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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcag

Basic information

species Vitis vinifera
transcript Vv13s0019g04470.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 8
TTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcag
||||||||||||| |||||||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || ||||| |    |    | |   | |   |     ||||||  | |  || |||||  |     ||| |  ||||     || ||       
TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatat---gatttgaacttggcattcctgttttact-agcagtttctgagattagttgttc--tattcctgtatgcag------

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 8
TTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcag
||||||||||||| |||| ||| ||| |||| |||||||| ||||| || ||||| || || | | | || |||||||||||||||||||| || ||||| |    |    | |   | |   |     ||||||  |    || || ||  |   | | | |  |||||    || ||       
TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatat---gatttgaacttggcattcctgttttact-ggcagtttttgagattaagtattc--tatttctgtatgcag------

upper sequence: Vv13s0019g04470.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 5
TTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcag
||||||||||||| ||| | ||||||||||| |||||||| ||||| || || || || || |  || || ||||| ||||| |||||||| || ||||| |    |      |  ||   || || | | |  | || |||    | |   |  |  | |   |||||     || ||       
TTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAGgttaaatat----gattggaaa-attgctgct-tcctattaaatgctgtttctgatactttatt--ttattcctgtatgcag------

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|110723004|gb|EE099818.1|EE099818
EST:     CCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|110406918|gb|EC972505.1|EC972505
EST:     CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|30329392|gb|CD012654.1|CD012654
EST:     TGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: TGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|22015287|gb|BQ800321.1|BQ800321
EST:     CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|110425226|gb|EC991608.1|EC991608
EST:     CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|110381672|gb|EC935088.1|EC935088
EST:     CGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
EST: gi|110382513|gb|EC946810.1|EC946810
EST:     CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAG                         GTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT
genomic: CCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttt ... tcacgtgcagGTCTTCATGATGAACCTTTCTGCTCCATTCATCTGTGAATTCTTCAAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAAAAGGCCAAATATTTCTATATTGCTGGTTTTTTCCTGACTGTGTCCCCTGAATCAATTCTACTCGTAGCTGAACATGCAGCTGCAAACAATAAGgtaattcttttcaagtcagattcatcgcagttgttttcttcaatagcttctgcaacccaatgtccattattttctcattcacgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC