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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctcaggctaacttgttattcttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC

Basic information

species Glycine max
transcript GLYMA05G00820.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 3'ss of exon 12
--------atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctcaggctaacttgttattcttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
           | | ||  |  |   |||   |  |     | ||| |  |    | || |  |||| |  |  |||||      |  | ||| |       ||||||||| | | |||||  |||  ||| ||  | |||||||||||||||||||||||||   ||| ||||| ||| | || ||||| |  ||||| ||||||||
ctgattgagcatatcttatttctgcattttttatcatcaaca-tatgtgtttgcttgttttggtatgtt--gcttaactc-----ttatgttgatcatgatgttgcagTTATCTCCACCCTCTTAACATTTGTAACAATGTTTCGGAAAGCACATGAAGAGAACCGCAAGCAAGCTGAGCTCGATAAGAAAAGGGCTGAAAAAGAGGC

upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G07760.1 (Arabidopsis thaliana), 3'ss of exon 25
----------atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctcaggc--taacttgttattcttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCA---CATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC---------------------------------------
          |  |   |     | || | ||  || |    ||| |  |      ||  |   || | |  ||    ||||     ||  |||| | | |  |   |||||||||| | |||||  | | |||| || | ||||||  || ||||   ||  |||||||| |||||||||| ||||| ||||||||||||||||  || || ||                                       
gtatacgatgaacttcatcatcctcatttgtgctaatatacataaaaagtggctggctcattgtttttacgtagctaataacaatacatgattatcgatattgc--ctgcagttaccgcgaccctcttgagttttgtaaggttgtttacgacagCAGCACACCAAGAGAATGTCAAACAAGCGGAGTTGGAGAAGAAGAAAGCTGCAAAGGAAGCAGAAATGGAGAAGACGAAGAAACGAGTCAGTCTCACTAA

upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G07780.1 (Arabidopsis thaliana), 3'ss of exon 13
atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctc-aggctaacttgttattcttat------tggt--ttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
              ||||  | | ||       | |  || ||||| | ||||| ||   |  |   |  ||  ||  |  ||       ||||  |  |    |||||||||| | || ||  | | ||||||| | ||||||  ||||||||||||||||||| |||| ||||| ||||| ||||||||||||||||  || |||||
-------------gtatgcctcggaaacaataaacttcatcctcatttattctaataccatagaaagtggctcattgctaataacatacatggtgatcgattgctgcagTTACCGCGACACTCTTGAGTTTTATAAGGTTGTTTAAGAAAGCACATGAAGAGAATGTCAAGCAAGCGGAGTTGGAGAAGAAGAAAGCTGCAAAGGAGGC

upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 15
--------------atgtgtgtttctgttatgtttggaaa------gagtggtaatatattctc-atcttttctattatgctcaggctaacttgttattc-------ttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
              || |    |||  |  | || |||||      ||  |  || | |||| | || | ||   ||| | |     |   ||||   |        |||   | |  |    ||||||||| |  || ||  | || ||||||   ||||||  ||||||||| ||||||||| | |||||||| || || ||||||||||||||   |||  ||  
gtatggcgtaaaatatataaacttcaatcttcttaggaaatacatagaaagaaaaaaaattccctatttgttactttaagttggaattgttttgtagctaacaataattacctgatggattgctgcagTTACTATGACTCTCTTTAACTTTATAAAGTTGTTTAAGAAAGCACACGAAGAGAATGTTAAACAAGCTGACTTGGAGAAGAAGAAAGCCATGAAGCAG--

upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 16
------------------------atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctcaggctaacttgttattcttattggttta---acaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
                        |  |    ||  |  ||   | |||| ||    | |   |  || |  |||   |     |       |  |  || |  ||  || | |   ||   |||||||||  |||||||  | ||||||||| | ||||||  ||||||||| ||||||||| |||| ||||| ||| |||||||||||||||||   || || ||
gtatgacgaggaatctataaacttaaatcctcttgggcaatacatagaaaaagaaaaagtccctaatcgttatttagttggaagtgttatgtagctaataataataccgggtaatggactgctgcagTTACTGCAACCCTCTTGAATTTTATAAGGTTGTTTAAGAAAGCACACGAAGAGAATGTCAAGCAAGCGGAGCTAGAGAAGAAGAAAGCTCTTAAGGAAGC

upper sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 18
atgtgtgtttctgttatgtttggaaagagtg-gtaatatattctcatcttttct---attatgctcaggc-taactt---gttattcttattggtttaaca-attgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
         |  || | |     || |  |  || ||  ||   ||| |||| |    | ||||| |  | |||||     | ||  ||||||||  |      |||||| ||   ||||||  |||| |||||| || |||| |||||||| |||||||||||   ||| ||||| || ||||||| |||||| ||| ||||||||| 
---------taagtcaagaactcaatgtttatgtgatccatatacattttttttttggtaatgctgaatcctaactctccatcatatttattggtgcattttgatgcagTCACTGTAACCCTCTTAAACTTTATAAGACTGTTCCGGAAAGCGCATGAAGAGAACTGCAAGCAAGCTGAATTAGAGAGGAAGAAGGCTCAGAAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttctattatgctcaggctaacttgttattcttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC
                         ttgttattcttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtgtttctgttatgtttggaaagagtggtaatatattctcatcttttctattatgctcaggctaacttgttattcttattggtttaacaattgcagTTACCACAACCCTGCTAAATTTTATACGATTGTTTCGGAAAGCACATGAAGAGAATATCAAACAAGCAGAGTTAGAGAAGAAGAAAGCTGAGAAAGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - gtttctg
- - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaact