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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATGGCTGTCTATGGAACTCATGTTTTATTTAAGTGTTCTTCCGCTCACACGTCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcctgtcacatttacttgctagcttgatttgatattagatatgacctaacagccagaggcctgcaactaatgttttttagtttattatttcag

Basic information

species Glycine max
transcript GLYMA01G39430.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39430.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G149802_T02 (Zea mays), 5'ss of exon 12
TGCATGGCTGTCTATGGAACTCATGTTTTATTTAAGTGTTCTTCCGCTCACACGTCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcctgtcacatttacttgctagcttgatttgatattagatatgacctaacagccagaggcc-tgcaactaatgttttttagtttattatttcag
||||||||| ||| |||| ||||||||| |||| |||||||| || || ||||| ||  | || || || ||||| || |||||||||||||| || ||||| |    | |||||  |||      |  |||  | | ||      | | | |  || |  || | | |    | ||||   |||  | ||         
TGCATGGCTTTCTTTGGAGCTCATGTTTCATTTGAGTGTTCTCCCACTGACACGACAATTAACCAACATTAGTGGTAACCTGTGGGGGAAAACACTCCAGgtaa----cagtcactattatcatgcatattgtgtagttaactaggaagtcgtg-catcttgacgtcatatctcaaatgaaatttcctgtag--------

upper sequence: GLYMA01G39430.1 (Glycine max), 5'ss of exon 13
lower sequence: AT5G67100.1 (Arabidopsis thaliana), 5'ss of exon 12
TGCATGGCTGTCTATGGAACTCATGTTTTATTTAAGTGTTCTTCCGCTCACACGTCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcctgtcacatttacttgctagcttgatttgatattagatatgacctaacagccagaggcctgcaactaatgttttttagtttattatttcag
||||||| | || ||||| ||||||||| || ||||||||||||| ||||| |  ||||| ||||| |||||||||||||| ||||||||||| ||||| || |       | ||  |  ||  |   |   ||  |  |  | |||||   ||     | ||  | ||||  |  ||||  | |              
TGCATGGTTATCCATGGAGCTCATGTTTCATCTAAGTGTTCTTCCTCTCACTCTCCAGCTTACTAACATAAGTGGCAATCTTTGGGGGAAAACACTTCAAgtaa-------tgactctccctctccctccc-atccggga--aaatatgtgttactgtgctgactcatgcattttttgttcatgaccag----------

upper sequence: GLYMA01G39430.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv07s0031g00470.t01 (Vitis vinifera), 5'ss of exon 11
TGCATGGCTGTCTATGGAACTCATGTTTTATTTAAGTGTTCTTCCGCTCACACGTCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcctgtcacatttacttgctagcttgatttgatattagatatgacctaacagccagaggcctgcaactaatgttttttagtttattatttcag
||||||| | || |||||||| |||||| |||| ||||||||||| || || ||||  ||||||||||| ||||| ||||| ||||| || ||||| || |||||  |   ||| || |  || ||    ||||||  |||    | || ||  |    ||       | || ||    |        | |  ||||||
TGCATGGTTATCCATGGAACTTATGTTTCATTTGAGTGTTCTTCCTCTTACTCGTCTTCTGACTAATATCAGTGGTAATCTCTGGGGAAAGACTCTCCAAgtgagtgct--tcaaatgtggtttctttaatgatttcttatgtattctgtcc--atgagcatgacatagaaagtacaact----gacatgtgttttcag

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|208028276|gb|GD826857.1|GD826857
EST:     TCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
genomic: TCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|208202098|gb|GD997077.1|GD997077
EST:     GGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCATGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|207739970|gb|GD716554.1|GD716554
EST:     GGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCATGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|193416446|gb|FK384952.1|FK384952
EST:     GGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|207823370|gb|GD795389.1|GD795389
EST:     GGGGGAAAACTCTCCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|193593256|gb|FK545788.1|FK545788
EST:     GGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
EST: gi|208225422|gb|GE025421.1|GE025421
EST:     TCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTACTTCAG                         GGTGCTCGAGCACAGAG
genomic: TCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACT-CTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAG
EST: gi|207712764|gb|GD693388.1|GD693388
EST:     GGGGGAAAACTCTTCAG                         GGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA
genomic: GGGGGAAAACTCTTCAGgtgagctcct ... attatttcagGGTGCTCGAGCACAGAGAGTGGAATATCTTTTGCTGCATACTTTCCACGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATGGCTGTCTATGGAACTCATGTTTTATTTAAGTGTTCTTCCGCTCACACGTCAGCTGACTAATATAAGTGGCAATCTGTGGGGGAAAACTCTTCAGgtgagctcctgtcacatttacttgctagcttgatttgatattagatatgacctaacagccagaggcctgcaactaatgttttttagtttattatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA