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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCTTGGTGCTGACTACTATGAAACCGACTCTGAAGTGGCATCACTGTTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaaaactttaaaactcgccgccccatttcttcatttgatctaattctttcactgatctttctcctatctcatggctcttcttattatgcttgtacag

Basic information

species Vitis vinifera
transcript Vv05s0020g02880.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G38820.1 (Glycine max), 5'ss of exon 13
TGATGCTTGGTGCTGACTACTATGAAACCGACTCTGAAGTGGCATCACTGTTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaaaactttaaaactcgccgccccatttcttcatttgatctaattctttcactgatctttctcctatctcatggctcttcttattatgcttgtacag
|||||||||||||||| || |||||||||||  | ||||||||| |||| || ||||| || || ||||| |||||||||||||||||||||| |||||||||   |    | ||   | ||| ||    || | ||| || | |  |   ||  |  || |  ||||| |                                 
TGATGCTTGGTGCTGATTATTATGAAACCGATGCAGAAGTGGCAGCACTCTTAGCTGAAGGAAGAGTTCCAATTGGAATAGGAGAAAATACAAAAATCAAgtatgaattgcaattctca-ctctcctaatcactactttatctcactttgctcactt-ctcacatttctgcag-------------------------------

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA17G01900.1 (Glycine max), 5'ss of exon 13
TGATGCTTGGTGCTGACTACTATGAAACCGACTCTGAAGTGGCATCACTGTTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaaaactttaaaactcgccgccccatttcttcatttgatctaattctttcactgatctttctcctatctcatggctcttcttattatgcttgtacag
|||||||||||||||| ||||||||||||||  | ||||||| | |||| || ||||| || || ||||| || ||||||||||||||||||| |||||||||   |    | ||   | ||| ||   ||||| |||  | | |  |   ||  |  || |  ||||| |                                 
TGATGCTTGGTGCTGATTACTATGAAACCGATGCAGAAGTGGTAGCACTCTTAGCTGAAGGAAGAGTTCCAATAGGAATAGGAGAAAATACAAAAATCAAgtatgaattgcaattctca-ctctcctaaccattactttctctcactttgctcactt-ctcacatttctacag-------------------------------
















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|351029658|gb|FQ427498.1|FQ427498
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351040871|gb|FQ438415.1|FQ438415
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351019209|gb|FQ429369.1|FQ429369
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351025236|gb|FQ433653.1|FQ433653
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351013646|gb|FQ429787.1|FQ429787
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTT-TTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351015482|gb|FQ447311.1|FQ447311
EST:     TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351034082|gb|FQ448000.1|FQ448000
EST:     TTAGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAACGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
EST: gi|351013342|gb|FQ425047.1|FQ425047
EST:     TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAA                         AGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC
genomic: TTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaa ... gcttgtacagAGACTGCATCATCGACAAAAATGCCAGAATTGGGAAGAATGTTGTTATTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCTTGGTGCTGACTACTATGAAACCGACTCTGAAGTGGCATCACTGTTGGCTGAGGGGAGGGTTCCTATTGGAATAGGAGAAAATACAAGAATCAAgtacagaaaaaactttaaaactcgccgccccatttcttcatttgatctaattctttcactgatctttctcctatctcatggctcttcttattatgcttgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA