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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag

Basic information

species Glycine max
transcript GLYMA01G42950.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv15s0046g02410.t01 (Vitis vinifera), 5'ss of exon 1
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggtttcatgttttaaagttatgcatg-ttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag
| | | |||||||||||  || |||||||  |||| || ||||| ||||||| ||| || |||||||| |  |||||||||||||||||||| || ||||||        | |||   | ||   |  ||   || ||  || |   ||   |    |        ||   ||  | | |     |   ||   | |||| |                                         
AAGTCCCCCAACAAGTGTGCTACTGTTGGTTTTCAGGGTATTGCTTGGGCTTGTGGGGGTATGATCTTCGTTCTTGTCTACTGCACTGCTGGTATCTCAGgtctgttctgtctttctctctctcttgctattcttttgtttgatctgctgagttctgcttttcctttgttttcttttttatt---ttccatggtggtttgata----------------------------------------

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv02s0025g03390.t01 (Vitis vinifera), 5'ss of exon 1
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataata--ttttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaaagtta-tgtatgtttgaattgttgttgggacag---------------------
| | |||||| || |||  |   |||||| ||||| || ||||| |||||||||||||| |||||||||||||||||||||||||||||||| || ||||||   ||  |    | ||  || |      |    |||    | |    || | |     |  | | ||   |   |    | |  ||   ||   || || ||| | ||    ||| ||| | ||| |     || ||| |                        
AAGTCACCCACCATGTGTGCCAGTGTTGGTATTCAGGGGATTGCTTGGGCTTTTGGTGGTATGATCTTTGCCCTTGTCTACTGCACTGCTGGTATCTCAGgtgtgcaccactgctcttccttcctcagcctttctttagctttttctgttaaacac-tttactgggttgctctaagttcttcttcttcctttagccttctgatgtgggttgctcttagtgtgttttttagcatctgatggaagttttgtgtggtttgttgtctcag

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv15s0046g02420.t01 (Vitis vinifera), 5'ss of exon 1
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggttt-catgttttaaagttatgcatgttaact-atatatacccaaagaggtgacgtcgatctcacc-tggtcagataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag
||| | |||| ||||||  |  ||||||| ||||| || ||||| ||||||||||| || |||||||||||||||||||||||||||||||| || ||||||        | | |   | |  ||||| |   |||     |||| | |  |   |  ||   |   ||   | | | |  || ||||    | |  |                                               
AGGTCCCCCAGCAAGTGTGCCACTGTTGGTATTCAGGGTATTGCTTGGGCTTTTGGGGGTATGATCTTTGCCCTTGTCTACTGCACTGCTGGTATCTCAGgtctgttctctgtctctctatatatgttcttttgtttgatctgttgagtcgtgcttttcctttgttttgttcttgttttttccatggtggtttgatatgc---------------------------------------------

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S305_12V6.1 (Physcomitrella patens), 5'ss of exon 1
-AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtc---agataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag-
 |  ||  |  |    ||| |    || ||||||||||||||||| ||||| || || |||||||| ||  |||| ||||||||||| |||||||| |||||| || |  ||    ||   |||| ||   ||||  ||||   | |  || | ||    |    |       |||||     | |    |  | ||| |    || || | |   |       ||||||  || || |||   |  
AATCGCGGC-GATGCCTGCGCGGGGGTCGGCATTCAAGGAATTGCGTGGGCCTTCGGCGGCATGATATTCACCCTCGTCTACTGCACCGCTGGAATTTCAGgtaaaga--atgcgctg--ctcat-ttcacaagtattgcagaatgatgatgtttatgtgatcttggtttccagatcttcgtagatttttatgtgagggtggtctgatgatgagcttgcccggggtttga--tgatgatggcttaag

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S102_107V6.1 (Physcomitrella patens), 5'ss of exon 1
-AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaa--agttatgtatgtttgaattgttgttgggacag
     |||   ||   ||||     || || |||||||| || || ||||| || ||||| ||||||||||| || ||||| ||||| || ||||| |||||||||   | ||  |    ||       | ||||| |  |   |  ||  |  || |   ||| ||  |    |   ||   ||| | || || |  | | ||  | |||  ||     ||||| |  |  |            
CGAAACACA-GACCCCTGCTTGGGGGTCGGAATTCAAGGCATCGCCTGGGCGTTCGGTGGAATGATCTTTGCGCTCGTCTATTGCACAGCAGGAATCTCAGgttaa---actacctccccttagcagcatgaagttttaaaaaatttctgcaagtatcatgagaagttgca---aaacca--gggttacattagctggtatagtgatctaacaaggccgttatgtctctacag------------

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ18960 (Selaginella moellendorffii), 5'ss of exon 1
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgt--taacataa-tattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag
   |  | || ||  |||  |   || ||||| || || || || ||||||||||| |||||||||||||| || |||||||||||||||||||| ||||||   || || | | |||| ||||| ||   | | ||   |  |   | ||| |  |       | |         |  | | |   || | |  ||| ||||        ||| ||                            
GTCGATCGCACCAGCTGCCTTGGAGTGGGCATCCAGGGCATCGCGTGGGCTTTTGGGGGCATGATCTTTGCTCTCGTCTACTGCACTGCTGGAATCTCAGgtaccaagatgagtttttttgtttcctg---tgaggtgtggtgttcgagctaaagtttgttcttgcga-------aactttatc---tcgggtgtggtgttgtc----ccgaaactt----------------------------

upper sequence: GLYMA01G42950.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ11572 (Selaginella moellendorffii), 5'ss of exon 1
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgt--taacataatattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtc----gatctcac--ctggtc-agataaggttttgttgttgtttaaagttatgtatgtttgaattgttgt-tgggacag-----------------------------------------
   |  | || ||  |||  |   || ||||| || || || || ||||||||||| |||||||||||||| || |||||||||||||| ||||| ||||||   || || |  |||| | |    |   ||||||  | | ||  ||   | ||   |    | ||||  |||     |  |     ||| || || ||| |||| |    | | ||  |||      |    | || | ||  | ||| |                                         
GTCGATCGCACCAGCTGCCTTGGAGTGGGCATCCAGGGCATCGCGTGGGCTTTTGGAGGCATGATCTTTGCTCTCGTCTACTGCACTGCCGGAATCTCAGgtaccaagatgagttttttggtgttcgagctaaagt-gttcttgcgaaac-tttacctcgggtgtggtgttgtcccgaaactttggtgctgttctagctaaagtttcgcgagt-tctagtgttcca---gcgaaagttttcgtgcgagactggaaaccatagctaaaagcttgacatgttttgtttttctcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|193493278|gb|FK463052.1|FK463052
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|298194408|gb|HO041056.1|HO041056
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|298188096|gb|HO032053.1|HO032053
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|207740733|gb|GD715791.1|GD715791
EST:     TCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|208113766|gb|GD913421.1|GD913421
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTC
EST: gi|193614264|gb|FK562264.1|FK562264
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|192305303|gb|FG997555.1|FG997555
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|298162974|gb|HO011707.1|HO011707
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|298167734|gb|HO012997.1|HO012997
EST:     TTCTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|192297908|gb|FG988364.1|FG988364
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|207775565|gb|GD749838.1|GD749838
EST:     TCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|151394697|gb|EV264568.1|EV264568
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|208167688|gb|GD963814.1|GD963814
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTT
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTT
EST: gi|208062226|gb|GD855936.1|GD855936
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATNTCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTT
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTT
EST: gi|207777239|gb|GD748334.1|GD748334
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|192312379|gb|FK003171.1|FK003171
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|208202537|gb|GD997866.1|GD997866
EST:     CACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: CACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|192312380|gb|FK003172.1|FK003172
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|193545096|gb|FK499445.1|FK499445
EST:     -TTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|193414940|gb|FK378780.1|FK378780
EST:     TGGTGGCATGAAATACTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TGGTGGCATG--AT-CTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|151403754|gb|EV273564.1|EV273564
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
EST: gi|298171802|gb|HO021394.1|HO021394
EST:     TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAG                         GTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC
genomic: TTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataa ... gttgggacagGTGGGCACATAAATCCGGCAGTGACGTTCGGTTTGTTTCTGGCTAGGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCACCCAACAAGTGCTCTTCTGTTGGCATTCAAGGAATTGCATGGGCTTTTGGTGGCATGATCTTTGCCCTTGTCTACTGCACTGCTGGAATATCAGgttaacataatattttggtttcatgttttaaagttatgcatgttaactatatatacccaaagaggtgacgtcgatctcacctggtcagataaggttttgttgttgtttaaagttatgtatgtttgaattgttgttgggacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA