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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatattcttaaatcgttaatcttctccgatctaatcgtacattatcatgttgtgctgattttggaatgtttttttggcagTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT

Basic information

species Arabidopsis thaliana
transcript AT2G18390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G07330.1 (Glycine max), 3'ss of exon 1
gtatgtcatattcttaaatcgttaatcttctccgat-ctaatcgtacat--tatcatgttgtgctgattttggaatgtttttttggcagTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT
||| ||  | ||||| |||    | |  |||  ||| ||   | | |||  ||   || | |  ||| |    | |  || ||  |||| ||| | || ||||||||||| || || || ||||| || ||||||||||| |||||||| || || ||||| || || || ||||||||||||||||| 
gtaagtttt-ttcttcaattccaatttctctttgattctctccattcataatacattgatatcttgaatc---agttgttgttctgcagCGGATTGGACAATTCTGGGAAAACCACAATCGTTCTAAAGATAAACGGAGAGGACACAAGCGTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATA

upper sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G38270.1 (Glycine max), 3'ss of exon 1
gtatgtcatattcttaaatcgttaatcttctccgat-ctaatcgtacattatcatgttgtgctgattttggaatgtttttttggcagTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT
||| ||  | | ||| |||    | |  |||  ||| ||   | | ||| ||    |    |      |    |||| || || ||| ||| | || ||||||||||| || || || ||| | || ||||||||||| ||||| || || || ||||| || || || ||||||||||||||||| 
gtaagttgt-tccttcaattccaatttctctttgattctctccattcataatacattaacaccttgaatcagttgttattctg-cagCGGATTGGACAATTCTGGGAAAACCACAATCGTTTTAAAGATAAACGGAGAGGACACCAGCGTCATCAGTCCCACGCTCGGCTTCAACATCAAAACCATA

upper sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g01820.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtcatattcttaaatcgttaatcttctccgatctaatcgtaca-ttatcatgttgtgctgattttggaatgtttttttggcagTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT
       || |||    |         ||| |       ||| || | | |   | ||   ||| |||      || |||| | ||| || ||||||||||| |||||||| || |||||  ||||||| || ||||| ||||| ||||| || ||||| || || || ||||| ||||||||||| 
-----gtatgttcaagcactccctgcattccctttctatatcatataatcagtgtttttgtctgctttaatggggtattttggacagGGGTCTTGATAATTCAGGGAAGACTACAATTGTGTTGAAAATCAATGGAGAGGACACTAGTGTTATCAGTCCCACCCTCGGCTTCAATATCAAAACCATC

upper sequence: AT2G18390.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S62_133V6.2 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------gtatgt-catattcttaaatcgttaatcttctccgatctaatcgtaca-ttatcatgttgtg---ctgattttggaatgtttttttggc---agTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT
                                                  || || |   ||  ||| || ||  |  |    |   | ||    || ||   ||| ||||    |||| | |   | | || |  ||   || ||  | || ||| | || || || || |||||   |   || || |||||||| ||||||   ||||| || |||||||||||||| ||||||||||| 
gtatgtgttcaactctgctgtttcagcttgtgatcggtgtccctgttctctaggttcgggttgataattcatttctggttgatgtcttcatttctcagttggtatgctgtgggtttgatgtagacgtttcttgtgtgcctcagAGGGTTGGACAATGCAGGAAAAACAACCATTGTGAAGCGGATTAATGGAGAAGATACAAGTAAAATTAGCCCTACTCTTGGATTCAATATCAAAACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatctaatcgtacattatcatgttgtgctgattttggaatgtttttttggcagTGGACTTGATAATTCTGGGAAGACGACGATTGTTCTGAAAATAAACGGAGAAGACACAAGTGTGATTAGTCCAACTCTTGGATTCAACATCAAAACCATT
                           tgctgat  putative branch site (score: 3)
                                         tgttttttt  putative PPT
                                       aatgttttttt  TA-rich tract