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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatctcttactctttaggatcaacatcttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

Basic information

species Arabidopsis thaliana
transcript AT5G15080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
-----------gtacgtatctc---ttactctttaggatcaacat--cttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
           || | |   |    ||||   ||     | |||    | | || |   |||||| ||   | ||     |  |  ||||| |||||||||||||| ||||||||||| |||||||||||||  ||||  |  | |||||| || || |||||| | || ||||| |||||||| ||||
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgta--tattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG

upper sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
------------gtacgtatctctta-ctctttaggatcaacatcttatatttgcaaattttt-taaccaataaat-cccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
            ||  |    ||  | |   |||| |        ||| |||   | ||| |  ||     |||||   |||| ||||||||||||||||||||| || ||||||||||| || |||||||  ||||| |  |  ||||| ||||| |||||| | || ||||| || ||||| ||||
gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
gtacgtatctcttactctttaggatcaacatcttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
||| | | || |       |   |  || || | ||   | ||||| | ||  | || | ||    || ||||||||| || |||||||| || |||||||||||||| |||||||  ||||| |  |  ||||| ||||| || |||||||| ||||| |||||||| ||||
gtaagcaactatattgaaatgttaaaaatat-tcattcatacaaatgtatttgctaacatattt--ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
----------gtacgtatctcttactctttaggatcaacatcttat--atttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
          | | ||||   ||| |  |||   ||| | ||  |   |   |||||  | | ||  || ||||    ||   |||| |||||||| || || || |||||||||||||||||||||| |||||| |  |  || || ||||| ||||| || |||||||| |||||||| ||||
gtatgtaggtgaaggtattaattatttcttat--tcatcctccaaccaaaaagcaaaaatctaaaaaaacaaat---gtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

upper sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
--gtacgtatctcttactctttaggatc---aacatcttatatttg----caaattttttaaccaataaatcccattgtc---agGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
   |  |  |     |      ||| |    |  || || |||       | ||  |   |||  | |||    |||||    |||| |||||||| ||||| || ||||||||||| |||||||||| |||||| |  |  || || ||  | || || || || ||||| |||||||| ||||
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaggatcaacatcttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
                             ttttaac  putative branch site (score: 2)
                                           tcccatt  putative PPT
              ttatatttgcaaattt  TA-rich tract