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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggctattgagttaaatttccttggtt...

Basic information

species Vitis vinifera
transcript Vv09s0002g04680.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgta-aaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggctattgagttaaatttccttggtt--
 ||||| ||| ||||||||||||| ||||| ||||| |||| ||| ||||| ||  | ||||| || ||||| || || ||||||||||||||||||||||||    | |  ||  ||   | |     ||| | | ||||   |||       | | ||   | |   | || | |||       | ||  ||  |  ||  
AGAACCAAGGAGGACAATGAATGCGAGTGAATGTGTTGCCAGGGGATGTGCGCTGGAGTGTGCTATCCTTAGTCCCACTTTTAAAGTGCGAGAGTTTCAGgtatgtgcccgctttcaccctgct---gccttctctgctttggctatctgcacaatacattaatagaaatcttgctgcttcatgccttaaaatctctaattaa

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggtt-gtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggct-attgagttaaatttccttggtt
||| || || || || |||||||||||||||||||| ||    || |||||||| || ||||| ||||| ||||| || || ||||||||||| || ||||||  |   | || | ||||  || |||| |   |||     |    ||   || | |||      ||  | ||   || |    | |   | | |||| | 
GGAGCCAAGACGAACCATGAATGCAAGTGAGTGTGTTGCGCGAGGATGTGCTCTTCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGAGAATTCCAGgtatcagctcctt-agcttaccttagtatatctgttttaagctactatgggttggattatactagactagtctatatcttaaactgctgtctatgcttgct-

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatg-tgttgcttttttacg-gctattgagttaaatttccttggtt
||| || || || || ||||||||||| |||||||| ||   |||||||||||| || ||||| ||||| ||||| || || |||||||| || || |||||| ||   | ||    ||   |  ||| || ||||      |    |   |  | |||  |  |||   | ||   | ||    ||    | | ||  || 
GGAGCCGAGACGAACCATGAATGCAAGCGAGTGTGTTGCGCGGGGCTGTGCTCTCCAGTGTGCTATTCTCAGCCCCACTTTCAAAGTGCGGGAATTCCAGgtataatctcattttttttct-tcctatgttgttttaagctatggcagggttagattattctagtgccggtctatatgatagactgtcgtctatgctccgt-

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggctattgagttaaatttccttggtt-----
||| |||||||||||||||||||| ||||||||||| |||| |||||||||  | || ||||||||||| |||||||| |||||||| || ||||||||||||||| |  |  |  |     || ||   | ||    ||||| | |   |  || | |      ||||||       || || || |   |  ||  ||     
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCCAGGGGCTGTGCATTGCAGTGTGCAATTCTCAGCCCAACTTTTAAAGTACGGGAGTTTCAGgtaaaaattttccctgcc---attataatgttttaaaattattcaatatgg--aactgttcagatctttttacgaatcatggacttcagcattttttattttttt

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggctattgagttaaatttccttggtt
||| |||||||||||||||||||| ||||||||||| |||| ||| |||||  | || ||||||||||| || ||||| |||||||| || ||||||||||||||  | |   |  ||    |  | |||  |||    |   |  || |  |   |||   |       | | ||   |         |||  ||  ||
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCCAGGGGTTGTGCATTGCAGTGTGCAATTCTCAGTCCAACTTTTAAAGTACGGGAGTTTCAGgtaaattttcccccggctgtattgctctctagtttgaaatgccttctgcaaagttttataattaaagggatcatggacttcagcagttgttttgttattt

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 1
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttcttt--atttatt-gaagtgaaatatg----tgttgcttttttacggctattgagttaaatttccttggtt
||| |||||||||||||||||||| ||||||||||| || | ||| |||||  |  |||||||||||||||| ||||| || ||||| ||||| |||||||||||  |  || |   || | ||||    |||||  |||  ||| |   | |     |||||    ||||| |||| || | || ||   |||  | || ||    
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCTAGGGGATGTGCGTTGGAATGTGCAATTCTTAGTCCAACGTTCAAAGTACGAGAATTTCAGgtaaagttttttgcg--ttggattgttctctatttcatttcaattcacaaggaccctcatatgccactgttggttttgtaggcctgtttgcttat-tgtcttt----

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 1
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtga---aatatg----tgttgcttttttacggctattgagttaaatttccttggtt
||| |||||||||||||||||||| ||||||||||| || | |||||||||  |  |||| ||||||||||| ||||| || ||||| ||||| |||||||||||  | | | |   || | ||||    |||||  |||   |   ||||       ||| |    ||||| |||| || |  |  |   |||  ||  |||    
GGAGCCTAGGCGGACAATGAATGCTAGTGAGTGTGTTGCTAGGGGCTGTGCGTTGGAATGCGCAATTCTTAGTCCAACGTTCAAAGTACGAGAATTTCAGgtaaagtttcatacg--ttggattgttctctatttcatttcaattcagaaggaccctcatacgccactgttggttttgtaagcttgcttgctta--ttgtcttc---

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaa--aactcctttcaac-ttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttac----ggctattgagttaaatttcct-tggtt------------------
||| || |||||||||||||||||||||||||||||| | | ||| |||||  | || ||||| ||||| || || || |||||||| || || || |||||||      | | || ||  |    |  || |  || | || || || |     | ||   | |   ||||| |||    |  |||     ||    |  | || ||                  
GGAGCCCAGGCGGACAATGAATGCAAGTGAGTGTGTGTCAAGGGGATGTGCCTTGCAGTGTGCCATTCTCAGTCCGACCTTTAAAGTTCGCGAATTCCAGgtaattggtgcatatctacgcttaagtaaatgtcgttattttcatgtacttgtaagcaactcgaga-acttttatactctagattatctgactagtcatattgtgatttattttttgttctcttag

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 2
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaa----actcctttcaacttaggttgtatcttattttctttatttatt--gaagtgaaatatgtgttgcttttttac-ggctattgagttaaatttcct-tggtt------------------
||| || ||||| |||||||||||||||||||||||| | | ||| |||||  | || ||||| ||||| || || || |||||||| || || || |||||||      |   | |   |||| ||   || |  || | || || || |   |||  |     |   || | |  | | || |||     ||    |  | || ||                  
GGAGCCCAGGCGTACAATGAATGCAAGTGAGTGTGTGTCGAGGGGATGTGCCTTGCAGTGTGCCATTCTCAGTCCGACCTTTAAAGTTCGCGAATTCCAGgtaatttgtgcatatctatgcttaagtaa-atgtcgttattttaatgtacttgtaagcaactcgagaactgttatactccaggttatctgactagtcatattatgatttattttttgttctcttag

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|351035450|gb|FQ463295.1|FQ463295
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351033537|gb|FQ447696.1|FQ447696
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|349825219|gb|FQ417940.1|FQ417940
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351026704|gb|FQ436357.1|FQ436357
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351056576|gb|FQ442404.1|FQ442404
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351021829|gb|FQ437214.1|FQ437214
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351015172|gb|FQ445456.1|FQ445456
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|30295926|gb|CB972720.1|CB972720
EST:     CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351016149|gb|FQ435469.1|FQ435469
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351014027|gb|FQ434179.1|FQ434179
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|349830554|gb|FQ416852.1|FQ416852
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351022620|gb|FQ447142.1|FQ447142
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351045993|gb|FQ441376.1|FQ441376
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|30295860|gb|CB972654.1|CB972654
EST:     CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351031000|gb|FQ439036.1|FQ439036
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351026139|gb|FQ428151.1|FQ428151
EST:     CCAACATTTAAAGTGCGAGAGTTTCAC                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|27579965|gb|CB002660.1|CB002660
EST:     CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351026310|gb|FQ428322.1|FQ428322
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|349832595|gb|FQ421953.1|FQ421953
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351044463|gb|FQ442994.1|FQ442994
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351016635|gb|FQ424062.1|FQ424062
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
EST: gi|351027160|gb|FQ440024.1|FQ440024
EST:     CCAACATTTAAAGTGCGAGAGTTTCAG                         GTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC
genomic: CCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcc ... ggttttgaagGTCAATGAAAGCTTCCCATTTACAATTGCTTTGACCTGGAAAGGCGATGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCTAGGCGGACAATGAATGCAAGTGAGTGTGTGGCCAAGGGCTGTGCTCTACAATGTGCAATTCTTAGCCCAACATTTAAAGTGCGAGAGTTTCAGgtaaaactcctttcaacttaggttgtatcttattttctttatttattgaagtgaaatatgtgttgcttttttacggctattgagttaaatttccttggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgaaa