttcagagcaagaccacaaataactctggatccaatccgcttggttttacaaggaaacctatcacacaatgggttctattcctgttttctgataagaaccactttattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG
                                                                            | | |   |  || | |  |   | |        | || || | |  | | |  |   |  |  |  | ||  ||  | | |||||||||||||||| | ||||||||||| || | ||||||||||
----------------------------------------------------------------------------gtacctccttgcatattttgccttgtggtgtagctatgttatgcatgaatgtgattaat--cctatcaatt--tctatttgtcagGGATATGAACTATTGCATCAAATGGAACCATATATTAATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctgataagaaccactttattcgctttctcacgagttcttccttctttcagGGATATGAACTACTACATCAAATGGAGCCTTTTATTAATCAG
                             ttctcac  putative branch site (score: 2)
                                       ttcttccttctttc  putative PPT
                 actttatt  TA-rich tract