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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacag

Basic information

species Vitis vinifera
transcript Vv11s0016g04620.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 14
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaat------tatacag
||   | ||||||||||| |||||||| ||||| || |||||||| || ||||| || ||||| || || || || |||||| | ||||| ||||||||||||||| |  | |   || |  || |  |   | |   ||   | ||| |   | ||     |  |||       || |||
TTGGAGGATTCCTTTGGTCAGTGACATACCAACTATTATATTTGGTGCAGATGTCACGCATCCTGAAACCGGGGAGGACTCTAGCCCATCCATTGCTGCTgtaaggctgagcatttctatggttac--atggccatcattttttttttaacctcttaccctctctaataagctgcatgcag

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 13
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggat----------------------atgaaaac-ctgtatttcccaaaatctacagttccatgt-ttgagtccatattgattacaattatacag---------
||   | ||||||||||| |||||||| ||||| || |||||||| || |||||||| || || || || || || |||||  |||||||||| ||||| |||||| |                      || || |     ||||   ||| || | ||  ||  ||| |||  |    | | ||  || | |||            
TTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacag

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA05G08170.1 (Glycine max), 5'ss of exon 13
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacag
||   |||| || ||||||||||||||||||||||| || |||||||| |||||||||||||||||  ||||||| ||| |||||||||| |||||||||||||| || |  |||    | |  |  | |     |  |   || |||| |||  |  |||||||  |||| |||
TTGGAGAATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACTCATCCAGAATCTGGAGAGGACCCTTGTCCATCCATTGCTGCTgtaagtatttccaaagtcctttaacttatagctggccat---atatttg-gtc--ttctgattactgttattcag

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA17G12850.1 (Glycine max), 5'ss of exon 14
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacag
||   | || || ||||||||||||||||||||||| || |||||||| |||||||| ||||||||  ||||||| ||| |||||||||| |||||||||||||| || |  |||    | |  |  | |     |  |   |  ||||  |   ||   || ||  |||| |||
TTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATCCAGAATCTGGAGAGGACCCTTGTCCATCCATTGCTGCTgtaagtatttccaaagtcctttaccttatagctggccat---acatttggttttcta---atcactgttattcag

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA06G23920.1 (Glycine max), 5'ss of exon 14
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacag
||   | |||||  |||||||||| ||||||||||| ||||||||||| |||||||||||||||||  | ||||| || ||||||||||| |||||||||||||| || |  ||||   ||| | |    |      || | ||| |||| |  ||| ||| |||  | || |||
TTGGAGGATTCCACTGGTTAGTGATATTCCAACAATAATATTTGGAGCTGATGTAACTCATCCAGAATCAGGAGAGGATTCTTGTCCATCCATTGCTGCTgtaagcatttccaaactcctatatacagctaagggatgtgctatgcttga-tatatactgaatacggtaatccag

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|33407837|gb|CF213464.1|CF213464
EST:     ACTCTTGTCCATCAATTGCTGCT                         GTAGTAGCCTCCCAAGNCTTGACAGAAGTCACCAAGTATGCTGGATTGGTA
genomic: ACTCTTGTCCATCAATTGCTGCTgtaaggatat ... aattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA
EST: gi|349828457|gb|FQ417199.1|FQ417199
EST:     ATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCT                         GTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA
genomic: ATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatat ... aattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCCAGAGACTGGAGATGACTCTTGTCCATCAATTGCTGCTgtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT