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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattcttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag

Basic information

species Glycine max
transcript GLYMA02G07830.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 1
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtc---attcttctcttctttg-attatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag------------------------------------------------------------------------------------------------
||| |  ||||| || || || ||||| ||||||||||| || || || ||||||||||| ||||| |||||||| |||||||| |||||||||||||||| |   |   | | | | | ||            |||    |  |    | |  |||        |   |  |  || |                                                                                                
GGCAGCCATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTCAAGAAGGTCCAGGAGGGCGTCGACGTCTTCGACAGCATCTGGAACAAGgcactcccccactttccccctccccacggcggcccgacccccccccccctcc--ctcgttttctcctccgtcgaattcgtctccccctcctgatgctgctttcggagaggttttggtttgtccctctgagattttgtttttttgtttcgctgctgcggcggtggggcttgtacag

upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 1
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt--cttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag------------
       ||||| || || || ||||| ||||||||||| || || || || |||||||| ||||| |||||||| ||||| || ||||||||||| |||| | | |     |  |    ||  | |||    |    |        ||   ||| |   |   |||| |   ||              
-------ATGGGCGCCAGCCGGAAGCTGCAGGGCGAGATCGACCGCGTCCTGAAGAAGgtccaggagggcgtcgatgtctttgacagcatctggaataaggcacgcccccagcgccctccctccgtttacccggcccctgccagaactttttctcgcgatttttgttgattttttttgtttgggggcag

upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 5'ss of exon 1
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattcttctcttctttgattatttcgattttcttctgttt-tcgactcacacatggcgttgctgcgttag------------------------
||| |  ||||| || || || ||  | || |||||||| ||||| || || ||||||||||| ||||| || || || ||||| ||||||||||||||||||     | |||    |     ||| | |  || || |||   |  | || |      |    || ||   | |                         
GGCTGTGATGGGTGCGAGCCGGAAATTACAAGGCGAGATAGATCGGGTGCTGAAGAAGGTTCAAGAAGGTGTTGATGTTTTCGACAGCATCTGGAACAAGgtaacgtttcctttctcttcacaattctctgtatattattccaataattgattgtttttttttcttcctttctcaattttgttaatcgttgatatcgaga

upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 5'ss of exon 1
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattcttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag
 |  | |||||| || |||||||| || || |||||||||||  | ||||| |||||||||||||||||||| || || |||||||| |||||||||||||||    || | ||   |||   ||  | | | || |    | ||     || | |  |    |   | | | ||
AGGTGGAATGGGGGCGAGTCGAAAACTACAAGGCGAGATTGACAGGGTTCTGAAGAAGGTTCAGGAAGGCGTGGATGTTTTCGATAGTATCTGGAACAAGgta----atgcctcgtatctcaaatcttattgtttattggttattcgtttctta-atctcctctctttacttcag

upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 5'ss of exon 2
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattct--tctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag-----------------------
       ||||| || |  || ||  | || || || |||||    ||||| ||||| || || ||||||||||| ||||||||||| ||||||||||||||   | | |||  | |||      | | | | || ||   | | |   |          ||   | ||||  |||                        
ATTCATCATGGGGGCGACACGGAAATTACAAGGAGAAATTGACAAAGTTCTGAAGAAAGTGCAAGAAGGCGTCGATGTCTTCGATAGTATCTGGAACAAGgtgaataagtctagtatctgtccaaactttgttgagttctgtgtttacacagagaggctgtgatatggctgttttacatccttttggtgcttattctgca

upper sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ20408 (Selaginella moellendorffii), 5'ss of exon 1
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattcttc--tcttctttgattatt--tcgattttcttctgttttcgactcacacatggcgttgctgcgttag
       ||||| || |  || ||||| ||||||||||| ||| | |||||||||||||| ||||| ||||| || |||||||| ||||||||||| |||||| |  | |||      |    |    |||  |||||       | ||||    || | ||                 
-------ATGGGCGCGACGCGGAAGCTCCAGGGCGAGATCGATAGAGTTCTCAAGAAGGTCCAGGAGGGCGTGGATGTCTTCGACAGCATCTGGAATAAGgtatggaaatctatggcgtcgcctcgccattgatcgatcgagaatttttttttcttctcgcag----------------

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|208191754|gb|GD991506.1|GD991506
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGA
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGA
EST: gi|193593248|gb|FK548902.1|FK548902
EST:     GTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAACGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTG
genomic: GTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTG
EST: gi|208301261|gb|GE098604.1|GE098604
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAATG
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAATG
EST: gi|208312936|gb|GE112622.1|GE112622
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAATG
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAATG
EST: gi|193689457|gb|FK630968.1|FK630968
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAA
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAA
EST: gi|213599213|gb|DB959995.1|DB959995
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTG
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAATGCCAACCAGAAGGAGAAGTTCGAGGCTGACCTG
EST: gi|193525804|gb|FK480189.1|FK480189
EST:     TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAG                         GTTTACGACACCGATAAT
genomic: TCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcatt ... gctgcgttagGTTTACGACACCGATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGAAATGGGAGCTAGTCGAAAGCTTCAGGGCGAGATTGATCGTGTTCTCAAGAAGGTTCAGGAAGGCGTCGAAGTCTTCGATAGCATCTGGAACAAGgtaggtcattcttctcttctttgattatttcgattttcttctgttttcgactcacacatggcgttgctgcgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG