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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgttaatacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC

Basic information

species Glycine max
transcript GLYMA06G03040.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 10
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaact-caaataatcgttaatacttg--acagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
 ||  |   || || ||    |  |  || |  | || |  |||    |||| | | |  |     |    ||| | | ||| ||   |   |  ||  ||||  | |||||||| || ||||||||||| || |||| ||| ||||| || || || ||| | |||||||| ||||||||||| ||||| ||||| || |||
-cttatatcttgtaaataaagaagtgtaattcatatcat--ttgaggtttgactcaatactgtaaggtggataagtgctaatgatgtgttccatgtggtacagTGTAGCCAAGTATCAAGAAGCAAATCCTGGAGTATTCACCATTGTGACTTTCCCTTTCTTATTTGCTGTCATGTTTGGTGATTGGGGCCATGGAATTTGC

upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 10
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactca--aataatcgttaat----acttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
          ||| |  |    ||||    |  ||    | |  |   |||  ||| || |  ||| | || |  |||   ||  || || ||    || |  |||  | ||||| || ||||| || |||||  |||||| ||||||||| || || || ||||| |||||||| ||||||||||||||||| ||||| || |||
-----caacctttcttgcttactttattttttcttctgcaatatccatttgtgttagtgttcgtct-cttgaatttcatggatcttctttgatcactacattgcagTGTGGCCAAATATCAGGAGGCCAATCCTAGTGTATTCACAATTGTTACCTTCCCCTTCCTGTTTGCTGTTATGTTTGGTGACTGGGGTCATGGAATCTGC

upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------actagtggattttatatccct---atttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgtt-------aa---tacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
                      |   | | ||||     |    | ||  |  |||  | | | ||        || | ||| ||  |||| | | ||||   | |  |||       ||   ||||   |||  | |||||||| |||||||| ||||| ||||||| ||| ||||| || || || |||||||| ||||| ||||||||||| ||||||||||| ||||||
gtaagtgtctttctggagcttttgacgcagtttaagaaacgggaaattgaagatagcctttgaattataagaaaatgtgttg-tagactgcgttttactcttgtcacagtttcctatgaactctactctgcagTGTGGCCAAGTATCAGGAAGCCAATCCAGGTGTATTCACCATTGTTACCTTCCCCTTCCTTTTCGCTGTTATGTTTGGTGATTGGGGGCATGGAATATGC

upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 3'ss of exon 10
actagtggattttatatccctatttacaactagt--ttcttagttgcttcttgatttattgataatctgcctgtaac--tcaaataat-cgttaatacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
  | ||   ||||  |    ||||  |   |||   | ||| | |   | || |  |    || |||     |||    |||| |||| |  ||||| ||  |||  | |||||||| |||||||  ||||| |||||||||   ||| | ||||| || |||||||||||||| ||||||||||| ||||| ||||| ||||||
--ttgttatttttcaaatggtattgccctatagaagtacttggctaaatgtttaagtggc-atcatccaatagtagagatcaactaattcaataatattt--cagGGTGGCCAAGTATCAGGAAGTGAATCCTGGTGTATACGTGATTATTACATTCCCTTTCCTTTTTGCTGTAATGTTTGGTGATTGGGGCCATGGAATATGC

upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------actagtggattttatatccctatttacaactagtttcttagttgcttcttgatt-tattgataatct-gcctgtaactca----aataatcgttaatacttg-acagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
                            | ||  ||   |   ||  |  ||    |||  || |||  ||      |||| |  | ||| | | || | |  | ||    | | ||| || | || || ||||| | |    ||| ||||| |||||||| |||   |  || ||  | |||||||||||||| || ||||| ||||||||||||||||| ||||| || |||
gtaggtgtggtgatcagtataattatgtcgaggagaagctg-gtctgtgatttttgcta--tttttaactgtcaagcgattgtggtcatatttttgcttctttcacacggtactgatcatttaaacatgtacagAGTGGGGCGGTATCAGGAGGCAAATCCTGGTTGTTTTACCATAATAACATTTCCATTCCTGTTCGCTGTTATGTTTGGTGACTGGGGCCATGGAATCTGC

upper sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ20446 (Selaginella moellendorffii), 3'ss of exon 9
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgttaatacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC-
                       | ||| | || |  ||      |||  | ||  ||  || | ||             |||  || | |       ||  | || |  ||| ||||||||||||| | ||| || ||||| || || ||||| || ||||| |||||||||||||| || |||||||| || || ||  
----------------------gtaacagcaagctctttctggctttcacgtttcgttcttactgtgt------------taactgtcagtgt-----agGGTGGCGAGATACAAGGAAGCAAATCCTGCTGTGTATACAATAGTTACTTTTCCGTTTCTTTTCGCTGTGATGTTTGGGGATTGGGGGCACGGGAT-TGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgatttattgataatctgcctgtaactcaaataatcgttaatacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC
      atttattgataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagtggattttatatccctatttacaactagtttcttagttgcttcttgatttattgataatctgcctgtaactcaaataatcgttaatacttgacagAATCGCCAAGTACCAGGAAGCAAATCCCGGTGTATACACAATTGTCACATTTCCATTCCTTTTTGCTGTGATGTTTGGTGACTGGGGGCATGGCATATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcaaa