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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttttgttctttggattttaggtcgcactttctgtagctcatgtttcttaaccttgcttgctcattgttccatgatag

Basic information

species Glycine max
transcript GLYMA13G43630.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 8
GGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttttgttctttggattttaggtcgcactttctgtagctcatgtttcttaaccttgcttgc-tcattgttccatgatag-------------------
|| | ||||||||||| ||||| |||||||| ||||| ||| |||||||||| || ||  |||| || || || |||| ||| ||||| || || |||||||| || ||   |  | |  |||  |  |  ||  |||   || |||| ||| ||         | |  | |||   ||  | |                    
GGTTAAGGGAGAAAAAGCAGCAGCAGGACTCACTTCCCAAACATGCCACCCCAGTCCTCCTGTCCGCCGATGTGAGAAGGAAGGCTGAGGCAGTTGACAGgtaatgattccatgatat--attccatattccatattc--aagttcattttttttgggtgacactacacctttgaaacaaaaaatgttgtctcaagtggcactc
















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|254322029|gb|GR837443.1|GR837443
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|192294395|gb|FG987324.1|FG987324
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|11117948|gb|BF219541.1|BF219541
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|23730841|gb|BU763524.1|BU763524
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|11687354|gb|BF595030.1|BF595030
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|6094746|gb|AW119475.1|AW119475
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|9563876|gb|BE473385.1|BE473385
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|12772061|gb|BG236988.1|BG236988
EST:     TTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: TTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|298183420|gb|HO028633.1|HO028633
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCGAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|254322030|gb|GR837444.1|GR837444
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|209705993|gb|BW664864.1|BW664864
EST:     CAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|298169033|gb|HO020393.1|HO020393
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|22931443|gb|BU548582.1|BU548582
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|8827941|gb|BE211671.1|BE211671
EST:     CTGTACTTGTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCT-TGGGACAG                         GTTTTGGGAGCCAATT-TGAAGAAACCCAAGCC
genomic: CTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGG-ACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCC
EST: gi|192301841|gb|FG997699.1|FG997699
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
EST: gi|6963487|gb|AW432180.1|AW432180
EST:     CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAG                         GTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC
genomic: CCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttt ... tccatgatagGTTTTGTAAGCCAATTATGACGAAACCAAAGCCACTGCCACCCAAGCCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCAGGGAGAAAAAACAGCATCAGGACTCGCTTCCAAAATATGCCACCCCTGTACTTTTGTCAGCTGACGTAAGAAAGAAAGCTGAAGCTGTGGACAGgtattgcttttgttctttggattttaggtcgcactttctgtagctcatgtttcttaaccttgcttgctcattgttccatgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG