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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatttttcagtttatgtttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

Basic information

species Glycine max
transcript GLYMA05G36910.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 3'ss of exon 15
---gttcatttttcagtttatgtttgaataagatatgcttctacg-----tggattgcatgatcatattttattcatgaa-----tggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
     || |||   |   | ||  || || | |  | ||  || |         |||||     |  ||| |    ||||     || ||| |     |||| || ||||| ||||||| |||  ||||||  |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||||
tactctcttttactaaactgtgcctggatgaca-gtactaatatgatcagctagttgcaaagagaggtttgaaaattgaaacatctgttctctgcttgcagGAGACATTGGTGAGTGGCAACCTGATGGAAGTATGAAAATCATAGATCGCAAAAAGAATATCTTCAAGCTTTCACAAGGAGAATATGTAGCAGTAGAAAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g48910.1 (Oryza sativa), 3'ss of exon 15
-gttcatttttcagtttat--gtttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaaca----------gGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
  ||||| |   |    |      ||   |    ||||||  || |      | ||||   ||  |  |  | |  ||   | ||  | |          || || ||||| |||||||   |  |||||| |||||| || |||||||| |||||||| || || ||||| || |||||||||||||| ||||| || ||
ttttcatatcaaaagagactgacctgttaacagaatgctttgacatttccccc-tgattgaatgcttcttgtaaccggctcactttgatatcttactgtagGAGACATTGGTGAGTGGCAGTCTGATGGAAGCATGAAGATCATTGATCGCAAGAAGAACATCTTCAAGCTCTCCCAAGGAGAATATGTCGCTGTGGAGAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM5G861300_T01 (Zea mays), 3'ss of exon 15
-----------------------------------------------------------------------------------------gttcatttttcagtttatgt---ttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaa-acagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
                                                                                          | ||   |||   | || |    |||  || || | ||  |  |||         || | |  | |  |||   ||    || |    |||| || ||||| ||||||| |||  ||||| | |||||||| || || || || ||||||||||| || |||||||| || |||||||| || ||||||||
gtagtgtgttgcccgttctactgctctgtttttacatagtgatcactattcatgacacacattgttagtagttaaaattccatgtagaaatccagggttccaatcatataccatgaccaaaatttcctattttgtgctcccgcctataaaacctgacacatc--tgcctcatctgttgcagGTGACATTGGTGAGTGGCAACCTGATGGATCTATGAAAATCATAGACCGTAAAAAGAATATATTCAAACTTTCACAGGGTGAATATGTGGCAGTTGAAAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 15
--gttcatttttc--agtttatgt----ttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggt-ctatttaaac----agGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
   ||  ||| ||  |  || | |    ||   ||  ||||   | |  || |   |     |  | ||   |||    |   | ||  ||| ||    ||| ||| |||| ||||||| |||  |||||| |||||| || |||||  ||||||||||||| ||||| || ||||||||||| |||||||| || || ||
gtatttctttctctgaacttgtatacaattagttagaatattggtttttgtagtccggtgagttcttttcagttctcacactctgcttcttatactctcagGTGATGTTGGTGAGTGGCAACCAGATGGAAGCATGAAGATAATTGACAGGAAGAAGAATATCTTTAAACTCTCACAAGGAGAGTATGTTGCGGTGGAGAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 3'ss of exon 15
----gttcatttttcagtttatgtttgaat-aagatatg----cttctac---gtggatt-gcatgatcat--attttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
    | |||| ||    ||| |  |||||| ||| | ||    | ||||    ||||||| |  |  | |   |  ||  | |||| |  ||| || |  |||||||| |||| ||||||| |||  |||| | |||||||||||| || || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||
gtttgctcatattggcatttcttcttgaattaagttttgaggtcctctattttgtggattcgtttctttaacaaccttgctgatgacttatcttttca--cagGGGATGTTGGTGAGTGGCAACCTGATGGGAGCATGAAAATTATCGACCGCAAGAAGAACATATTCAAGCTTTCACAAGGAGAATACGTTGCCGTTGAGAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S47_161V6.1 (Physcomitrella patens), 3'ss of exon 15
---gttcatttttcagtttatgtttgaataag-atatgcttctacgtggat-------tgcatgat--catattttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
   |  |  || |     ||||||  ||  |  ||     | |  || |||       |  |||||  ||||    | |  |   || | | | ||  |||| |||||||||||||||| |    ||||  |  |||| ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| || |||||
caggggctgttcttgaaatatgttgaaaggattatccatctttgggtcgatgaataagtcaatgatgacatagacaagttctttgtgatgtgtgtat-cagGCGATATTGGAGAGTGGCAAAAAGATGGTGCTTTGAAGATTATTGATCGCAAGAAGAACATCTTCAAGCTTTCTCAAGGAGAATACGTTGCAGTCGAAAA

upper sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 15
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------gttcatttttcagtttatgtttgaataagatatgcttctacgtggattgcatgatcatatttt-attcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
                      |   | ||||||||||   ||  |    ||||     | |||  ||       |||| | |||| |  ||  |  ||  || |||| ||||||||||||||||   |  |||| | |||||| |||||||| || ||||||||||| || |||||||| || ||||||||| |||| || |||||
gtcaccaatatacgtggaaaaaacgatgcagtttatgt--aaacgaatggtgctg----gaggagagcgctgatgtattctgattcttttataatgcatg-aatcagGTGATATTGGAGAGTGGCAGGCAGATGGTAGCATGAAGATTATTGACCGTAAGAAGAATATTTTCAAGCTTTCTCAGGGAGAATATATTGCAGTCGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA
                                          tctattt  CT-rich tract
                       atattttattcatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatttttcagtttatgtttgaataagatatgcttctacgtggattgcatgatcatattttattcatgaatggtctatttaaacagGGGATATTGGAGAGTGGCTACCCAATGGAACCATGAAAATTATTGATCGGAAGAAGAATATATTTAAGCTTTCACAAGGAGAATATGTTGCTGTTGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT