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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgaaaaagtttccattttatcttcacaaattgtctcttctctctctatctctcttaaccaaaagaaggatttatgttgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG

Basic information

species Arabidopsis thaliana
transcript AT4G27910.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 20
gtgagttgaaaaagtttccattttatcttcacaaattgtctcttctctctctatctctcttaaccaaaagaaggatttat-gttg-------------cagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
 | |   || | | | |   ||| |  || |  | | || ||       | ||  || | |||    ||       |||| | ||             ||||||||||| ||||| || |||||||| |||||||| ||||||||||| ||  | || ||  | || |||||||| 
atcatacgatagactcttattttgaaatttatga-tggtatccctatcttataattcgcctaatattaattgcatcttattgctgtcttttgtattctcagCTTTTCAAAATCAGCGAGGAAGTAGTCGTTGATGCCACAGATAAAGGAAACGTGGCACGCTTGATTAATCATTCT

upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 21
gtgagttgaa-----aaagtttccattttatcttcaca--aattgtc-tcttctctctctatctctcttaacc--aaaagaaggatttatgt---tgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
||||||| |       | || | | |||||    ||||    |  || | || | | | |     | | ||||  ||| |    | |  |||   ||||||| || ||||| ||||||||||| ||||| ||||| || ||||||||||||||||||||||| || |||||||| 
gtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT

upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 21
gtgagttgaaa-----aagtttccattttatcttcacaa-----attgtctcttctctctctatctctcttaacc--aaaagaaggatttatg---ttgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
||||||| |       | || | | | ||| |  ||||      ||  | |  | | | | |     | | ||||  ||| |    | |  ||   |||||||| || ||||| ||||||||||| ||||| ||||| || ||||||||||||||||||||||| || |||||||| 
gtgagttaattcctctatgtctgcctattaacagcacactggtcatcatattatttatatgttatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATTAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT

upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA19G17460.2 (Glycine max), 3'ss of exon 12
gtgagttgaaaaagtttccattttatcttcac--aaattgtctcttct-----ctctctatctctcttaaccaaaagaag----gatttatgt-------tgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
     || |  |  || ||| | | ||   |   || || |||  |||      | | | | |||| | ||   ||   |    | ||| | |       |||||||||||||||| ||||||||||| || || ||||| || |||||||| |||||||| ||||| || || ||||| 
-----ttcattattttcccactgtttccctatttaagttttctgctcttctaattttttgtatctcatgacattaaattgtcctggtttctttatttttttgcagCTTTTCAAGATAAGTGAAGAAGTGGTAGTAGATGCCACTGATAAAGGAAATATAGCACGGCTAATTAACCATTCT

upper sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 21
----------------------gtgagttgaaaaagtttccat------tttatcttcacaaattgtctcttctctctctatctctcttaaccaaaagaaggat-ttatgtt-gcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
                      |||   | ||||     |||          |   |   | |||  ||| ||| |||  |   |  | ||  |||   |   | || |||| |||||| || ||||||||||||||||| || || ||||||||||||||||| || || || || || ||||| || |||
gtgagaatctttctctttctttgtgttctaaaaagaccaccaaaaacaaccaaaacttttacatttcctcatctttcttgagagcattaaaataaattgatattgttgtgtttgcagCTCTTTAAGATCAGTGAAGAAGTGGTAGTCGATGCTACAGATAAAGGAAACATTGCCCGCCTAATCAACCACTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtctcttctctctctatctctcttaaccaaaagaaggatttatgttgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
                         tcttaac  putative branch site (score: 2)
                                          atttatgtt  TA-rich tract