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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAATTTATGTTTCCGTGGGGCGCCAATAGAAGATCTCTGTCTGGATTTCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgcataccctcttgaatgcctcttcaaaattttgatggattttttttcccctttggcatatttgtgttgtttgcaaagatgttcctgaaagatctcctcatttgtttaatttttcag

Basic information

species Vitis vinifera
transcript Vv03s0038g02340.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 11
TGCTAATTTATGTTTCCGTGGGGCGCCAATAGAAGATCTCTGTCTGGATTTCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgcataccctcttgaatgcctcttcaaaattttgatggattttttttcccctttggcatatttgtgttgtttgcaaagatgttcctgaaagatctcctcatttgtttaatttttcag
|||||||||   ||| |||||||| |||||||||||||||||  |||| ||||| ||||||||||||||||| ||||| |||||||| ||||| |||| ||||   || || |  |||     |  | ||      ||   ||| |||| |||    | ||      || |||   |   ||| ||     ||||       || | |   | ||  ||||||
TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgta---tgtattcagtct-----gtttttt------ttacctggtttttgttttggttctga-----ttctgtctgtaataaaaattgctttgaa-------cttactg--tcaaactttcag

upper sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA11G11490.2 (Glycine max), 5'ss of exon 11
TGCTAATTTATGTTTCCGTGGGGCGCCAATAGAAGATCTCTGTCTGGATTTCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgcataccctcttgaatgcctcttcaaaattttgatggattttttttcccctttggcatatttgtgttgtttgcaaagatgttcctgaaagatctcctcatttgtttaatttttcag
|||||||||   ||| |||||||| |||||||||||||||||  |||| ||||| ||||||||||||||||| ||||| |||||||| ||||| |||| ||||   || || |  ||| |  |   |   |    ||||| |    || |  | |  | ||      || ||    ||||   ||  || |||  | |  |||                    
TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgta---tgtattcagtct-gtttctattacctggtttttgttttggttctgattctgtctg------ttatgaaaattgctttgaacttactgtcaaacttccag------------------
















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|37185673|gb|CF605026.1|CF605026
EST:     TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
genomic: TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
EST: gi|71879155|gb|DT028210.1|DT028210
EST:     CTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
genomic: CTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
EST: gi|110376562|gb|EC941621.1|EC941621
EST:     TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
genomic: TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
EST: gi|161714276|gb|FC064167.1|FC064167
EST:     TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
genomic: TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
EST: gi|30126932|gb|CB912271.1|CB912271
EST:     TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
genomic: TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC
EST: gi|110684682|gb|EE062237.1|EE062237
EST:     TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAAT                         GTGGATATTAATAACTTGGAGGAGTATATATCTTTGGTTGTTGATGCAACC
genomic: TCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgca ... aatttttcagGTGGATATTAATAACTTGGAGGAATATATATCTTTGGTCGTTGATGCAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTAATTTATGTTTCCGTGGGGCGCCAATAGAAGATCTCTGTCTGGATTTCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgcataccctcttgaatgcctcttcaaaattttgatggattttttttcccctttggcatatttgtgttgtttgcaaagatgttcctgaaagatctcctcatttgtttaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA