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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG

Basic information

species Arabidopsis thaliana
transcript AT3G20040.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
                                                       |||    |        |||| |||    |  ||| ||||    |     ||  ||  | ||||  |   |||||| ||||||||||| ||||||||||||||||||||||   | |||||||| ||||||||| |||| |||||||| |||||    ||| |||||||   |
----------------------------------------------------gtctttgccctttcttcttttcactttt---gttttgcttttggacttgccgtgtaacccttttataat---ttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG

upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 5
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
                                                 |       |   |||    |  ||   ||||   |  ||| ||||    |   | ||  ||  | |||| ||   |||||| ||||||||||| ||||||||||||||||| ||||   | |||||||| || |||||| |||| |||||||| |||||    ||| |||||||   |
------------------------------------------------gttttgccctttcttcttttgacttttgtttatt-gttttgcttttgaacttgctgtgtaacccttttatatt---ttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCCTCTCACTTACCAAGAACGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAG

upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
                                                   |  ||| |  ||    |   ||||||||     | |   | || | ||     |  ||      |  | | | |||||| || |||||||| |||||||||||||||||||||| | | |||||||| || |||||  |||| || ||  | || ||    ||| |||||||   |
-------------------------------------------------gtactgttcatgttttttaattttcaattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG

upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
                  | |   ||  |      |||||  |      |    ||||   || |||    ||   ||||   | |||| |||  || |  |    ||  | ||||      | |||||| || |||||||| |||||||||||||||||||||| | | |||||||| || |||||  |||| || ||  | || ||    ||| |||||||   |
-----------------acatcttatgatattgatttagactctttttttgtttgtttttttttcac----ttttgtttatt-gtcttgttttgatcctagtataaatcttctgtt------tattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG

upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S3_571V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaataactattaagaatcgttacatagttca-tccttagaaaccagccatcaaagtt-tagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG-
                      ||  | |  | || ||  | | | |||    | ||   | ||      | ||||    |   ||  ||| |     ||  |||| | |   || |    |||   |||||| ||||||||||||||||||| |||||||| || | | ||||  | || |     |||      ||||||   |||||| ||||| ||   || ||  
---------------------gacgaaatcgaatctttctagagctgcctctcatgtaacatatgatgttgaattc---ctggtagg-ttggtagcaactaatttaaggt---ttatgcccttga--tagGTGATCAATATGGAGTGGGGAAATTTTTGGTCGTCACATTTGCCTCGGACCTACGTGGACGAGCTATTGGATAACGAGAGTCTGAATCCAGGAGA-ATAC

upper sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S401_23V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttatt--ttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGA-GTTGGATGCAGAGAGTATGAATTCAAATGACATG-
                        |  | ||     ||| |     |  |   | ||| |  |     || || ||| |  |  || |    ||   |      |||||  | |||  |     ||  ||||| ||||||||||||||||||||||||||||||| | | ||||  | || | || ||     |   ||||||   |||||  |  || ||   || ||  
------------------------actgctctcgtgtaggatatgac--ttggaatttcgggt----gggtttgaatattgaccacgtacccttacataacaagtgatatatggttcctgaccttggcagGTGATCAATATGGAGTGGGGAAACTTTTGGTCATCACATTTGCCTCGGACCT-ATGTGGATGAGTTATTGGATAGCGAGAGCCTCCATCCAGGAGA-ATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG
           acttgat  putative branch site (score: 5)
                                         ttatttt  putative PPT
                           tttatgatactttgtt  TA-rich tract