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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag

Basic information

species Vitis vinifera
transcript Vv01s0127g00260.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G04120.2 (Glycine max), 5'ss of exon 11
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag
||||||||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||| || ||||| |||||||| |   |||    | | |||||| |   |  |      |    || ||  | ||  |  |||    |  || |  ||||    |  | |   
TGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTCGGGCATTGAAGGAGAAGgtaagtctatgatcaatagagcttagttcagatgtatgatgagaatcttcttgtagtagttaattgagtgttgagctattgcaattcaggag-

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G04120.1 (Glycine max), 5'ss of exon 11
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag
||||||||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||| || ||||| |||||||| |   |||    | | |||||| |   |  |   ||| ||  | | | |||  |  | | | | ||| | | ||   |||||   |  |||
TGATGGCCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTCGGGCATTGAAGGAGAAGgtaagtctatgatcaatagagcttagttcagatgt-atgatgagaatcttcttgtagtagtta-attgagtgt-tgagctattgca-attcag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA01G03530.1 (Glycine max), 5'ss of exon 11
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag
||||| ||  |||||||||||||| || |||||||| ||||| |||||||||||||||||||| || |||| ||| |||||||| || ||||| |||||||| | | |||    ||  ||| || |      |   ||| ||  | | | |||  |  | | | | ||| | | ||   |||||   |  |||
TGATGACCAGAAGAGAGCTCTTGTGATAGGAGGAGGCATAGCCAACTTTACTGATGTTGCTGCCACATTTAGTGGTATAATTCGGGCATTGAAGGAGAAGgtaagcctatgatcata-gagattggttcggatgt-atgatgagaatcttcttctagtagtta-attgagtgt-tgagctattgca-attcag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G17010.2 (Glycine max), 5'ss of exon 10
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag
||||||||  ||| |||| ||||| || || || |||||||||||||||||||||||||||||||| || | |||||||||||| ||| |||| |||||||||| | |||    ||   ||||||||   ||      ||    ||||   | ||  | |    | ||| | |      ||||    || |||
TGATGGCCAAAAGCGAGCCCTTGTGATAGGTGGGGGAATAGCTAACTTTACTGATGTTGCTGCTACGTTCAGTGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctatcatcatg-aagctttgctctataatatcgtattaatttgcttatattagagttaattgattgttgaccctattaca-aaccag

upper sequence: Vv01s0127g00260.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA15G42140.1 (Glycine max), 5'ss of exon 11
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag
||||||||  ||| |||| |||||  | || ||||||||||||||||||||||||||||||||||| || |  ||||||||||| ||| |||| |||||||||| | |||    ||   ||||||||   ||    ||  |   | ||| |||  |  |     | |  |||  ||   ||||    || |||
TGATGGCCAAAAGCGAGCCCTTGTGGTAGGTGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctatcatcatg-aagctttgctctataat-atcatattaatttgcttagagtagagttaattgattgttgacctattaca-aaccag

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|110363218|gb|EC926793.1|EC926793
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAAAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|71882514|gb|DT031569.1|DT031569
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGG
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGG
EST: gi|111125104|gb|EE253722.1|EE253722
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGTGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|32247604|gb|CD713423.1|CD713423
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|351054175|gb|FQ450257.1|FQ450257
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACCTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|71888760|gb|DT037815.1|DT037815
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAAAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|30325227|gb|CD008489.1|CD008489
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110698225|gb|EE075525.1|EE075525
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|349820930|gb|FQ408638.1|FQ408638
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110702653|gb|EE078810.1|EE078810
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|32271862|gb|CD721021.1|CD721021
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|351035742|gb|FQ463587.1|FQ463587
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|32271741|gb|CD720900.1|CD720900
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110389062|gb|EC953874.1|EC953874
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|349822202|gb|FQ412466.1|FQ412466
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGGATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110421990|gb|EC988298.1|EC988298
EST:     TTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: TTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110416323|gb|EC982295.1|EC982295
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|110422467|gb|EC988792.1|EC988792
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|32272154|gb|CD721313.1|CD721313
EST:     CTGACGTCGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|71882170|gb|DT031225.1|DT031225
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|46910213|gb|CN545588.1|CN545588
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
EST: gi|351044803|gb|FQ449057.1|FQ449057
EST:     CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAG                         GAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttat ... gtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGCCTTAAGAGAGCTCTTGTAATTGGAGGAGGAATAGCTAACTTTACTGATGTTGCTGCTACTTTTAATGGCATAATTCGCGCTTTGAAAGAGAAGgtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA