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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG

Basic information

species Arabidopsis thaliana
transcript AT1G50460.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 5
gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaag-aaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
             ||||    |||  ||||          | | |           ||| || |      ||   |||| |||| ||| |||| || |||||||| |||||||| |||||||||||||| || || ||||| ||||||||||||||||||||||| |||||  ||||| ||||||||  |
----------gttttgccctttcttcttttgacttttgtttattgttttgcttttgaacttgctg-----tgtaacccttttatattttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCCTCTCACTTACCAAGAACGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAG

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G43650.1 (Glycine max), 3'ss of exon 5
gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
          || ||||    |||  ||||  |     | |||        |     | |||  ||        |||| ||||  || |||| || |||||||| |||||||| |||||||| ||||| || || ||||| || ||||||||||| |||||||| |||||  | ||| ||||||||  |
---------gtctttgccctttcttcttttc-acttttgttttgcttttggacttgccgtgt--aa--------cccttttataatttagGTTGTCAATATGGAATGGGGAAACTTTTGGTCATCTCACTTACCAAGAACATCATATGACATTGATTTGGATGCTGAGAGCCCTAATCCAAATGATCAG

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
       | |   || |||| | | |  ||   ||     ||||    | |  |      | |||  ||     | ||  | | | | |||| ||||||||||| |||||||| |||||||| |||||||| || ||||| || ||||| ||||| || ||  | || ||  | ||| ||||||||  |
-------gtactgtt-catgttttttaattttcaattttgtttattgtctattgttttgagcttattataa---ctcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G02450.1 (Glycine max), 3'ss of exon 5
--gtactaaga-atcattgcatggtctatttttagaaaccagctttagacccaaaagaaacat----gtttaagattgattc---cctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
   |  || || ||   |  |   ||| |||||          |||  ||        |   |     ||| |   |  |      ||  | | | | |||| ||||||||||| |||||||| |||||||| |||||||| || ||||| || ||||| ||||| || ||  | || ||  | ||| ||||||||  |
acatcttatgatattgatttagactctttttttgtttgtttttttttcacttttgtttattgtcttgttttgatcctagtataaatcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S3_571V6.1 (Physcomitrella patens), 3'ss of exon 4
gtactaa---gaatcattgcatggtctatttttagaaacca---gctttagacccaaaagaaacatgtttaagattgattccct-cttatgtttc----agGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG-
  || ||   ||||| ||  |  |     | | |   | ||   | | | ||       | |   || |    | | |||      |||||        ||||| | |||||||||||||||||||||||||| || ||||||||| | || |     |||      ||||||   ||||||   ||| ||   || ||  
-gacgaaatcgaatctttctagagctgcctctcatgtaacatatgatgttgaattcctggtaggttggtagcaactaatttaaggtttatgcccttgatagGTGATCAATATGGAGTGGGGAAATTTTTGGTCGTCACATTTGCCTCGGACCTACGTGGACGAGCTATTGGATAACGAGAGTCTGAATCCAGGAGA-ATAC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S414_10V6.1 (Physcomitrella patens), 3'ss of exon 4
-------gtactaagaatc--attgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtt-taagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG-
        |  || || ||  ||   ||| | | |||   |||   | ||   |        | ||   ||  |   ||  ||    |    | |  |||||| |||| ||||||||||| ||||| ||||| || ||||||||||| ||||     ||      |||||||   |||||||  ||  ||   || ||  
acgttgtttcatatgattcccatgagatgatatttttgacgaactaaactagtgctattgttgcaatgcgtcatctaatctataggatgaattttgacagGTGATAAACATGGAGTGGGGGAATTTCTGGTCATCACATTTGCCTAGGACTTATGTGGATGAATCCTTGGATAACGAGAGTTTGAACCCAGGAGA-ATAC

upper sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S401_23V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGA-TATG
                 || || |       | |  |   |||  | |    |     ||||  |   |||| ||   | || | | |   | |  |   |||||| | ||||||||||||||||| |||||||| || ||||||||| | || |     ||       ||||||   |||||     || ||   || ||| 
actgctctcgtgtaggatatgacttggaatttcgggtgggtttgaatattgaccacgtacccttacataacaagtgatatatggttcctgaccttgg---cagGTGATCAATATGGAGTGGGGAAACTTTTGGTCATCACATTTGCCTCGGACCTATGTGGATGAGTTATTGGATAGCGAGAGCCTCCATCCAGGAGAATAT-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG
                               gattgat  putative branch site (score: 4)
                                     ttccctcttatgtttc  CT-rich tract
                          tttaagatt  TA-rich tract