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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttcctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG

Basic information

species Arabidopsis thaliana
transcript AT5G55040.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G05000.1 (Glycine max), 3'ss of exon 6
tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttc-ctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
||  |||      ||  |||   | |  |  |  ||    || |   |||   |||     ||| |||   |  |  ||       | || |||||||||||  |||||||| || ||||||||||||||||||||||||||| |  |||| ||| | ||| | ||||||
taacactttgactgtccattaatttgtcttcttaattgagtaaaa-attggaagacaagattttgctataattatactgactggtgaattgttgaatgcagATTGATGTCTTTTTAATTTGCTCAAATGCAATGCAATACAATGCACCAGAGACTATATACCACAAACAG

upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G43050.1 (Glycine max), 3'ss of exon 5
--tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttc-ctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
  |    |||  || ||| |||   |    || |   | |   | |   |||   |||     |||||||   |  |  ||       | || || ||||||||  |||||||| || ||||||||||||||||||||||||||| |  |||| ||| | ||| | ||||||
attttgtctgtgct-gtgcattaattgtcttcctaattgactaaaa--attggaagacaagattttactataattatactgacttgtgaattgttaaatgcagACTGATGTCTTTTTAATTTGCTCAAATGCAATGCAATACAATGCACCAGAGACTATATACCACAAACAG

upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G02590.1 (Glycine max), 3'ss of exon 5
-tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttcctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
 ||  |    |  |    ||||   |     |  |||  |||      ||   ||| ||        ||   | |  |   | || |  | |||||||||||| ||||| || ||||||| ||||||||||||||||| |||| |  | || ||  | ||| | ||||||
ttattatcatttgaac-catttttaaaacgtacatattgtcttcctgatttagtgattttgaaaggcaaatagatgatttgaatgcaactgttgaatgcagAGTGATGTATTTTTGATTTCCTCAAATGCAATGCAATTCAATGCGGCGGAGACCATATACCACAAACAG

upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G10890.1 (Glycine max), 3'ss of exon 4
-tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttcctttactaa-cctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
 ||  |        |   |||   |    || |   | |   | |   |||   |||    ||||| || |   |  |||  | || | || |||||||||||| ||||| || || |||||||||||||||||||| |||||| |  | || ||| | ||| | ||||| 
ctatcatcttaactgcacattaattgttttcctacttgagtaaaa--attggaagacaatatttacaaaacactgacttgtgaatgaaattgttgaatgcagAGTGATGTATTTTTAATTTGCTCAAATGCAATGCAGTACAATGCACCGGAGACTATATACCACAAACA-

upper sequence: AT5G55040.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G10850.1 (Glycine max), 3'ss of exon 5
--tagaactgctctagtgtatttgctaggatcatgtataatctataccgttgcttgacttcctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
  ||  |        |   |||   |    || |   | |   | |   |||   |||    ||||| | |   |  ||| || || | || |||||||||||| ||||| || || |||||||||||||||||||| |||||| |  | || ||| | ||| | ||||||
tctatcatcttaactgcacattaattgttttcctacttgagtaaaa--attggaagacaatatttacaatcactgacttgtaaatgaaattgttgaatgcagAGTGATGTATTTTTAATTTGCTCAAATGCAATGCAGTACAATGCACCGGAGACTATATACCACAAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttgcttgacttcctttactaacctggttttggaactgtatttcttgaatgcagAGCGATGTCTTATTGATTTGCTCAAATGCAATGCAATACAATTCCTCAGACACTGTCTACTATAAACAG
                 tactaac  putative branch site (score: 0)
                                       tatttctt  putative PPT
               tttactaa  TA-rich tract