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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA

Basic information

species Glycine max
transcript GLYMA13G41060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 3'ss of exon 4
--------tcatgcatttgtgcactccccctagaaatt--agaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA----------------------------------
        ||     ||    || |     |    | |  |  || |  | ||||| | | ||||||  ||    || | |  ||| |  | ||||       ||||||||||||||| || ||||||||||| ||||| || || || || ||||| || ||||||||||| | |                                  
ctatattctctgtttttcagacattttttttcctcactccaagatttgttcttgatgtag-caatttgctacaagtactga--atgtgatatttgt-------aatgcagATGTGGATAGCAAAGGCAGAGTATGATGAATCTGGGCCATCTATTGTGCATAGGAAATGCTTCTAAATTGGCCAGATGGGGGAGGTAGAAGAAAGCCAGT

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
-----tcatgcat-ttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA----------------------------------
     || |  || ||       |    | | |   | ||| |  |||| ||||      |||       || |  ||  ||| |   | |  |||     ||||||||||||| |||||| | |||||||| || ||||| || |||||||| ||  ||||||||||||                                    
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttt----tgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 5
-----------------------tcatgcattt-gtgcactccccctagaaattagaatgttgttt--tgatatggtcaatttagtagggatattaat-------ga---tgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA----------------------------------
                          ||||||| |||   |       |   | |     ||||||  | | ||| ||   || || | |    ||||       ||   | |  |  ||  || | |   |||||||||||||||||||| | |||||||||||||| ||||| |||||||| |||||||| || || |                                    
gtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcagATGTGGATTGCGAAGTCGGAGTACGATGAGTCAGGTCCATCAATTGTGCACAGGAAGTGTTTCTAGAGCAGTGCGACACATCTTTTGCTTTTTTCAGCAC

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatatt-aatgatgaggcac-ttgtttttg--gaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA----------------------------------
                                     |  |  || | || ||| |   |            |   |||   |||| |       || ||   |||   || |    ||  ||||| ||   |   ||||||||||||| |||||  |||||||||| ||||| ||||| |||||||| || ||||| || || |                                    
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatat-tgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAGGTAAGATGTATGTACCGCTTGACTTTTTCATGAC

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S372_48V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatatt-aatgatgaggcac-ttgtttttg--gaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA
                                     |  |  || | || ||| |   |            |   |||   |||| |       || ||   |||   || |    ||  ||||| ||   |   ||||||||||||| |||||  |||||||||| ||||| ||||| |||||||| || ||||| || || |  
gtaaactgagtttgcatgatattttctacgttggacgtggtaaatat-tgaacttcttttcagttagcagtcggaatttgagtatgtttcgagaggttggttaattcggtgtttgcacatattgttctttctgtggtgcagATGTGGATCGCGAAATCAGAGTACGACGAGTCAGGTCCATCAATTGTGCATAGGAAGTGTTTCTAG

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 3
tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA
                           |  | ||  || ||||| |  | |    |||  ||   | ||  |  |       || |||||      ||||||||||||||| ||| | |||||||||||||| ||||| || ||||| ||||| || ||||| |  
-------------------------gtaccacaacattcttttgct-cgtttttcttatcagccttgtttttctt------tttctttttt----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG

upper sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA
                           |  | ||  || ||||| |  | |    |||  ||   | ||  |  |       | |||| |      ||||||||||||||| ||| | |||||||||||||| ||||| || ||||| ||||| || ||||| |  
-------------------------gtaccacaacattcttttgct-cgtttttcttatcagccttgtttttcttt-----ttcgtttct-----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA
                    tattaat  putative branch site (score: 2)
                   atattaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgcatttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA

tcatgca
- - - -tttgtgc
- - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaggc