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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACAACACTGAGCAAAGTGCAGAAATCATCTTTGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctctcaacctgcggttttcaacttatcattaattccaaggattcgagatggatccagatatttgtcctttaagattctgcctgattaggttga...

Basic information

species Vitis vinifera
transcript Vv10s0003g05770.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g05770.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G14360.1 (Glycine max), 5'ss of exon 4
AAACAACACTGAGCAAAGTGCAGAAATCATCTTTGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctctcaacctgcggtttt--caacttatcattaat-tccaaggattcgagatggatccagatatttgtcctttaagattctgcctgattaggttga-
|||||||| ||| ||||||| |||||||||||||  | || || |||||||||||||||||||||||||| ||||| ||||||||    |   || |  |    |||   ||  || | ||| || |        | |   | ||   | ||||  || |||||    | ||  ||| | ||||   
AAACAACATTGAACAAAGTGGAGAAATCATCTTTAATGCTTGCATATGAGGTTAATGCAGTGGGTCCTATCTTAGTTATCAAGgtaacataaatctaattttaatttcaacacttttttatttatctatttatgatagttttagaagtaaatataggttcttta----tatgtatgagtgggttata

upper sequence: Vv10s0003g05770.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G03440.1 (Glycine max), 5'ss of exon 5
AAACAACACTGAGCAAAGTGCAGAAATCATCTTTGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtg-cgctctctcaacctgcggttttcaacttatca--ttaattccaaggattcgagatggatccagatatttgtcctttaagattctgcctgattaggttga-
|||||||| ||| ||||||| |||||||||||||  | || || |||||||||||||||||||||||||| ||||| ||||||||  |        ||  | |  |    || ||||    |||  |        | |   | ||   | ||||  || |||||    | ||  |||    |||   
AAACAACATTGAACAAAGTGGAGAAATCATCTTTAATGCTTGCGTATGAGGTTAATGCAGTGGGTCCTATCTTAGTTATCAAGgtaacatcaatctaattttcattacaaaagttatttatttatctgtttatgatagttttagaagtaaatataggttcttta----tatgtatgagggagttata
















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|71871481|gb|DT020536.1|DT020536
EST:     TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAG                         CATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
genomic: TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctc ... gtcctagcagCATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
EST: gi|294964556|gb|GW838359.1|GW838359
EST:     TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAG                         CATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
genomic: TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctc ... gtcctagcagCATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
EST: gi|77585998|gb|DV222098.1|DV222098
EST:     TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAG                         CATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
genomic: TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctc ... gtcctagcagCATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
EST: gi|110416872|gb|EC982880.1|EC982880
EST:     TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAG                         CATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
genomic: TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctc ... gtcctagcagCATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
EST: gi|71873455|gb|DT022510.1|DT022510
EST:     TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAG                         CATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT
genomic: TGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctc ... gtcctagcagCATATGTGGCCTCTTCTAACGGCTGGAGGAGGCTCTGGGACTGAAAGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACAACACTGAGCAAAGTGCAGAAATCATCTTTGCTTCTAGCCTATGAGGTTAATGCAGTGGGTCCTATTTTAGTGATCAAGgtgcgctctctcaacctgcggttttcaacttatcattaattccaaggattcgagatggatccagatatttgtcctttaagattctgcctgattaggttga

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