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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatttattgcag

Basic information

species Vitis vinifera
transcript Vv01s0010g00950.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 5
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatttattgcag
|||||||||||||||||||| || ||||||||||| || |  || || |||||  | |||||||||||||| |||||| || |      ||   ||    |  ||   ||     | ||     || | | |   | | ||||    |    | ||||  | |||
ACTTTTGATGCTGTTGATGGTAAACAAGCAAGGCGCACTAGCTCATCAAGTCCTCTAGGAGAACTTTTTGATCATGgtaatgtgttaaggtttaatgctct--ttccacacccacatgtct---atcttatactcaca-atatgcaaatttgtcattt--tacag

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G08720.1 (Glycine max), 5'ss of exon 6
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatttattgcag------
|| |||||||||||||||||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||||||||| ||    |  | | | | ||| |    ||||  | || || ||  |   |   | |||  ||  | |  |  |  | || |       
ACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATGgtgattttcctgcattgtttttttcattctattgtttttca-ttatgcatacct--gtttgttattaatgaagatgttttcaactgtatttgcag

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G14210.1 (Glycine max), 5'ss of exon 6
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagt---tctgaatttcaaagggagatatatattgacacatgatttattgcag
|| |||||||||||||| ||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||||||||| ||    |  | | | | ||| |   |||||  | |     |   | |  |      ||  | ||     ||    |  ||||||
ACATTTGATGCTGTTGACGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATGgtgattttcctgcattgtgtttttcattctattatttttcattatgcttacctgtttattattaatgaagatgttttcaactgtatttgcag

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 5'ss of exon 5
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatt---tattgcag
|| |||||||| ||||||||||||||||||||  |||||||||||||||| ||  | ||||| || || || |||||||||||    ||  ||| |  ||  |||    || |    ||| | | |||       |||| | |  |||||  || |    ||||||||
ACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATGgtgatttatttttcccatgttcctcctttgattatct----gttttcagttt-gtttctagattttt-ctgacatgtgttccaatattgcag

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S269_30V6.1 (Physcomitrella patens), 5'ss of exon 6
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtca---tatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatttattgcag--------
|| |||||||||||||||||||| ||||| |||||||||||||| || |||||  | |||||||||||||| || ||| |    |  |  | |     ||   |  |   | ||||   ||   ||   | |    |   |  |||     |  | |   | || ||         
ACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACGgtaaacagctttgttgaactcgtaagctgctggtggatttatcaggcatgttgtcccttagttcacttatcagtgcgtaggcactcttacatatgtaaat

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 5'ss of exon 5
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgt----gatttccccttgtcatatatcttattttggcatt-ttgaagttctgaatttcaaagggagat--atatattgacacatgatttat---tgcag-
|||||||||||||||||||| |||||||| ||||||||||| || || || ||  | ||||| |||||||| || |||    ||| |  |          || | ||| | | | | ||  ||   | | | |  ||    | |  |||| ||      |  |||||   || |  
ACTTTTGATGCTGTTGATGGCAAGCAAGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACGgtagaggatcttacggaactcacaatttgattgtagaaatattagagacatcactctacaatctcgttcaatattttttagattcgtttatgtatgtaaa

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|351028084|gb|FQ425985.1|FQ425985
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|351043445|gb|FQ444045.1|FQ444045
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|349829684|gb|FQ421202.1|FQ421202
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|349824351|gb|FQ417738.1|FQ417738
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|110708043|gb|EE085132.1|EE085132
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|110694296|gb|EE071276.1|EE071276
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|351040557|gb|FQ434690.1|FQ434690
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|351014955|gb|FQ444244.1|FQ444244
EST:     AGCAAGGCGGACAAACTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|351029069|gb|FQ435269.1|FQ435269
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG
EST: gi|110687900|gb|EE065836.1|EE065836
EST:     AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG                         GATGTGATGCCCTTGCATGTGCG
genomic: AGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccc ... tttattgcagGATGTGATGCCCTTGCATGTGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATGgtgatttccccttgtcatatatcttattttggcattttgaagttctgaatttcaaagggagatatatattgacacatgatttattgcag

- - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA